title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-10 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics link: https://peerj.com/articles/2603 last-modified: 2016-10-27 description: Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils. creator: Elena R. Schroeter creator: Caroline J. DeHart creator: Mary H. Schweitzer creator: Paul M. Thomas creator: Neil L. Kelleher uri: https://doi.org/10.7717/peerj.2603 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Schroeter et al. title: A new species of Brachycephalus (Anura: Brachycephalidae) from Santa Catarina, southern Brazil link: https://peerj.com/articles/2629 last-modified: 2016-10-27 description: A new species of Brachycephalus (Anura: Brachycephalidae) is described from the Atlantic Forest of northeastern state of Santa Catarina, southern Brazil. Nine specimens (eight adults and a juvenile) were collected from the leaf litter of montane forests 790–835 m above sea level (a.s.l.). The new species is a member of the pernix group by its bufoniform shape and the absence of dermal co-ossification and is distinguished from all its congeners by a combination of its general coloration (dorsal region of head, dorsum, legs, arms, and flanks light, brownish green to dark, olive green, with darker region in the middle of the dorsum and a white line along the vertebral column in most specimens) and by its smooth dorsum. The geographical distribution of the new species is highly reduced (extent of occurrence estimated as 25.04 ha, or possibly 34.37 ha). In addition, its habitat has experienced some level of degradation, raising concerns about the future conservation of the species. Preliminary density estimates suggest one calling individual every 3–4 m2 at 815–835 m a.s.l. and every 100 m2 at 790 m a.s.l. Together with the recently described B. boticario and B. fuscolineatus, the new species is among the southernmost species of Brachycephalus known to date. creator: Marcos R. Bornschein creator: Luiz F. Ribeiro creator: David C. Blackburn creator: Edward L. Stanley creator: Marcio R. Pie uri: https://doi.org/10.7717/peerj.2629 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bornschein et al. title: Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse) link: https://peerj.com/articles/2617 last-modified: 2016-10-27 description: Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens) of Peromyscus eremicus (Cactus mouse), a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse) and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss. creator: Lauren L. Kordonowy creator: Matthew D. MacManes uri: https://doi.org/10.7717/peerj.2617 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kordonowy and MacManes title: Synthetic lung surfactants containing SP-B and SP-C peptides plus novel phospholipase-resistant lipids or glycerophospholipids link: https://peerj.com/articles/2635 last-modified: 2016-10-27 description: BackgroundThis study examines the biophysical and preclinical pulmonary activity of synthetic lung surfactants containing novel phospholipase-resistant phosphonolipids or synthetic glycerophospholipids combined with Super Mini-B (S-MB) DATK and/or SP-Css ion-lock 1 peptides that replicate the functional biophysics of surfactant proteins (SP)-B and SP-C. Phospholipase-resistant phosphonolipids used in synthetic surfactants are DEPN-8 and PG-1, molecular analogs of dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG), while glycerophospholipids used are active lipid components of native surfactant (DPPC:POPC:POPG 5:3:2 by weight). The objective of the work is to test whether these novel lipid/peptide synthetic surfactants have favorable preclinical activity (biophysical, pulmonary) for therapeutic use in reversing surfactant deficiency or dysfunction in lung disease or injury.MethodsSurface activity of synthetic lipid/peptide surfactants was assessed in vitro at 37 °C by measuring adsorption in a stirred subphase apparatus and dynamic surface tension lowering in pulsating and captive bubble surfactometers. Shear viscosity was measured as a function of shear rate on a Wells-Brookfield micro-viscometer. In vivo pulmonary activity was determined by measuring lung function (arterial oxygenation, dynamic lung compliance) in ventilated rats and rabbits with surfactant deficiency/dysfunction induced by saline lavage to lower arterial PO2 to <100 mmHg, consistent with clinical acute respiratory distress syndrome (ARDS).ResultsSynthetic surfactants containing 5:3:2 DPPC:POPC:POPG or 9:1 DEPN-8:PG-1 combined with 3% (by wt) of S-MB DATK, 3% SP-Css ion-lock 1, or 1.5% each of both peptides all adsorbed rapidly to low equilibrium surface tensions and also reduced surface tension to ≤1 mN/m under dynamic compression at 37 °C. However, dual-peptide surfactants containing 1.5% S-MB DATK + 1.5% SP-Css ion-lock 1 combined with 9:1 DEPN-8:PG-1 or 5:3:2 DPPC:POPC:POPG had the greatest in vivo activity in improving arterial oxygenation and dynamic lung compliance in ventilated animals with ARDS. Saline dispersions of these dual-peptide synthetic surfactants were also found to have shear viscosities comparable to or below those of current animal-derived surfactant drugs, supporting their potential ease of deliverability by instillation in future clinical applications.DiscussionOur findings support the potential of dual-peptide synthetic lipid/peptide surfactants containing S-MB DATK + SP-Css ion-lock 1 for treating diseases of surfactant deficiency or dysfunction. Moreover, phospholipase-resistant dual-peptide surfactants containing DEPN-8/PG-1 may have particular applications in treating direct forms of ARDS where endogenous phospholipases are present in the lungs. creator: Robert H. Notter creator: Rohun Gupta creator: Adrian L. Schwan creator: Zhengdong Wang creator: Mohanad Gh Shkoor creator: Frans J. Walther uri: https://doi.org/10.7717/peerj.2635 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Notter et al. title: Risk and clinical predictors of osteoporotic fracture in East Asian patients with chronic obstructive pulmonary disease: a population-based cohort study link: https://peerj.com/articles/2634 last-modified: 2016-10-27 description: IntroductionOsteoporosis is becoming an impending epidemic in the Asia-Pacific region. The association between risk of osteoporotic fracture (OTPF) and chronic obstructive pulmonary disease (COPD) in East Asian patients is yet to be fully examined. We conducted a nationwide population-based retrospective cohort study of 98,700 patients aged ≥50 years with or without COPD using a national administrative claims dataset.Materials and MethodsThe patients were divided into COPD and comparison groups comprising 19,740 and 78,960 patients, respectively. The groups were 1 to 4 matched for age, gender, index date, diabetes mellitus, pre-existing osteoporosis and chronic kidney disease. Information such as the geographic area where southern part represented more sunshine exposure, smoking-related diagnoses, alcohol use disorder, whether there was regular use of inhaled corticosteroids and oral corticosteroids, vitamin D prescriptions, Charlson-Deyo comorbidity index score, and other relevant medical comorbidities were extracted for analysis. They were followed up until OTPF or the end of the year 2013. The outcome measure was an osteoporotic vertebral fracture and other long-bone fractures. A multivariate Cox model was constructed to derive adjusted hazard ratios (aHR) for OTPF with corresponding 95% confidence intervals (CI) after controlling for age, sex, insurance premium category, vitamin D prescription, osteoporosis, and coronary heart disease (CHD). Kaplan–Meier curves of the probability of OTPF-free survival for each cohort were compared using the log-rank test. Patients with OTPF during the first follow-up year were excluded from the overall risk calculation. Contributing factors to the increased risk of OTPF in COPD patients were examined in a sensitivity analysis.ResultsAfter a total follow-up of 68,743 patient-years for the COPD group and 278,051 patient-years for the matched comparison group, the HR for OTPF was 1.24 (95% CI [1.02–1.51]; P = 0.0322) in COPD patients. The aHR was increased by 30% for vertebral OTPF (aHR = 1.297, 95% CI [1.020–1.649]; P = 0.0339). Differential lag time sensitivity analysis revealed a progressively elevated risk up to 8-fold increase in women (aHR = 8.0 (95% CI [1.81–35.4]; P < 0.01)) during the fifth follow-up year. COPD patients with pre-existing osteoporosis or given vitamin D prescription harbor a sustained increased risk up to the 5th (aHR, 4.1; 95% CI [1.61–10.35]) and third (aHR, 2.97; 95% CI [1.48–5.97]) follow-up year, respectively.ConclusionsOur nationwide population-based cohort study demonstrates that East Asian COPD patients aged 50 and beyond do harbor a modestly increased risk for osteoporotic vertebral fractures particularly for those who are female, have pre-existing osteoporosis or require vitamin D prescription. creator: Ping-Hsueh Lee creator: Victor C. Kok creator: Po-Liang Chou creator: Ming-Chang Ku creator: Yu-Ching Chen creator: Jorng-Tzong Horng uri: https://doi.org/10.7717/peerj.2634 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lee et al. title: Alcohol consumption and risk of fatty liver disease: a meta-analysis link: https://peerj.com/articles/2633 last-modified: 2016-10-27 description: BackgroundObservational studies have shown inconsistent results regarding alcohol consumption and risk of fatty liver. We performed a meta-analysis of published literature to investigate the association between alcohol consumption and fatty liver disease (FLD).MethodsWe searched Medline, Embase, Web of Science, and several Chinese databases, identifying studies that reported an association between alcohol consumption and the risk of FLD.ResultsA total of 16 studies with 76,608 participants including 13 cross-sectional studies, two cross-sectional following longitudinal studies, and one cohort study met the inclusion criteria. For light to moderate alcohol consumption (LMAC), there was a 22.6% reduction in risk of FLD (odds ratio [OR] = 0.774, 95% confidence interval CI [0.695–0.862], P <0.001), and subgroup analysis showed that a greater reduction in risk of FLD was found in the female drinkers (30.2%) and the drinkers with BMI ≥25 kg/m2(31.3%) compared with the male drinkers (22.6%) and the drinkers with BMI <25 kg/m2(21.3%), respectively. For heavy alcohol consumption, there was no significant influence on risk of FLD (OR = 0.869, 95% CI [0.553–1.364], P = 0.541) in Japanese women, but there was a 33.7% reduction in risk of FLD (OR = 0.663, 95% CI [0.574–0.765], P < 0.001) in Japanese men and a significant increased risk of FLD (OR = 1.785, 95% CI [1.064–2.996], P = 0.028) in Germans.ConclusionLMAC is associated with a significant protective effect on FLD in the studied population, especially in the women and obese population. However, the effect of heavy alcohol consumption on FLD remains unclear due to limited studies and small sample sizes. creator: Guoli Cao creator: Tingzhuang Yi creator: Qianqian Liu creator: Min Wang creator: Shaohui Tang uri: https://doi.org/10.7717/peerj.2633 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cao et al. title: Social buffering and contact transmission: network connections have beneficial and detrimental effects on Shigella infection risk among captive rhesus macaques link: https://peerj.com/articles/2630 last-modified: 2016-10-27 description: In social animals, group living may impact the risk of infectious disease acquisition in two ways. On the one hand, social connectedness puts individuals at greater risk or susceptibility for acquiring enteric pathogens via contact-mediated transmission. Yet conversely, in strongly bonded societies like humans and some nonhuman primates, having close connections and strong social ties of support can also socially buffer individuals against susceptibility or transmissibility of infectious agents. Using social network analyses, we assessed the potentially competing roles of contact-mediated transmission and social buffering on the risk of infection from an enteric bacterial pathogen (Shigella flexneri) among captive groups of rhesus macaques (Macaca mulatta). Our results indicate that, within two macaque groups, individuals possessing more direct and especially indirect connections in their grooming and huddling social networks were less susceptible to infection. These results are in sharp contrast to several previous studies that indicate that increased (direct) contact-mediated transmission facilitates infectious disease transmission, including our own findings in a third macaque group in which individuals central in their huddling network and/or which initiated more fights were more likely to be infected. In summary, our findings reveal that an individual’s social connections may increase or decrease its chances of acquiring infectious agents. They extend the applicability of the social buffering hypothesis, beyond just stress and immune-function-related health benefits, to the additional health outcome of infectious disease resistance. Finally, we speculate that the circumstances under which social buffering versus contact-mediated transmission may occur could depend on multiple factors, such as living condition, pathogen-specific transmission routes, and/or an overall social context such as a group’s social stability. creator: Krishna Balasubramaniam creator: Brianne Beisner creator: Jessica Vandeleest creator: Edward Atwill creator: Brenda McCowan uri: https://doi.org/10.7717/peerj.2630 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Balasubramaniam et al. title: Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights link: https://peerj.com/articles/2647 last-modified: 2016-10-27 description: BackgroundAbundant pan-trionychid (soft-shell) turtles specimens have been found in Eocene sequences of central Europe, particularly from two localities in Germany, the Messel Pit (a UNESCO World Natural Heritage Site) and Geiseltal, traditionally attributed to Trionyx messelianus or Rafetoides austriacus. Over the last two decades new specimens of this taxon from these two localities have been discovered and fully prepared. However, they have remained unstudied, as well as their phylogenetic position inside Pan-Trionychidae is unknown.ResultsFive new specimens of Palaeoamyda messeliana nov. comb. from Messel Pit and Geiseltal localities are fully described here. A revised diagnosis for the species is also presented here, together with its inclusion in a phylogenetic analysis of Pan-Trionychidae that shows that this species is sister to the extant Amyda cartilaginea, one of the most abundant pan-trionychid (soft-shell) turtles from Asia, both members of the clade Chitrini. The specimens described in here are among the best and most complete fossil pan-trionychid skeletons so far known. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.2647 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cadena title: Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast link: https://peerj.com/articles/2628 last-modified: 2016-10-27 description: Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites. creator: Josefine Larsson creator: Mikael Lönn creator: Emma E. Lind creator: Justyna Świeżak creator: Katarzyna Smolarz creator: Mats Grahn uri: https://doi.org/10.7717/peerj.2628 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Larsson et al. title: Widespread dieback of riparian trees on a dammed ephemeral river and evidence of local mitigation by tributary flows link: https://peerj.com/articles/2622 last-modified: 2016-10-27 description: Ephemeral rivers act as linear oases in drylands providing key resources to people and wildlife. However, not much is known about these rivers’ sensitivities to human activities. We investigated the landscape-level determinants of riparian tree dieback along the Swakop River, a dammed ephemeral river in Namibia, focusing on the native ana tree (Faidherbia albida) and the invasive mesquite (Prosopis spp.). We surveyed over 1,900 individual trees distributed across 24 sites along a 250 km stretch of the river. General linear mixed models were used to test five hypotheses relating to three anthropogenic threats: river flow disruption from damming, human settlement and invasive species. We found widespread dieback in both tree populations: 51% mortality in ana tree, with surviving trees exhibiting 18% canopy death (median); and 26% mortality in mesquite, with surviving trees exhibiting 10% canopy death. Dieback in the ana tree was most severe where trees grew on drier stretches of the river, where tributary flow was absent and where mesquite grew more abundantly. Dieback in the mesquite, a more drought-tolerant taxon, did not show any such patterns. Our findings suggest that dieback in the ana tree is primarily driven by changes in river flow resulting from upstream dam creation and that tributary flows provide a local buffer against this loss of main channel flow. The hypothesis that the invasive mesquite may contribute to ana tree dieback was also supported. Our findings suggest that large dams along the main channels of ephemeral rivers have the ability to cause widespread mortality in downstream riparian trees. To mitigate such impacts, management might focus on the maintenance of natural tributary flows to buffer local tree populations from the disruption to main channel flow. creator: Caitlin M. S. Douglas creator: Mark Mulligan creator: Xavier A. Harrison creator: Joh R. Henschel creator: Nathalie Pettorelli creator: Guy Cowlishaw uri: https://doi.org/10.7717/peerj.2622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Douglas et al. title: Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses link: https://peerj.com/articles/2620 last-modified: 2016-10-27 description: The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. One PeTIFY belongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins of Arabidopsis and Oryza sativa indicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship between P. edulis, O. sativa, and B. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication of PeTIFY may have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among the P. edulis-O. sativa, P. edulis-B. distachyon, and O. sativa-B. distachyon was approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% of PeTIFY genes could be up-regulated by cold and dehydration stresses, and some PeTIFYs also share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress. creator: Zhuo Huang creator: Si-Han Jin creator: Han-Du Guo creator: Xiao-Juan Zhong creator: Jiao He creator: Xi Li creator: Ming-Yan Jiang creator: Xiao-Fang Yu creator: Hai Long creator: Ming-Dong Ma creator: Qi-Bing Chen uri: https://doi.org/10.7717/peerj.2620 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huang et al. title: The PARA-suite: PAR-CLIP specific sequence read simulation and processing link: https://peerj.com/articles/2619 last-modified: 2016-10-27 description: BackgroundNext-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein–RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth.MethodsWe here compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. We developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows–Wheeler Aligner algorithm and CLIP read clustering for binding site detection.ResultsWe show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. We examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. We demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. Our processing pipeline allowed the improvement of both alignment and binding site detection accuracy.AvailabilityThe PARA-suite toolkit and the PARA-suite aligner are available at https://github.com/akloetgen/PARA-suite and https://github.com/akloetgen/PARA-suite_aligner, respectively, under the GNU GPLv3 license. creator: Andreas Kloetgen creator: Arndt Borkhardt creator: Jessica I. Hoell creator: Alice C. McHardy uri: https://doi.org/10.7717/peerj.2619 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kloetgen et al. title: Human altruistic tendencies vary with both the costliness of selfless acts and socioeconomic status link: https://peerj.com/articles/2610 last-modified: 2016-10-27 description: Altruism toward strangers is considered a defining feature of humans. However, manifestation of this behaviour is contingent on the costliness of the selfless act. The extent of altruistic tendencies also varies cross-culturally, being more common in societies with higher levels of market integration. However, the existence of local variation in selfless behaviour within populations has received relatively little empirical attention. Using a ‘lost letter’ design, we dropped 300 letters (half of them stamped, half of them unstamped) in 15 residential suburbs of the greater Perth area that differ markedly in socioeconomic status. The number of returned letters was used as evidence of altruistic behaviour. Costliness was assessed by comparing return rates for stamped vs. unstamped letters. We predicted that there is a positive association between suburb socioeconomic status and number of letters returned and that altruistic acts decrease in frequency when costs increase, even minimally. Both predictions were solidly supported and demonstrate that socioeconomic deprivation and elevated performance costs independently impinge on the universality of altruistic behaviour in humans. creator: Cyril C. Grueter creator: Jesse A. Ingram creator: James W. Lewisson creator: Olivia R. Bradford creator: Melody Taba creator: Rebecca E. Coetzee creator: Michelle A. Sherwood uri: https://doi.org/10.7717/peerj.2610 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Grueter et al. title: Specialization on pollen or nectar in bumblebee foragers is not associated with ovary size, lipid reserves or sensory tuning link: https://peerj.com/articles/2599 last-modified: 2016-10-27 description: Foraging specialization allows social insects to more efficiently exploit resources in their environment. Recent research on honeybees suggests that specialization on pollen or nectar among foragers is linked to reproductive physiology and sensory tuning (the Reproductive Ground-Plan Hypothesis; RGPH). However, our understanding of the underlying physiological relationships in non-Apis bees is still limited. Here we show that the bumblebee Bombus terrestris has specialist pollen and nectar foragers, and test whether foraging specialization in B. terrestris is linked to reproductive physiology, measured as ovarian activation. We show that neither ovary size, sensory sensitivity, measured through proboscis extension response (PER), or whole-body lipid stores differed between pollen foragers, nectar foragers, or generalist foragers. Body size also did not differ between any of these three forager groups. Non-foragers had significantly larger ovaries than foragers. This suggests that potentially reproductive individuals avoid foraging. creator: Adam R. Smith creator: Peter Graystock creator: William O.H. Hughes uri: https://doi.org/10.7717/peerj.2599 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Smith et al. title: Evolution of genes involved in feeding preference and metabolic processes in Calliphoridae (Diptera: Calyptratae) link: https://peerj.com/articles/2598 last-modified: 2016-10-27 description: BackgroundThe genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae). Closely related species in this family exhibit distinct larval feeding habits, most notably necro-saprophagy and obligate parasitism.MethodsTo understand the genetic and molecular bases underlying these habits, expression levels of eight candidate genes for feeding behavior—Cyp6g2, foraging, glutamate dehydrogenase, Jonah65aiv, Malvolio, PGRP-SC2, RPS6-p70-protein kinase, and smooth—were measured in four species using qPCR. Moreover we used expression values and sequence information to reconstruct the relationship among species and the dN/dS rate to infer possible sites under selection.ResultsFor most candidate genes, no statistically significant differences were observed, indicating a high degree of conservation in expression. However, Malvolio was differentially expressed between habits. Evolutionary analyses based on transcript levels and nucleotide sequences of Malvolio coding region suggest that transcript levels were correlated to feeding habit preferences among species, although deviations under a strictly neutral model were also observed in statistical tests.DiscussionMalvolio was the only gene demonstrating a possible connection to feeding habit. Differences in gene expression may be involved in (or be a result of) the genetic regulation of Calliphoridae feeding habit. Our results are the first steps towards understanding the genetic basis and evolution of feeding behavior in Calliphoridae using a functional approach. creator: Gisele Antoniazzi Cardoso creator: Marco Antonio Tonus Marinho creator: Raquel Dietsche Monfardini creator: Ana Maria Lima de Azeredo Espin creator: Tatiana Teixeira Torres uri: https://doi.org/10.7717/peerj.2598 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cardoso et al. title: The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance link: https://peerj.com/articles/2595 last-modified: 2016-10-27 description: Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria. creator: Katherine H. Tanaka creator: Antony T. Vincent creator: Mélanie V. Trudel creator: Valérie E. Paquet creator: Michel Frenette creator: Steve J. Charette uri: https://doi.org/10.7717/peerj.2595 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Tanaka et al. title: Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod link: https://peerj.com/articles/2593 last-modified: 2016-10-27 description: Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs. creator: Alan J. Couch creator: Peter J. Unmack creator: Fiona J. Dyer creator: Mark Lintermans uri: https://doi.org/10.7717/peerj.2593 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Couch et al. title: Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences link: https://peerj.com/articles/2594 last-modified: 2016-10-27 description: Comparative efforts to understand the body plan evolution of stalked jellyfishes are scarce. Most characters, and particularly internal anatomy, have neither been explored for the class Staurozoa, nor broadly applied in its taxonomy and classification. Recently, a molecular phylogenetic hypothesis was derived for Staurozoa, allowing for the first broad histological comparative study of staurozoan taxa. This study uses comparative histology to describe the body plans of nine staurozoan species, inferring functional and evolutionary aspects of internal morphology based on the current phylogeny of Staurozoa. We document rarely-studied structures, such as ostia between radial pockets, intertentacular lobules, gametoducts, pad-like adhesive structures, and white spots of nematocysts (the last four newly proposed putative synapomorphies for Staurozoa). Two different regions of nematogenesis are documented. This work falsifies the view that the peduncle region of stauromedusae only retains polypoid characters; metamorphosis from stauropolyp to stauromedusa occurs both at the apical region (calyx) and basal region (peduncle). Intertentacular lobules, observed previously in only a small number of species, are shown to be widespread. Similarly, gametoducts were documented in all analyzed genera, both in males and females, thereby elucidating gamete release. Finally, ostia connecting adjacent gastric radial pockets appear to be universal for Staurozoa. Detailed histological studies of medusozoan polyps and medusae are necessary to further understand the relationships between staurozoan features and those of other medusozoan cnidarians. creator: Lucília S. Miranda creator: Allen G. Collins creator: Yayoi M. Hirano creator: Claudia E. Mills creator: Antonio C. Marques uri: https://doi.org/10.7717/peerj.2594 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Miranda et al. title: Pacing during an ultramarathon running event in hilly terrain link: https://peerj.com/articles/2591 last-modified: 2016-10-27 description: PurposeThe dynamics of speed selection as a function of distance, or pacing, are used in recreational, competitive, and scientific research situations as an indirect measure of the psycho-physiological status of an individual. The purpose of this study was to determine pacing on level, uphill and downhill sections of participants in a long (>80 km) ultramarathon performed on trails in hilly terrain.MethodsFifteen ultramarathon runners competed in a  173 km event (five finished at  103 km) carrying a Global-Positioning System (GPS) device. Using the GPS data, we determined the speed, relative to average total speed, in level (LEV), uphill (UH) and downhill (DH) gradient categories as a function of total distance, as well as the correlation between overall performance and speed variability, speed loss, and total time stopped.ResultsThere were no significant differences in normality, variances or means in the relative speed in 173-km and 103-km participants. Relative speed decreased in LEV, UH and DH. The main component of speed loss occurred between 5% and 50% of the event distance in LEV, and between 5% and 95% in UH and DH. There were no significant correlations between overall performance and speed loss, the variability of speed, or total time stopped.ConclusionsPositive pacing was observed at all gradients, with the main component of speed loss occurring earlier (mixed pacing) in LEV compared to UH and DH. A speed reserve (increased speed in the last section) was observed in LEV and UH. The decrease in speed and variability of speed were more important in LEV and DH than in UH. The absence of a significant correlation between overall performance and descriptors of pacing is novel and indicates that pacing in ultramarathons in trails and hilly terrain differs to other types of running events. creator: Hugo A. Kerhervé creator: Tom Cole-Hunter creator: Aaron N. Wiegand creator: Colin Solomon uri: https://doi.org/10.7717/peerj.2591 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kerhervé et al. title: The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant link: https://peerj.com/articles/2581 last-modified: 2016-10-27 description: Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana. Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant. creator: Sarah-Anne Jeanetta Selier creator: Rob Slotow creator: Enrico Di Minin uri: https://doi.org/10.7717/peerj.2581 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Selier et al. title: A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000 link: https://peerj.com/articles/2564 last-modified: 2016-10-27 description: Outbreaks of porcine epidemic diarrhea (PED) were first recorded in England in the 1970s and continued to be confirmed until 2002. Retrospective analysis of archived material from one of the last confirmed cases in England in the year 2000 demonstrates the previous existence of a very diverse PED virus strain. Following the outbreaks of PED in North America in 2013, there has been renewed interest in phylogenetic analysis of sequences from PEDV strains worldwide. There is a gap in the available sequence data between the mid 1980s and the mid 2000s. This work is an example of how this gap can be at least partially filled by the examination of archived material. creator: Falko Steinbach creator: Akbar Dastjerdi creator: Julie Peake creator: S. Anna La Rocca creator: Frank P. Tobin creator: Jean-Pierre Frossard creator: Susanna Williamson uri: https://doi.org/10.7717/peerj.2564 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Steinbach et al. title: Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies link: https://peerj.com/articles/2631 last-modified: 2016-10-26 description: The role of kin-selection in the evolution of post-reproductive life is controversial. While anthropological and demographic studies strongly suggest that humans and a few other species experience kin selection for significant post-reproductive survival, these results are necessarily correlational. Understanding could therefore be advanced by the development of a globally available, field and laboratory tractable experimental model of kin-selected post-reproductive survival. In only one invertebrate (Quadrartus yoshinomiyai, a gall-forming aphid endemic to Japan) have individuals too old to reproduce been shown to be both numerous in natural habitats and able to help close relatives survive or reproduce. Pea aphids, (Acyrthosiphon pisum), common, tractable organisms, frequently outlive their reproductive ages in laboratories, live in tight interacting groups that are often clonal, and therefore should be evaluated as potential model organisms for the study of adaptive post-reproductive life. The first major step in this process is to identify an optimal method for assessing if a parthenogenetic adult is post-reproductive. We evaluated three methods, relying respectively on isolation in clip cages, visual examination for embryonic eyespots, and dissection. In every case each method identified the same individuals as reproductive versus post-reproductive. While the clip-cage method requires a multi-day wait to produce data, and dissection is inevitably fatal, the eyespot method is quick (under one minute per individual) easy, and non-invasive. This method makes it possible to accurately assess the post-reproductive status of a large number of parthenogenetic pea aphids. We demonstrate the usefulness of the eyespot method in showing that while reproductively valuable adults tend to place themselves near the centers of clonal colonies, less valuable post-reproductive adults are more often at or beyond the edges of colonies. These encouraging early results provide both impetuous and aid for further investigations into the post-reproductive lives of pea aphids. creator: Erik T. Saberski creator: Julia Daisy Diamond creator: Nathaniel Fath Henneman creator: Daniel A. Levitis uri: https://doi.org/10.7717/peerj.2631 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Saberski et al. title: Early evolution of polyisoprenol biosynthesis and the origin of cell walls link: https://peerj.com/articles/2626 last-modified: 2016-10-26 description: After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor. creator: Jonathan Lombard uri: https://doi.org/10.7717/peerj.2626 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lombard title: In silico study on anti-Chikungunya virus activity of hesperetin link: https://peerj.com/articles/2602 last-modified: 2016-10-26 description: BackgroundThe re-emerging, Aedes spp. transmitted Chikungunya virus (CHIKV) has recently caused large outbreaks in a wide geographical distribution of the world including countries in Europe and America. Though fatalities associated with this self-remitting disease were rarely reported, quality of patients’ lives have been severely diminished by polyarthralgia recurrence. Neither effective antiviral treatment nor vaccines are available for CHIKV. Our previous in vitro screening showed that hesperetin, a bioflavonoid exhibits inhibitory effect on the virus intracellular replication. Here, we present a study using the computational approach to identify possible target proteins for future mechanistic studies of hesperetin.Methods3D structures of CHIKV nsP2 (3TRK) and nsP3 (3GPG) were retrieved from Protein Data Bank (PDB), whereas nsP1, nsP4 and cellular factor SPK2 were modeled using Iterative Threading Assembly Refinement (I-TASSER) server based on respective amino acids sequence. We performed molecular docking on hesperetin against all four CHIKV non-structural proteins and SPK2. Proteins preparation and subsequent molecular docking were performed using Discovery Studio 2.5 and AutoDock Vina 1.5.6. The Lipinski’s values of the ligand were computed and compared with the available data from PubChem. Two non-structural proteins with crystal structures 3GPG and 3TRK in complexed with hesperetin, demonstrated favorable free energy of binding from the docking study, were further explored using molecular dynamics (MD) simulations.ResultsWe observed that hesperetin interacts with different types of proteins involving hydrogen bonds, pi-pi effects, pi-cation bonding and pi-sigma interactions with varying binding energies. Among all five tested proteins, our compound has the highest binding affinity with 3GPG at −8.5 kcal/mol. The ligand used in this study also matches the Lipinski’s rule of five in addition to exhibiting closely similar properties with that of in PubChem. The docking simulation was performed to obtain a first guess of the binding structure of hesperetin complex and subsequently analysed by MD simulations to assess the reliability of the docking results. Root mean square deviation (RMSD) of the simulated systems from MD simulations indicated that the hesperetin complex remains stable within the simulation timescale.DiscussionThe ligand’s tendencies of binding to the important proteins for CHIKV replication were consistent with our previous in vitro screening which showed its efficacy in blocking the virus intracellular replication. NsP3 serves as the highest potential target protein for the compound’s inhibitory effect, while it is interesting to highlight the possibility of interrupting CHIKV replication via interaction with host cellular factor. By complying the Lipinski’s rule of five, hesperetin exhibits drug-like properties which projects its potential as a therapeutic option for CHIKV infection. creator: Adrian Oo creator: Pouya Hassandarvish creator: Sek Peng Chin creator: Vannajan Sanghiran Lee creator: Sazaly Abu Bakar creator: Keivan Zandi uri: https://doi.org/10.7717/peerj.2602 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Oo et al. title: Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae) link: https://peerj.com/articles/2627 last-modified: 2016-10-25 description: BackgroundThe chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum.MethodsThe Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed.ResultsThe 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site.DiscussionOur results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites. creator: Jean-Simon Brouard creator: Monique Turmel creator: Christian Otis creator: Claude Lemieux uri: https://doi.org/10.7717/peerj.2627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Brouard et al. title: A 12-year record of intertidal barnacle recruitment in Atlantic Canada (2005–2016): relationships with sea surface temperature and phytoplankton abundance link: https://peerj.com/articles/2623 last-modified: 2016-10-25 description: On the Gulf of St. Lawrence coast of Nova Scotia (Canada), recruitment of the barnacle Semibalanus balanoides occurs in May and June. Every year in June between 2005 and 2016, we recorded recruit density for this barnacle at the same wave-exposed rocky intertidal location on this coast. During these 12 years, mean recruit density was lowest in 2015 (198 recruits dm−2) and highest in 2007 (969 recruits dm−2). The highest recruit density observed in a single quadrat was 1,457 recruits dm−2 (in 2011) and the lowest was 34 recruits dm−2 (in 2015). Most barnacle recruits appear during May, which suggests that most pelagic larvae (which develop over 5–6 weeks before benthic settlement) are in the water column in April. An AICc-based model selection approach identified sea surface temperature (SST) in April and the abundance of phytoplankton (food for barnacle larvae, measured as chlorophyll-a concentration –Chl-a–) in April as good explanatory variables. Together, April SST and April Chl-a explained 51% of the observed interannual variation in recruit density, with an overall positive influence. April SST was positively related to March–April air temperature (AT). April Chl-a was negatively related to the April ratio between the number of days with onshore winds (which blow from phytoplankton-limited offshore waters) and the number of days with alongshore winds (phytoplankton is more abundant on coastal waters). Therefore, this study suggests that climatic processes affecting April SST and April Chl-a indirectly influence intertidal barnacle recruitment by influencing larval performance. creator: Ricardo A. Scrosati creator: Julius A. Ellrich uri: https://doi.org/10.7717/peerj.2623 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Scrosati and Ellrich title: Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats link: https://peerj.com/articles/2614 last-modified: 2016-10-25 description: Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health. creator: Massimo Ponti creator: Francesca Fratangeli creator: Nicolò Dondi creator: Marco Segre Reinach creator: Clara Serra creator: Michael J. Sweet uri: https://doi.org/10.7717/peerj.2614 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ponti et al. title: A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex link: https://peerj.com/articles/2609 last-modified: 2016-10-25 description: The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type. creator: Hao Zhang creator: Balázs Brankovics creator: Theo A.J. van der Lee creator: Cees Waalwijk creator: Anne A.D. van Diepeningen creator: Jin Xu creator: Jingsheng Xu creator: Wanquan Chen creator: Jie Feng uri: https://doi.org/10.7717/peerj.2609 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhang et al. title: Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California link: https://peerj.com/articles/2583 last-modified: 2016-10-25 description: The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf. creator: Erika Magallón-Gayón creator: Pindaro Diaz-Jaimes creator: Manuel Uribe-Alcocer uri: https://doi.org/10.7717/peerj.2583 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Magallón-Gayón et al. title: The impact of IL-6 and IL-28B gene polymorphisms on treatment outcome of chronic hepatitis C infection among intravenous drug users in Croatia link: https://peerj.com/articles/2576 last-modified: 2016-10-25 description: BackgroundSeveral genes and their single nucleotide polymorphisms (SNPs) are associated with either spontaneous resolution of hepatitis C infection or better treatment-induced viral clearance. We tested a cohort of intravenous drug users (IVDU) diagnosed with chronic hepatitis C virus (HCV) for treatment response and its association with the SNPs in the interleukin-6 (rs1800795-IL6) and the interleukin-28B (rs12979860-IL28B) genes.MethodsThe study included 110 Croatian IVDU positive for anti-HCV antibody. Genotyping was performed by polymerase chain reaction (PCR) based approach. Patients were treated by standard pegylated-interferon/ribavirin and followed throughout a period of four years, during which sustained virological response (SVR) was determined. All data were analysed with statistical package SPSS 19.0 (IBM Corp, Armonk, NY, USA) and PLINK v1.07 software.ResultsPatients showed a significantly better response to treatment according to the number of copies of the C allele carried at rs1800795-IL6 (P = 0.034). All but one of the patients with CC genotype achieved SVR (93%), whereas the response rate of patients with GG genotype was 64%. The association of rs1800795-IL6 with SVR status remained significant after further adjustment for patients’ age, fibrosis staging, and viral genotype (OR 2.15, 95% CI 1.16–4.68, P = 0.019). Distributions of allele frequencies at the locus rs12979860-IL28B among the study cohort and the underlying general population were suggestive of a protective effect of CC genotype in acquiring chronic hepatitis C in the Croatian IVDU population.DiscussionThe rs1800795-IL6 polymorphism is associated with positive response to treatment in IVDU patients positive for HCV infection. A protective role of rs12979860-IL28B CC genotype in acquiring chronic hepatitis C is suggested for Croatian IVDU population. creator: Zoran Bogdanović creator: Ivana Marinović-Terzić creator: Sendi Kuret creator: Ana Jerončić creator: Nikola Bradarić creator: Gea Forempoher creator: Ozren Polašek creator: Šimun Anđelinović creator: Janoš Terzić uri: https://doi.org/10.7717/peerj.2576 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bogdanović et al. title: Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity link: https://peerj.com/articles/2570 last-modified: 2016-10-25 description: The majority of bacterial foliar plant pathogens must invade the apoplast of host plants through points of ingress, such as stomata or wounds, to replicate to high population density and cause disease. How pathogens navigate plant surfaces to locate invasion sites remains poorly understood. Many bacteria use chemical-directed regulation of flagellar rotation, a process known as chemotaxis, to move towards favorable environmental conditions. Chemotactic sensing of the plant surface is a potential mechanism through which foliar plant pathogens home in on wounds or stomata, but chemotactic systems in foliar plant pathogens are not well characterized. Comparative genomics of the plant pathogen Pseudomonas syringae pathovar tomato (Pto) implicated annotated chemotaxis genes in the recent adaptations of one Pto lineage. We therefore characterized the chemosensory system of Pto. The Pto genome contains two primary chemotaxis gene clusters, che1 and che2. The che2 cluster is flanked by flagellar biosynthesis genes and similar to the canonical chemotaxis gene clusters of other bacteria based on sequence and synteny. Disruption of the primary phosphorelay kinase gene of the che2 cluster, cheA2, eliminated all swimming and surface motility at 21 °C but not 28 °C for Pto. The che1 cluster is located next to Type IV pili biosynthesis genes but disruption of cheA1 has no observable effect on twitching motility for Pto. Disruption of cheA2 also alters in planta fitness of the pathogen with strains lacking functional cheA2 being less fit in host plants but more fit in a non-host interaction. creator: Christopher R. Clarke creator: Byron W. Hayes creator: Brendan J. Runde creator: Eric Markel creator: Bryan M. Swingle creator: Boris A. Vinatzer uri: https://doi.org/10.7717/peerj.2570 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Clarke et al. title: Antimicrobial activity of Tachyplesin 1 against Burkholderia pseudomallei: an in vitro and in silico approach link: https://peerj.com/articles/2468 last-modified: 2016-10-25 description: Burkholderia pseudomallei, the causative agent of melioidosis, is intrinsically resistant to many conventional antibiotics. Therefore, alternative antimicrobial agents such as antimicrobial peptides (AMPs) are extensively studied to combat this issue. Our study aims to identify and understand the mode of action of the potential AMP(s) that are effective against B. pseudomallei in both planktonic and biofilm state as well as to predict the possible binding targets on using in vitro and in silico approaches. In the in vitro study, 11 AMPs were tested against 100 B. pseudomallei isolates for planktonic cell susceptibility, where LL-37, and PG1, demonstrated 100.0% susceptibility and TP1 demonstrated 83% susceptibility. Since the B. pseudomallei activity was reported on LL-37 and PG1, TP1 was selected for further investigation. TP1 inhibited B. pseudomallei cells at 61.69 μM, and membrane blebbing was observed using scanning electron microscopy. Moreover, TP1 inhibited B. pseudomallei cell growth, reaching bactericidal endpoint within 2 h post exposure as compared to ceftazidime (CAZ) (8 h). Furthermore, TP1 was shown to suppress the growth of B. pseudomallei cells in biofilm state at concentrations above 221 μM. However, TP1 was cytotoxic to the mammalian cell lines tested. In the in silico study, molecular docking revealed that TP1 demonstrated a strong interaction to the common peptide or inhibitor binding targets for lipopolysaccharide of Escherichia coli, as well as autolysin, pneumolysin, and pneumococcal surface protein A (PspA) of Streptococcus pneumoniae. Homology modelled B. pseudomallei PspA protein (YDP) also showed a favourable binding with a strong electrostatic contribution and nine hydrogen bonds. In conclusion, TP1 demonstrated a good potential as an anti-B. pseudomallei agent. creator: Lyn-Fay Lee creator: Vanitha Mariappan creator: Kumutha Malar Vellasamy creator: Vannajan Sanghiran Lee creator: Jamuna Vadivelu uri: https://doi.org/10.7717/peerj.2468 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lee et al. title: A pilot study examining the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular risk factors in cancer survivors link: https://peerj.com/articles/2613 last-modified: 2016-10-20 description: Purpose The aim of this study was to evaluate the effects of low-volume high-intensity interval training and continuous low to moderate intensity training on quality of life, functional capacity and cardiovascular disease risk factors in cancer survivors.MethodsCancer survivors within 24 months post-diagnosis were randomly assigned into the low-volume high-intensity interval training group (n = 8) or the continuous low to moderate intensity training group (n = 8) group for 36 sessions (12 weeks) of supervised exercise. The low-volume high-intensity interval training (LVHIIT) group performed 7 × 30 s intervals (≥85% maximal heart rate) and the continuous low to moderate intensity training (CLMIT) group performed continuous aerobic training for 20 min (≤55% maximal heart rate) on a stationary bike or treadmill.ResultsSignificant improvements (time) were observed for 13 of the 23 dependent variables (ES 0.05–0.61, p ≤ 0.05). An interaction effect was observed for six minute walk test (18.53% [32.43–4.63] ES 0.50, p ≤ 0.01) with the LVHIIT group demonstrating greater improvements.ConclusionThese preliminary findings suggest that both interventions can induce improvements in quality of life, functional capacity and selected cardiovascular disease risk factors. The LVHIIT program was well tolerated by the participants and our results suggest that LVHIIT is the preferred modality to improve fitness (6MWT); it remains to be seen which intervention elicits the most clinically relevant outcomes for patients. A larger sample size with a control group is required to confirm the significance of these findings. creator: Kellie Toohey creator: Kate L. Pumpa creator: Leonard Arnolda creator: Julie Cooke creator: Desmond Yip creator: Paul S. Craft creator: Stuart Semple uri: https://doi.org/10.7717/peerj.2613 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Toohey et al. title: Nonlinear temperature effects on multifractal complexity of metabolic rate of mice link: https://peerj.com/articles/2607 last-modified: 2016-10-20 description: Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so, we examine the multifractal temporal scaling properties of the rate of change in oxygen consumption r(VO2), in the laboratory mouse Mus musculus, assessing their long range correlation properties across seven different environmental temperatures, ranging from 0 °C to 30 °C. To do so, we applied multifractal detrended fluctuation analysis (MF-DFA), finding that r(VO2) fluctuations show two scaling regimes. For small time scales below the crossover time (approximately 102 s), either monofractal or weak multifractal dynamics are observed depending on whether Ta < 15 °C or Ta > 15 °C respectively. For larger time scales, r(VO2) fluctuations are characterized by an asymptotic scaling exponent that indicates multifractal anti-persistent or uncorrelated dynamics. For both scaling regimes, a generalization of the multiplicative cascade model provides very good fits for the Renyi exponents τ(q), showing that the infinite number of exponents h(q) can be described by only two independent parameters, a and b. We also show that the long-range correlation structure of r(VO2) time series differs from randomly shuffled series, and may not be explained as an artifact of stochastic sampling of a linear frequency spectrum. These results show that metabolic rate dynamics in a well studied micro-endotherm are consistent with a highly non-linear feedback control system. creator: Fabio A. Labra creator: Jose M. Bogdanovich creator: Francisco Bozinovic uri: https://doi.org/10.7717/peerj.2607 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Labra et al. title: Taxonomy of Platypterygius campylodon and the diversity of the last ichthyosaurs link: https://peerj.com/articles/2604 last-modified: 2016-10-20 description: A complex and confusing taxonomy has concealed the diversity dynamics of Cretaceous ichthyosaurs (Reptilia) for decades. The near totality of Albian-Cenomanian remains from Eurasia has been assigned, by default, to the loosely defined entity Platypterygius campylodon, whose holotype was supposed to be lost. By thoroughly examining the Cenomanian ichthyosaur collections from the UK, I redescribe the syntypic series of Platypterygius campylodon. This material, along with a handful of other coeval remains, is diagnostic and seemingly differs from the vast majority of Cretaceous remains previously assigned to this taxon. A lectotype for Platypterygius campylodon is designated and I reassign this species to Pervushovisaurus campylodon nov. comb. The feeding ecology of this species is assessed and conforms to the scenario of an early Cenomanian diversity drop prior to the latest Cenomanian final extinction. creator: Valentin Fischer uri: https://doi.org/10.7717/peerj.2604 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fischer title: Effects of 14-day oral low dose selenium nanoparticles and selenite in rat—as determined by metabolite pattern determination link: https://peerj.com/articles/2601 last-modified: 2016-10-20 description: Selenium (Se) is an essential element with a small difference between physiological and toxic doses. To provide more effective and safe Se dosing regimens, as compared to dosing with ionic selenium, nanoparticle formulations have been developed. However, due to the nano-formulation, unexpected toxic effects may occur. We used metabolite pattern determination in urine to investigate biological and/or toxic effects in rats administered nanoparticles and for comparison included ionic selenium at an equimolar dose in the form of sodium selenite. Low doses of 10 and 100 fold the recommended human high level were employed to study the effects at borderline toxicity. Evaluations of all significantly changed putative metabolites, showed that Se nanoparticles and sodium selenite induced similar dose dependent changes of the metabolite pattern. Putative identified metabolites included increased decenedioic acid and hydroxydecanedioic acid for both Se formulations whereas dipeptides were only increased for selenite. These effects could reflect altered fatty acid and protein metabolism, respectively. creator: Niels Hadrup creator: Katrin Loeschner creator: Kasper Skov creator: Gitte Ravn-Haren creator: Erik H. Larsen creator: Alicja Mortensen creator: Henrik R. Lam creator: Henrik L. Frandsen uri: https://doi.org/10.7717/peerj.2601 license: http://creativecommons.org/licenses/by/3.0/ rights: ©2016 Hadrup et al. title: Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic link: https://peerj.com/articles/2597 last-modified: 2016-10-20 description: Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery. creator: Diego Lirman creator: Stephanie Schopmeyer uri: https://doi.org/10.7717/peerj.2597 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lirman and Schopmeyer title: A revision of Sanpasaurus yaoi Young, 1944 from the Early Jurassic of China, and its relevance to the early evolution of Sauropoda (Dinosauria) link: https://peerj.com/articles/2578 last-modified: 2016-10-20 description: The Early Jurassic of China has long been recognized for its diverse array of sauropodomorph dinosaurs. However, the contribution of this record to our understanding of early sauropod evolution is complicated by a dearth of information on important transitional taxa. We present a revision of the poorly known taxon Sanpasaurus yaoiYoung, 1944 from the late Early Jurassic Ziliujing Formation of Sichuan Province, southwest China. Initially described as the remains of an ornithopod ornithischian, we demonstrate that the material catalogued as IVPP V156 is unambiguously referable to Sauropoda. Although represented by multiple individuals of equivocal association, Sanpasaurus is nonetheless diagnosable with respect to an autapomorphic feature of the holotypic dorsal vertebral series. Additional material thought to be collected from the type locality is tentatively referred to Sanpasaurus. If correctly attributed, a second autapomorphy is present in a referred humerus. The presence of a dorsoventrally compressed pedal ungual in Sanpasaurus is of particular interest, with taxa possessing this typically ‘vulcanodontid’ character exhibiting a much broader geographic distribution than previously thought. Furthermore, the association of this trait with other features of Sanpasaurus that are broadly characteristic of basal eusauropods underscores the mosaic nature of the early sauropod–eusauropod transition. Our revision of Sanpasaurus has palaeobiogeographic implications for Early Jurassic sauropods, with evidence that the group maintained a cosmopolitan Pangaean distribution. creator: Blair W. McPhee creator: Paul Upchurch creator: Philip D. Mannion creator: Corwin Sullivan creator: Richard J. Butler creator: Paul M. Barrett uri: https://doi.org/10.7717/peerj.2578 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 McPhee et al. title: Predictions of potential geographical distribution and quality of Schisandra sphenanthera under climate change link: https://peerj.com/articles/2554 last-modified: 2016-10-20 description: Climate change will significantly affect plant distribution as well as the quality of medicinal plants. Although numerous studies have analyzed the effect of climate change on future habitats of plants through species distribution models (SDMs), few of them have incorporated the change of effective content of medicinal plants. Schisandra sphenanthera Rehd. et Wils. is an endangered traditional Chinese medical plant which is mainly located in the Qinling Mountains. Combining fuzzy theory and a maximum entropy model, we obtained current spatial distribution of quality assessment for S. spenanthera. Moreover, the future quality and distribution of S. spenanthera were also projected for the periods 2020s, 2050s and 2080s under three different climate change scenarios (SRES-A1B, SRES-A2 and SRES-B1 emission scenarios) described in the Special Report on Emissions Scenarios (SRES) of IPCC (Intergovernmental Panel on Climate Change). The results showed that the moderately suitable habitat of S. sphenanthera under all climate change scenarios remained relatively stable in the study area. The highly suitable habitat of S. sphenanthera would gradually decrease in the future and a higher decline rate of the highly suitable habitat area would occur under climate change scenarios SRES-A1B and SRES-A2. The result suggested that in the study area, there would be no more highly suitable habitat areas for S. sphenanthera when the annual mean temperature exceeds 20 °C or its annual precipitation exceeds 1,200 mm. Our results will be influential in the future ecological conservation and management of S. sphenanthera and can be taken as a reference for habitat suitability assessment research for other medicinal plants. creator: Yanlong Guo creator: Haiyan Wei creator: Chunyan Lu creator: Bei Gao creator: Wei Gu uri: https://doi.org/10.7717/peerj.2554 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Guo et al. title: Single-agent maintenance therapy for advanced non-small cell lung cancer (NSCLC): a systematic review and Bayesian network meta-analysis of 26 randomized controlled trials link: https://peerj.com/articles/2550 last-modified: 2016-10-20 description: BackgroundThe benefit of maintenance therapy has been confirmed in patients with non-progressing non-small cell lung cancer (NSCLC) after first-line therapy by many trials and meta-analyses. However, since few head-to-head trials between different regimens have been reported, clinicians still have little guidance on how to select the most efficacious single-agent regimen. Hence, we present a network meta-analysis to assess the comparative treatment efficacy of several single-agent maintenance therapy regimens for stage III/IV NSCLC.MethodsA comprehensive literature search of public databases and conference proceedings was performed. Randomized clinical trials (RCTs) meeting the eligible criteria were integrated into a Bayesian network meta-analysis. The primary outcome was overall survival (OS) and the secondary outcome was progression free survival (PFS).ResultsA total of 26 trials covering 7,839 patients were identified, of which 24 trials were included in the OS analysis, while 23 trials were included in the PFS analysis. Switch-racotumomab-alum vaccine and switch-pemetrexed were identified as the most efficacious regimens based on OS (HR, 0.64; 95% CrI, 0.45–0.92) and PFS (HR, 0.54; 95% CrI, 0.26–1.04) separately. According to the rank order based on OS, switch-racotumomab-alum vaccine had the highest probability as the most effective regimen (52%), while switch-pemetrexed ranked first (34%) based on PFS.ConclusionsSeveral single-agent maintenance therapy regimens can prolong OS and PFS for stage III/IV NSCLC. Switch-racotumomab-alum vaccine maintenance therapy may be the most optimal regimen, but should be confirmed by additional evidence. creator: Qinxue Wang creator: Haobin Huang creator: Xiaoning Zeng creator: Yuan Ma creator: Xin Zhao creator: Mao Huang uri: https://doi.org/10.7717/peerj.2550 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer link: https://peerj.com/articles/2542 last-modified: 2016-10-20 description: BackgroundBreast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis.MethodsA discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities.ResultsIn-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC.ConclusionThe in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC. creator: Samra Khalid creator: Rumeza Hanif creator: Samar H.K. Tareen creator: Amnah Siddiqa creator: Zurah Bibi creator: Jamil Ahmad uri: https://doi.org/10.7717/peerj.2542 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Khalid et al. title: The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes link: https://peerj.com/articles/2539 last-modified: 2016-10-20 description: The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for “true” Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships. creator: Alice M. Clement creator: Tom J. Challands creator: John A. Long creator: Per E. Ahlberg uri: https://doi.org/10.7717/peerj.2539 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Clement et al. title: Climate-related environmental stress in intertidal grazers: scaling-up biochemical responses to assemblage-level processes link: https://peerj.com/articles/2533 last-modified: 2016-10-20 description: BackgroundOrganisms are facing increasing levels of environmental stress under climate change that may severely affect the functioning of biological systems at different levels of organization. Growing evidence suggests that reduction in body size is a universal response of organisms to global warming. However, a clear understanding of whether extreme climate events will impose selection directly on phenotypic plastic responses and how these responses affect ecological interactions has remained elusive.MethodsWe experimentally investigated the effects of extreme desiccation events on antioxidant defense mechanisms of a rocky intertidal gastropod (Patella ulyssiponensis), and evaluated how these effects scaled-up at the population and assemblage levels.ResultsWith increasing levels of desiccation stress, limpets showed significant lower levels of total glutathione, tended to grow less and had reduced per capita interaction strength on their resources.DiscussionResults suggested that phenotypic plasticity (i.e., reduction in adults’ body size) allowed buffering biochemical responses to stress to scale-up at the assemblage level. Unveiling the linkages among different levels of biological organization is key to develop indicators that can anticipate large-scale ecological impacts of climate change. creator: Elena Maggi creator: Mario Cappiello creator: Antonella Del Corso creator: Francesca Lenzarini creator: Eleonora Peroni creator: Lisandro Benedetti-Cecchi uri: https://doi.org/10.7717/peerj.2533 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Maggi et al. title: The influence of flight style on the aerodynamic properties of avian wings as fixed lifting surfaces link: https://peerj.com/articles/2495 last-modified: 2016-10-20 description: The diversity of wing morphologies in birds reflects their variety of flight styles and the associated aerodynamic and inertial requirements. Although the aerodynamics underlying wing morphology can be informed by aeronautical research, important differences exist between planes and birds. In particular, birds operate at lower, transitional Reynolds numbers than do most aircraft. To date, few quantitative studies have investigated the aerodynamic performance of avian wings as fixed lifting surfaces and none have focused upon the differences between wings from different flight style groups. Dried wings from 10 bird species representing three distinct flight style groups were mounted on a force/torque sensor within a wind tunnel in order to test the hypothesis that wing morphologies associated with different flight styles exhibit different aerodynamic properties. Morphological differences manifested primarily as differences in drag rather than lift. Maximum lift coefficients did not differ between groups, whereas minimum drag coefficients were lowest in undulating flyers (Corvids). The lift to drag ratios were lower than in conventional aerofoils and data from free-flying soaring species; particularly in high frequency, flapping flyers (Anseriformes), which do not rely heavily on glide performance. The results illustrate important aerodynamic differences between the wings of different flight style groups that cannot be explained solely by simple wing-shape measures. Taken at face value, the results also suggest that wing-shape is linked principally to changes in aerodynamic drag, but, of course, it is aerodynamics during flapping and not gliding that is likely to be the primary driver. creator: John J. Lees creator: Grigorios Dimitriadis creator: Robert L. Nudds uri: https://doi.org/10.7717/peerj.2495 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lees et al. title: Intranodal signal suppression in pelvic MR lymphography of prostate cancer patients: a quantitative comparison of ferumoxtran-10 and ferumoxytol link: https://peerj.com/articles/2471 last-modified: 2016-10-20 description: ObjectivesThe key to MR lymphography is suppression of T2* MR signal in normal lymph nodes, while retaining high signal in metastatic nodes. Our objective is to quantitatively compare the ability of ferumoxtran-10 and ferumoxytol to suppress the MR signal in normal pelvic lymph nodes.MethodsIn 2010, a set of consecutive patients who underwent intravenous MR Lymphography (MRL) were included. Signal suppression in normal lymph nodes in T2*-weighted images due to uptake of USPIO (Ultra-Small Superparamagnetic Particles of Iron Oxide) was quantified. Signal suppression by two USPIO contrast agents, ferumoxtran-10 and ferumoxytol was compared using Wilcoxon’s signed rank test.ResultsForty-four patients were included, of which all 44 had a ferumoxtran-10 MRL and 4 had additionally a ferumoxytol MRL. A total of 684 lymph nodes were identified in the images, of which 174 had been diagnosed as metastatic. USPIO-induced signal suppression in normal lymph nodes was significantly stronger in ferumoxtran-10 MRL than in ferumoxytol MRL (p < 0.005).ConclusionsT2* signal suppression in normal pelvic lymph nodes is significantly stronger with ferumoxtran-10 than with ferumoxytol, which may affect diagnostic accuracy. creator: Oscar A. Debats creator: Ansje S. Fortuin creator: Hanneke J.M. Meijer creator: Thomas Hambrock creator: Geert J.S. Litjens creator: Jelle O. Barentsz creator: Henkjan J. Huisman uri: https://doi.org/10.7717/peerj.2471 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Debats et al. title: Expression and characterization of thermotolerant lipase with broad pH profiles isolated from an Antarctic Pseudomonas sp strain AMS3 link: https://peerj.com/articles/2420 last-modified: 2016-10-20 description: A gene encoding a thermotolerant lipase with broad pH was isolated from an Antarctic Pseudomonas strain AMS3. The recombinant lipase AMS3 was purified by single-step purification using affinity chromatography, yielding a purification fold of approximately 1.52 and a recovery of 50%. The molecular weight was approximately ∼60 kDa including the strep and affinity tags. Interestingly, the purified Antarctic AMS3 lipase exhibited broad temperature profile from 10–70 °C and stable over a broad pH range from 5.0 to pH 10.0. Various mono and divalent metal ions increased the activity of the AMS3 lipase, but Ni2+ decreased its activity. The purified lipase exhibited the highest activity in the presence of sunflower oil. In addition, the enzyme activity in 25% v/v solvents at 50 °C particularly to n-hexane, DMSO and methanol could be useful for catalysis reaction in organic solvent and at broad temperature. creator: Wahhida Latip creator: Raja Noor Zaliha Raja Abd Rahman creator: Adam Thean Chor Leow creator: Fairolniza Mohd Shariff creator: Mohd Shukuri Mohamad Ali uri: https://doi.org/10.7717/peerj.2420 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Latip et al. title: Spotted hyaena space use in relation to human infrastructure inside a protected area link: https://peerj.com/articles/2596 last-modified: 2016-10-19 description: Increasing human population growth has led to elevated levels of human-carnivore conflict. However, some carnivore populations have adapted to urban environments and the resources they supply. Such associations may influence carnivore ecology, behaviour and life-history. Pockets of urbanisation sometimes occur within protected areas, so that anthropogenic influences on carnivore biology are not necessarily confined to unprotected areas. In this study we evaluated associations between human infrastructure and related activity and space use of spotted hyaenas within one of the largest protected areas in South Africa, the Kruger National Park. Home range size was smaller for the dominant female of a clan living in close proximity to humans than that of the dominant female of a clan without direct access to human infrastructure. The home range including human infrastructure was also used less evenly during the night, presumably when the animals were active. Within this home range, a village area was preferred during the night, when the least modified areas within the village were preferred and administration and highly modified areas were avoided. During the day, however, there were no preference or avoidance of the village area, but all habitats except unmodified habitats within the village area were avoided. We suggest that human infrastructure and associated activity influenced hyaena space use, primarily through alterations in the spatial distribution of food. However, these effects may have been indirectly caused by habitat modification that generated favourable hunting habitat rather than a direct effect caused by access to human food such as garbage. Because of the often pivotal effects of apex predators in terrestrial ecosystems, we encourage further work aimed to quantify how human presence influences large carnivores and associated ecosystem processes within protected areas. creator: Lydia E. Belton creator: Elissa Z. Cameron creator: Fredrik Dalerum uri: https://doi.org/10.7717/peerj.2596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Belton et al. title: A reappraisal of Theroteinus (Haramiyida, Mammaliaformes) from the Upper Triassic of Saint-Nicolas-de-Port (France) link: https://peerj.com/articles/2592 last-modified: 2016-10-19 description: The earliest mammaliaforms are difficult to assess because the fossil record is poor and because their distinctive morphologies cannot be directly compared with more recent mammaliaforms. This is especially true for the haramiyid genus Theroteinus, only known in the Saint-Nicolas-de-Port locality (Rhaetian, France). This study presents a new definition of the type-species Theroteinus nikolai. A new species Theroteinus rosieriensis, sp. nov., is named and distinguished by the lingual shift of distal cusps, a larger size, and a stockier occlusal outline. Comparisons with Eleutherodon, Megaconus and Millsodon suggest that Theroteinus has potential close relatives among the Jurassic haramiyids. creator: Maxime Debuysschere uri: https://doi.org/10.7717/peerj.2592 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Debuysschere title: Green synthesis of silver nanoparticles in aloe vera plant extract prepared by a hydrothermal method and their synergistic antibacterial activity link: https://peerj.com/articles/2589 last-modified: 2016-10-19 description: BackgroundThere is worldwide interest in silver nanoparticles (AgNPs) synthesized by various chemical reactions for use in applications exploiting their antibacterial activity, even though these processes exhibit a broad range of toxicity in vertebrates and invertebrates alike. To avoid the chemical toxicity, biosynthesis (green synthesis) of metal nanoparticles is proposed as a cost-effective and environmental friendly alternative. Aloe vera leaf extract is a medicinal agent with multiple properties including an antibacterial effect. Moreover the constituents of aloe vera leaves include lignin, hemicellulose, and pectins which can be used in the reduction of silver ions to produce as AgNPs@aloe vera (AgNPs@AV) with antibacterial activity.MethodsAgNPs were prepared by an eco-friendly hydrothermal method using an aloe vera plant extract solution as both a reducing and stabilizing agent. AgNPs@AV were characterized using XRD and SEM. Additionally, an agar well diffusion method was used to screen for antimicrobial activity. MIC and MBC were used to correlate the concentration of AgNPs@AV its bactericidal effect. SEM was used to investigate bacterial inactivation. Then the toxicity with human cells was investigated using an MTT assay.ResultsThe synthesized AgNPs were crystalline with sizes of 70.70 ± 22-192.02 ± 53 nm as revealed using XRD and SEM. The sizes of AgNPs can be varied through alteration of times and temperatures used in their synthesis. These AgNPs were investigated for potential use as an antibacterial agent to inhibit pathogenic bacteria. Their antibacterial activity was tested on S. epidermidis and P. aeruginosa. The results showed that AgNPs had a high antibacterial which depended on their synthesis conditions, particularly when processed at 100 oC for 6 h and 200 oC for 12 h. The cytotoxicity of AgNPs was determined using human PBMCs revealing no obvious cytotoxicity. These results indicated that AgNPs@AV can be effectively utilized in pharmaceutical, biotechnological and biomedical applications.DiscussionAloe vera extract was processed using a green and facile method. This was a hydrothermal method to reduce silver nitrate to AgNPs@AV. Varying the hydrothermal temperature provided the fine spherical shaped nanoparticles. The size of the nanomaterial was affected by its thermal preparation. The particle size of AgNPs could be tuned by varying both time and temperature. A process using a pure AG phase could go to completion in 6 h at 200 oC, whereas reactions at lower temperatures required longer times. Moreover, the antibacterial effect of this hybrid nanomaterial was sufficient that it could be used to inhibit pathogenic bacteria since silver release was dependent upon its particle size. The high activity of the largest AgNPs might have resulted from a high concentration of aloe vera compounds incorporated into the AgNPs during hydrothermal synthesis. creator: Patcharaporn Tippayawat creator: Nutthakritta Phromviyo creator: Parichart Boueroy creator: Apiwat Chompoosor uri: https://doi.org/10.7717/peerj.2589 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tippayawat et al. title: Residency in white-eared hummingbirds (Hylocharis leucotis) and its effect in territorial contest resolution link: https://peerj.com/articles/2588 last-modified: 2016-10-19 description: BackgroundTerritory owners usually defeat intruders. One explanation for this observation is the uncorrelated asymmetry hypothesis which argues that contests might be settled by an arbitrary convention such as “owners win.” We studied the effect of territorial residency on contest asymmetries in the white-eared hummingbird (Hylocharis leucotis) in a fir forest from central Mexico.MethodsTwenty white-eared male adult hummingbird territories were monitored during a winter season, recording the territorial behavior of the resident against intruding hummingbirds. The size and quality of the territory were related to the probability that the resident would allow the use of flowers by the intruder. Various generalized models (logistical models) were generated to describe the probabilities of victory for each individual resident depending on the different combinations of three predictor variables (territory size, territory quality, and intruder identity).ResultsIn general, small and low quality territory owners tend to prevent conspecific intruders from foraging at a higher rate, while they frequently fail to exclude heterospecific intruders such as the magnificent hummingbird (Eugenes fulgens) or the green violetear hummingbird (Colibri thalassinus) on any territory size. Our results showed that the identity of the intruder and the size and quality of the territory determined the result of the contests, but not the intensity of defense.DiscussionInitially, the rule that “the resident always wins” was supported, since no resident was expelled from its territory during the study. Nevertheless, the resident-intruder asymmetries during the course of a day depended on different factors, such as the size and quality of the territory and, mainly, the identity of the intruders. Our results showed that flexibility observed in contest tactics suggests that these tactics are not fixed but are socially plastic instead and they can be adjusted to specific circumstances. creator: Verónica Mendiola-Islas creator: Carlos Lara creator: Pablo Corcuera creator: Pedro Luis Valverde uri: https://doi.org/10.7717/peerj.2588 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mendiola-Islas et al. title: Performance of joint modelling of time-to-event data with time-dependent predictors: an assessment based on transition to psychosis data link: https://peerj.com/articles/2582 last-modified: 2016-10-19 description: Joint modelling has emerged to be a potential tool to analyse data with a time-to-event outcome and longitudinal measurements collected over a series of time points. Joint modelling involves the simultaneous modelling of the two components, namely the time-to-event component and the longitudinal component. The main challenges of joint modelling are the mathematical and computational complexity. Recent advances in joint modelling have seen the emergence of several software packages which have implemented some of the computational requirements to run joint models. These packages have opened the door for more routine use of joint modelling. Through simulations and real data based on transition to psychosis research, we compared joint model analysis of time-to-event outcome with the conventional Cox regression analysis. We also compared a number of packages for fitting joint models. Our results suggest that joint modelling do have advantages over conventional analysis despite its potential complexity. Our results also suggest that the results of analyses may depend on how the methodology is implemented. creator: Hok Pan Yuen creator: Andrew Mackinnon uri: https://doi.org/10.7717/peerj.2582 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Yuen and Mackinnon title: Systematic review on the conservation genetics of African savannah elephants link: https://peerj.com/articles/2567 last-modified: 2016-10-19 description: BackgroundIn this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1) what are the research trends concerning the conservation genetics of Loxodonta africana? (2) Do richer countries conduct more research on the genetics of African elephants? (3) Which attributes influence where scholars conduct their research?Materials and MethodsWe examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS), Scopus and Google Scholar (GS), and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks.ResultsWe found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species.ConclusionsResearch in this field should be expanded to additional countries harboring elephant populations to enable a more comprehensive understanding of the population structure and genetic differentiation of the species, and to cope with challenges associated with the conservation of the species such as illegal hunting, habitat fragmentation, species reintroduction and climate change. creator: Daniel Zacarias creator: Luis Mauricio Bini creator: Rafael Loyola uri: https://doi.org/10.7717/peerj.2567 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zacarias et al. title: A small molecule targeting protein translation does not rescue spatial learning and memory deficits in the hAPP-J20 mouse model of Alzheimer’s disease link: https://peerj.com/articles/2565 last-modified: 2016-10-19 description: A small molecule named ISRIB has recently been described to enhance memory in rodents. In this study we aimed to test whether ISRIB would reverse learning and memory deficits in the J20 mouse model of human amyloid precursor protein (hAPP) overexpression, a model that simulates many aspects of Alzheimer’s disease in which memory deficits are a hallmark feature. We did not observe a significant rescue effect with ISRIB treatment on spatial learning and memory as assessed in the Morris water maze in J20 mice. We also did not observe a significant enhancement of spatial learning or memory in nontransgenic mice with ISRIB treatment, although a trend emerged for memory enhancement in one cohort of mice. Future preclinical studies with ISRIB would benefit from additional robust markers of target engagement in the brain. creator: Erik C.B. Johnson creator: Jing Kang uri: https://doi.org/10.7717/peerj.2565 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Johnson and Kang title: Beech cupules as keystone structures for soil fauna link: https://peerj.com/articles/2562 last-modified: 2016-10-19 description: Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, ‘keystone structures’, which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals—springtails, mites and enchytraeids—during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered ‘keystone structures’ that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers. creator: Nereida Melguizo-Ruiz creator: Gerardo Jiménez-Navarro creator: Jordi Moya-Laraño uri: https://doi.org/10.7717/peerj.2562 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Melguizo-Ruiz et al. title: Determining the distribution loss of brown eared-pheasant (Crossoptilon mantchuricum) using historical data and potential distribution estimates link: https://peerj.com/articles/2556 last-modified: 2016-10-19 description: We analyzed the synchronous relationship between forest cover and species distribution to explain the contraction in the distribution range of the brown eared-pheasant (Crossoptilon mantchuricum) in China. Historical resources can provide effective records for reconstructing long-term distribution dynamics. The brown eared-pheasant’s historical distribution from 25 to 1947 CE, which included the three provinces of Shaanxi, Shanxi, and Hebei based on this species’ habitat selection criteria, the history of the forests, ancient climate change records, and fossil data. The current species distribution covers Shaanxi, Shanxi, and Hebei provinces, as well as Beijing city, while Shanxi remains the center of the distribution area. MaxEnt model indicated that the suitable conditions of the brown eared-pheasant had retreated to the western regions of Shanxi and that the historical distribution area had reduced synchronously with the disappearance of local forest cover in Shanxi. We built a correlative relationship between the presence/absence of brown eared-pheasants and forest coverage and found that forest coverage in the north, northeast, central, and southeast areas of the Shanxi province were all less than 10% in 1911. Wild brown eared-pheasants are stable in the Luliang Mountains, where forest coverage reached 13.2% in 2000. Consequently, we concluded that the distribution of this species is primarily determined by vegetation conditions and that forest cover was the most significant determining factor. creator: Yilin Li creator: Xinhai Li creator: Zitan Song creator: Changqing Ding uri: https://doi.org/10.7717/peerj.2556 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Li et al. title: Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant link: https://peerj.com/articles/2585 last-modified: 2016-10-18 description: Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group. creator: Victoria M. Pearson creator: S. Brian Caudle creator: Darin R. Rokyta uri: https://doi.org/10.7717/peerj.2585 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pearson et al. title: VSEARCH: a versatile open source tool for metagenomics link: https://peerj.com/articles/2584 last-modified: 2016-10-18 description: BackgroundVSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.MethodsWhen searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.ResultsVSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.DiscussionVSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community. creator: Torbjørn Rognes creator: Tomáš Flouri creator: Ben Nichols creator: Christopher Quince creator: Frédéric Mahé uri: https://doi.org/10.7717/peerj.2584 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rognes et al. title: Divergent relationship of circulating CTRP3 levels between obesity and gender: a cross-sectional study link: https://peerj.com/articles/2573 last-modified: 2016-10-18 description: C1q TNF Related Protein 3 (CTRP3) is a novel adipose tissue derived secreted factor, or adipokine, which has been linked to a number of beneficial biological effects on metabolism, inflammation, and survival signaling in a variety of tissues. However, very little is known about CTRP3 in regards to human health. The purpose of this project was to examine circulating CTRP3 levels in a clinical population, patients with symptoms requiring heart catheterization in order to identify the presence of obstructive coronary artery disease (CAD). It was hypothesized that serum CTRP3 levels would be decreased in the presence of CAD.MethodsBody mass index (BMI), diabetes status, and plasma samples were collected from 100 patients who were >30 years of age and presented at the East Tennessee State University Heart Clinic with symptoms requiring heart catheterization in order to identify the presence of cardiovascular blockages (n = 52 male, n = 48 female). Circulating CTRP3 levels were quantified using commercially available ELISA.ResultsCirculating CTRP3 levels had no relationship to the presence of CAD regardless of gender. However, circulating concentrations of CTRP3 were significantly higher in normal weight (BMI < 30) females (0.88 ± 0.12 µg/ml) compared with males (0.54 ± 0.06 µg/ml). Further, obesity (BMI > 30) resulted in an increase in circulating CTRP3 levels in male subjects (0.74 ± 0.08 µg/ml) but showed a significant decrease in female subjects (0.58 ± 0.07 µg/ml). Additionally, there was a significant reduction in circulating CTRP3 levels in female subjects who were diagnosed with Type 2 diabetes compared with patients without (0.79 ± 0.08 vs. 0.42 ± 0.10 µg/ml). There was no relationship between diabetes status and circulating CTRP3 levels in male subjects.ConclusionCirculating CTRP3 levels had a different relationship with diabetes and obesity status between male and female patients. It is possible that circulating CTRP3 levels are controlled by hormonal status, however more research is needed to explore this relationship. Nevertheless, future studies examining the relationship between CTRP3 levels and disease status should treat gender as an independent variable. creator: Roy Marshal Wagner creator: Kamesh Sivagnanam creator: William Andrew Clark creator: Jonathan M. Peterson uri: https://doi.org/10.7717/peerj.2573 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wagner et al. title: The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data link: https://peerj.com/articles/2571 last-modified: 2016-10-18 description: In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage >0.025. In both projects, CC8 and CC30 were the most common S. aureus clonal complexes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage often associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are possibly associated with S. aureus carriage but there was limited power to identify factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. creator: Sandeep J. Joseph creator: Ben Li creator: Robert A. Petit III creator: Zhaohui S. Qin creator: Lyndsey Darrow creator: Timothy D. Read uri: https://doi.org/10.7717/peerj.2571 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Joseph et al. title: Molecular phylogeny of the megadiverse insect infraorder Bibionomorpha sensu lato (Diptera) link: https://peerj.com/articles/2563 last-modified: 2016-10-18 description: The phylogeny of the insect infraorder Bibionomorpha (Diptera) is reconstructed based on the combined analysis of three nuclear (18S, 28S, CAD) and three mitochondrial (12S, 16S, COI) gene markers. All the analyses strongly support the monophyly of Bibionomorpha in both the narrow (sensu stricto) and the broader (sensu lato) concepts. The major lineages of Bibionomorpha sensu lato (Sciaroidea, Bibionoidea, Anisopodoidea, and Scatopsoidea) and most of the included families are supported as monophyletic groups. Axymyiidae was not found to be part of Bibionomorpha nor was it found to be its sister group. Bibionidae was paraphyletic with respect to Hesperinidae and Keroplatidae was paraphyletic with respect to Lygistorrhinidae. The included Sciaroidea incertae sedis (except Ohakunea Edwards) were found to belong to one clade, but the relationships within this group and its position within Sciaroidea require further study. creator: Jan Ševčík creator: David Kaspřák creator: Michal Mantič creator: Scott Fitzgerald creator: Tereza Ševčíková creator: Andrea Tóthová creator: Mathias Jaschhof uri: https://doi.org/10.7717/peerj.2563 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ševčík et al. title: Does regional diversity recover after disturbance? A field experiment in constructed ponds link: https://peerj.com/articles/2455 last-modified: 2016-10-18 description: The effects of disturbance on local species diversity have been well documented, but less recognized is the possibility that disturbances can alter diversity at regional spatial scales. Since regional diversity can dictate which species are available for recolonization of degraded sites, the loss of diversity at regional scales may impede the recovery of biodiversity following a disturbance. To examine this we used a chemical disturbance of rotenone, a piscicide commonly used for fish removal in aquatic habitats, on small fishless freshwater ponds. We focused on the non-target effects of rotenone on aquatic invertebrates with the goal of assessing biodiversity loss and recovery at both local (within-pond) and regional (across ponds) spatial scales. We found that rotenone caused significant, large, but short-term losses of species at both local and regional spatial scales. Using a null model of random extinction, we determined that species were selectively removed from communities relative to what would be expected if species loss occurred randomly. Despite this selective loss of biodiversity, species diversity at both local and regional spatial scales recovered to reference levels one year after the addition of rotenone. The rapid recovery of local and regional diversity in this study was surprising considering the large loss of regional species diversity, however many aquatic invertebrates disperse readily or have resting stages that may persist through disturbances. We emphasize the importance of considering spatial scale when quantifying the impacts of a disturbance on an ecosystem, as well as considering how regional species loss can influence recovery from disturbance. creator: Lauren M. Woods creator: Elizabeth G. Biro creator: Muxi Yang creator: Kevin G. Smith uri: https://doi.org/10.7717/peerj.2455 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Woods et al. title: Histological variability in the limb bones of the Asiatic wild ass and its significance for life history inferences link: https://peerj.com/articles/2580 last-modified: 2016-10-13 description: The study of bone growth marks (BGMs) and other histological traits of bone tissue provides insights into the life history of present and past organisms. Important life history traits like longevity or age at maturity, which could be inferred from the analysis of these features, form the basis for estimations of demographic parameters that are essential in ecological and evolutionary studies of vertebrates. Here, we study the intraskeletal histological variability in an ontogenetic series of Asiatic wild ass (Equus hemionus) in order to assess the suitability of several skeletal elements to reconstruct the life history strategy of the species. Bone tissue types, vascular canal orientation and BGMs have been analyzed in 35 cross-sections of femur, tibia and metapodial bones of 9 individuals of different sexes, ages and habitats. Our results show that the number of BGMs recorded by the different limb bones varies within the same specimen. Our study supports that the femur is the most reliable bone for skeletochronology, as already suggested. Our findings also challenge traditional beliefs with regard to the meaning of deposition of the external fundamental system (EFS). In the Asiatic wild ass, this bone tissue is deposited some time after skeletal maturity and, in the case of the femora, coinciding with the reproductive maturity of the species. The results obtained from this research are not only relevant for future studies in fossil Equus, but could also contribute to improve the conservation strategies of threatened equid species. creator: Carmen Nacarino-Meneses creator: Xavier Jordana creator: Meike Köhler uri: https://doi.org/10.7717/peerj.2580 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nacarino-Meneses et al. title: Exclusions for resolving urban badger damage problems: outcomes and consequences link: https://peerj.com/articles/2579 last-modified: 2016-10-13 description: Increasing urbanisation and growth of many wild animal populations can result in a greater frequency of human-wildlife conflicts. However, traditional lethal methods of wildlife control are becoming less favoured than non-lethal approaches, particularly when problems involve charismatic species in urban areas. Eurasian badgers (Meles meles) excavate subterranean burrow systems (setts), which can become large and complex. Larger setts within which breeding takes place and that are in constant use are known as main setts. Smaller, less frequently occupied setts may also exist within the social group’s range. When setts are excavated in urban environments they can undermine built structures and can limit or prevent safe use of the area by people. The most common approach to resolving these problems in the UK is to exclude badgers from the problem sett, but exclusions suffer a variable success rate. We studied 32 lawful cases of badger exclusions using one-way gates throughout England to evaluate conditions under which attempts to exclude badgers from their setts in urban environments were successful. We aimed to identify ways of modifying practices to improve the chances of success. Twenty of the 32 exclusion attempts were successful, but success was significantly less likely if a main sett was to be excluded in comparison with another type of sett and if vegetation was not completely removed from the sett surface prior to exclusion attempts. We recommend that during exclusions all vegetation is removed from the site, regardless of what type of sett is involved, and that successful exclusion of badgers from a main sett might require substantially more effort than other types of sett. creator: Alastair I. Ward creator: Jason K. Finney creator: Sarah E. Beatham creator: Richard J. Delahay creator: Peter A. Robertson creator: David P. Cowan uri: https://doi.org/10.7717/peerj.2579 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ward et al. title: Judgement bias in goats (Capra hircus): investigating the effects of human grooming link: https://peerj.com/articles/2485 last-modified: 2016-10-13 description: Animal emotional states can be investigated by evaluating their impact on cognitive processes. In this study, we used a judgement bias paradigm to determine if short-term positive human-animal interaction (grooming) induced a positive affective state in goats. We tested two groups of goats and trained them to discriminate between a rewarded and a non-rewarded location over nine training days. During training, the experimental group (n = 9) was gently groomed by brushing their heads and backs for five min over 11 days (nine training days, plus two testing days, total time 55 min). During training, the control group (n = 10) did not experience any direct interaction with the experimenter, but was kept unconstrained next to him for the same period of time. After successful completion of the training, the responses (latency time) of the two groups to reach ambiguous locations situated between the two reference locations (i.e., rewarded/non-rewarded) were compared over two days of testing. There was not a positive bias effect after the animals had been groomed. In a second experiment, 10 goats were tested to investigate whether grooming induced changes in physiological activation (i.e., heart rate and heart rate variability). Heart rate increased when goats were groomed compared to the baseline condition, when the same goats did not receive any contact with the experimenter. Also, subjects did not move away from the experimenter, suggesting that the grooming was positively accepted. The very good care and the regular positive contacts that goats received from humans at the study site could potentially account for the results obtained. Good husbandry outcomes are influenced by animals’ perception of the events and this is based on current circumstances, past experiences and individual variables. Taking into account animals’ individual characteristics and identifying effective strategies to induce positive emotions could increase the understanding and reliability of using cognitive biases paradigms to investigate and promote animal welfare. creator: Luigi Baciadonna creator: Christian Nawroth creator: Alan G. McElligott uri: https://doi.org/10.7717/peerj.2485 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baciadonna et al. title: Metabolic control in patients with type 2 diabetes mellitus in a public hospital in Peru: a cross-sectional study in a low-middle income country link: https://peerj.com/articles/2577 last-modified: 2016-10-13 description: ObjectiveThe objective of this study was to assess patients’ achievement of ADA (American Diabetes Association) guideline recommendations for glycosylated hemoglobin, lipid profile, and blood pressure in a type 2 diabetes mellitus (T2DM) outpatient clinic in a low-middle income country (LMIC) setting.MethodsThis is a descriptive cross-sectional study with 123 ambulatory T2DM patients who are being treated at a public hospital in Lima, Peru. Data was gathered via standardized interviews, clinical surveys, and anthropomorphic measurements for each patient. Blood samples were drawn in fasting state for measures of glucose, glycosylated hemoglobin (HbA1c), and lipid profile. Laboratory parameters and blood pressure were evaluated according to ADA recommendations.ResultsOf the 123 patients, 81 were women and the mean age was 61.8 years. Glycemic control was abnormal in 82 (68.33%) participants, and 45 (37.50%) were unable to control their blood pressure. Lipid profile was abnormal in 73 (60.83%) participants. Only nine (7.50%) participants fulfilled ADA recommendations for glycemic, blood pressure, and lipid control.ConclusionsAmongst individuals with type 2 diabetes, there was poor attainment of the ADA recommendations (HbA1c, blood pressure and LDL-cholesterol) for ambulatory T2DM patients. Interventions are urgently needed in order to prevent long-term diabetic complications. creator: Irma Elizabeth Huayanay-Espinoza creator: Felix Guerra-Castañon creator: María Lazo-Porras creator: Ana Castaneda-Guarderas creator: Nimmy Josephine Thomas creator: Ana-Lucia Garcia-Guarniz creator: Augusto A. Valdivia-Bustamante creator: Germán Málaga uri: https://doi.org/10.7717/peerj.2577 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Huayanay-Espinoza et al. title: YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance link: https://peerj.com/articles/2574 last-modified: 2016-10-13 description: Plants respond to neighbor shade by increasing stem and petiole elongation. Shade, sensed by phytochrome photoreceptors, causes stabilization of PHYTOCHROME INTERACTING FACTOR proteins and subsequent induction of YUCCA auxin biosynthetic genes. To investigate the role of YUCCA genes in phytochrome-mediated elongation, we examined auxin signaling kinetics after an end-of-day far-red (EOD-FR) light treatment, and found that an auxin responsive reporter is rapidly induced within 2 hours of far-red exposure. YUCCA2, 5, 8, and 9 are all induced with similar kinetics suggesting that they could act redundantly to control shade-mediated elongation. To test this hypothesis we constructed a yucca2, 5, 8, 9 quadruple mutant and found that the hypocotyl and petiole EOD-FR and shade avoidance responses are completely disrupted. This work shows that YUCCA auxin biosynthetic genes are essential for detectable shade avoidance and that YUCCA genes are important for petiole shade avoidance. creator: Patricia Müller-Moulé creator: Kazunari Nozue creator: Melissa L. Pytlak creator: Christine M. Palmer creator: Michael F. Covington creator: Andreah D. Wallace creator: Stacey L. Harmer creator: Julin N. Maloof uri: https://doi.org/10.7717/peerj.2574 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Müller-Moulé et al. title: Variation in habitat soundscape characteristics influences settlement of a reef-building coral link: https://peerj.com/articles/2557 last-modified: 2016-10-13 description: Coral populations, and the productive reef ecosystems they support, rely on successful recruitment of reef-building species, beginning with settlement of dispersing larvae into habitat favourable to survival. Many substrate cues have been identified as contributors to coral larval habitat selection; however, the potential for ambient acoustic cues to influence coral settlement responses is unknown. Using in situ settlement chambers that excluded other habitat cues, larval settlement of a dominant Caribbean reef-building coral, Orbicella faveolata, was compared in response to three local soundscapes, with differing acoustic and habitat properties. Differences between reef sites in the number of larvae settled in chambers isolating acoustic cues corresponded to differences in sound levels and reef characteristics, with sounds at the loudest reef generating significantly higher settlement during trials compared to the quietest site (a 29.5 % increase). These results suggest that soundscapes could be an important influence on coral settlement patterns and that acoustic cues associated with reef habitat may be related to larval settlement. This study reports an effect of soundscape variation on larval settlement for a key coral species, and adds to the growing evidence that soundscapes affect marine ecosystems by influencing early life history processes of foundational species. creator: Ashlee Lillis creator: DelWayne Bohnenstiehl creator: Jason W. Peters creator: David Eggleston uri: https://doi.org/10.7717/peerj.2557 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lillis et al. title: Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen link: https://peerj.com/articles/2552 last-modified: 2016-10-13 description: BackgroundReference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues.MethodsThe study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase, GAPDH; β-actin, ACTB; 18S rRNA, 18S; 28S rRNA, 28S; and ribosomal protein L13A, RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUS software.ResultsGene stability for juvenile and adult tissue samples combined show that GAPDH was most stable in liver and lung tissue, and 18S in small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except 28S were stable for lung and only 18S and 28S were stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTB and GAPDH) and adults (18S and 28S), and RPL13A was not stable for juvenile small intestine tissue. Except for 28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue.DiscussionBased on expression stability, ACTB and GAPDH are suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults but RPL13A was not suitable in juveniles. creator: Oselyne T.W. Ong creator: Lauren J. Young creator: Julie M. Old uri: https://doi.org/10.7717/peerj.2552 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ong et al. title: Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes link: https://peerj.com/articles/2551 last-modified: 2016-10-13 description: BackgroundAssembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes.MethodsWe employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms.ResultsThe unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition.DiscussionVariation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. creator: Laura M. Cisneros creator: Matthew E. Fagan creator: Michael R. Willig uri: https://doi.org/10.7717/peerj.2551 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cisneros et al. title: Aboveground and belowground arthropods experience different relative influences of stochastic versus deterministic community assembly processes following disturbance link: https://peerj.com/articles/2545 last-modified: 2016-10-13 description: BackgroundUnderstanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces.MethodsUsing a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies abundance, diversity, and composition. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models comparing observed vs. expected levels of species turnover (Beta diversity) among samples.ResultsTree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors.DiscussionOur results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a spatially co-occurring ground-dwelling arthropod community following disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of stochastic and deterministic processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory and considering conservation strategies. creator: Scott Ferrenberg creator: Alexander S. Martinez creator: Akasha M. Faist uri: https://doi.org/10.7717/peerj.2545 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ferrenberg et al. title: Highly divergent mussel lineages in isolated Indonesian marine lakes link: https://peerj.com/articles/2496 last-modified: 2016-10-13 description: Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago. creator: Leontine E. Becking creator: Christiaan A. de Leeuw creator: Bram Knegt creator: Diede L. Maas creator: Nicole J. de Voogd creator: Abdunnur creator: Iwan Suyatna creator: Katja T.C.A. Peijnenburg uri: https://doi.org/10.7717/peerj.2496 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Becking et al. title: Ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae link: https://peerj.com/articles/2536 last-modified: 2016-10-12 description: Parrotfish are fundamental species in controlling algal phase-shifts and ensuring the resilience of coral reefs. Nevertheless, little is known on their ecological role in the south-western Atlantic Ocean. The present study analysed the ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae using behavioural observation and benthic composition analyses. We found a significant negative relationship between fish size and feeding rates for S. zelindae individuals. Thus, terminal phase individuals forage with lower feeding rates compared to juveniles and initial phase individuals. The highest relative foraging frequency of S. zelindae was on epilithic algae matrix (EAM) with similar values for juveniles (86.6%), initial phase (88.1%) and terminal phase (88.6%) individuals. The second preferred benthos for juveniles was sponge (11.6%) compared with initial (4.5%) and terminal life phases (1.3%). Different life phases of S. zelindae foraged on different benthos according to their availability. Based on Ivlev’s electivity index, juveniles selected EAM and sponge, while initial phase and terminal phase individuals only selected EAM. Our findings demonstrate that the foraging frequency of the endemic parrotfish S. zelindae is reduced according to body size and that there is a slight ontogenetic change in feeding selectivity. Therefore, ecological knowledge of ontogenetic variations on resource use is critical for the remaining parrotfish populations which have been dramatically reduced in the Southwestern Atlantic Ocean. creator: Pedro H.C. Pereira creator: Marcus Santos creator: Daniel L. Lippi creator: Pedro Silva uri: https://doi.org/10.7717/peerj.2536 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pereira et al. title: LIMK1/2 inhibitor LIMKi 3 suppresses porcine oocyte maturation link: https://peerj.com/articles/2553 last-modified: 2016-10-12 description: LIMKi 3 is a specific selective LIMK inhibitor against LIMK1 and LIMK2, while LIMK1 and LIMK2 are the main regulators of actin cytoskeleton to participate in many cell activities. However, the effect of LIMKi 3 in porcine oocyte meiosis is still unclear. The present study was designed to investigate the effects of LIMKi 3 and potential regulatory role of LIMK1/2 on porcine oocyte meiotic maturation. Immunofluorescent staining of p-LIMK1/2 antibody showed that LIMK1/2 was localized mainly to the cortex of porcine oocyte, which co-localized with actin. After LIMKi 3 treatment, the diffusion of COCs became weak and the rate of polar body extrusion was decreased. This could be rescued by moving oocytes to fresh medium. After prolonging the culture time of oocytes, the maturation rate of porcine oocyte increased in LIMKi 3 groups, indicating that LIMKi 3 may suppress the cell cycle during porcine oocyte maturation. We also found that after LIMKi 3 treatment actin distribution was significantly disturbed at porcine oocyte membranes and cytoplasm, indicating the conserved roles of LIMK1/2 on actin dynamics. Next we examined the meiotic spindle positioning in porcine oocyte, and the results showed that a majority of spindles were not attached to the cortex of porcine oocyte, indicating that LIMKi 3 may affect actin-mediated spindle positioning. Taken together, these results showed that LIMK1/2 inhibitor LIMKi 3 had a repressive role on porcine oocyte meiotic maturation. creator: Ru-Xia Jia creator: Xing Duan creator: Si-Jing Song creator: Shao-Chen Sun uri: https://doi.org/10.7717/peerj.2553 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jia et al. title: Common metabolic constraints on dive duration in endothermic and ectothermic vertebrates link: https://peerj.com/articles/2569 last-modified: 2016-10-12 description: Dive duration in air-breathing vertebrates is thought to be constrained by the volume of oxygen stored in the body and the rate at which it is consumed (i.e., “oxygen store/usage hypothesis”). The body mass-dependence of dive duration among endothermic vertebrates is largely supportive of this model, but previous analyses of ectothermic vertebrates show no such body mass-dependence. Here we show that dive duration in both endotherms and ectotherms largely support the oxygen store/usage hypothesis after accounting for the well-established effects of temperature on oxygen consumption rates. Analyses of the body mass and temperature dependence of dive duration in 181 species of endothermic vertebrates and 29 species of ectothermic vertebrates show that dive duration increases as a power law with body mass, and decreases exponentially with increasing temperature. Thus, in the case of ectothermic vertebrates, changes in environmental temperature will likely impact the foraging ecology of divers. creator: April Hayward creator: Mariela Pajuelo creator: Catherine G. Haase creator: David M. Anderson creator: James F. Gillooly uri: https://doi.org/10.7717/peerj.2569 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hayward et al. title: Invasion of the tropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Oligochaeta) in temperate grasslands link: https://peerj.com/articles/2572 last-modified: 2016-10-12 description: The tropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Oligochaeta) presents a broad distribution (e.g., 56 countries from four continents). It is generally assumed that temperature appears to limit the success of tropical exotic species in temperate climates. However, the distribution range of this species could advance towards higher elevations (with lower temperatures) where no tropical species currently occur. The aim of this study was to evaluate the soil and climatic variables that could be closely associated with the distribution of P. corethrurus in four sites along an altitudinal gradient in central Veracruz, Mexico. We predicted that the distribution of P. corethrurus would be more related to climate variables than edaphic parameters. Five sampling points (in the grassland) were established at each of four sites along an altitudinal gradient: Laguna Verde (LV), La Concepción (LC), Naolinco (NA) and Acatlán (AC) at 11–55, 992–1,025, 1,550–1,619 y 1,772–1,800 masl, respectively. The climate ranged from tropical to temperate along the altitudinal gradient. Ten earthworm species (5 Neotropical, 4 Palearctic and 1 Nearctic) were found along the gradient, belonging to three families (Rhinodrilidae, Megascolecide and Lumbricidae). Soil properties showed a significant association (positive for Ngrass, pH, permanent wilting point, organic matter and P; and negative for Total N, K and water-holding capacity) with the abundance of the earthworm community. Also there seems to be a relationship between climate and earthworm distribution along the altitudinal gradient. P. corethrurus was recorded at tropical (LV and LC) and temperate sites (NA) along the altitudinal gradient. Our results reveal that soil fertility determines the abundance of earthworms and site (climate) can act as a barrier to their migration. Further research is needed to determine the genetic structure and lineages of P. corethrurus along altitudinal gradients. creator: Diana Ortiz-Gamino creator: Paulino Pérez-Rodríguez creator: Angel I. Ortiz-Ceballos uri: https://doi.org/10.7717/peerj.2572 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ortiz-Gamino et al. title: Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes link: https://peerj.com/articles/2438 last-modified: 2016-10-12 description: Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources. creator: Alba Ardura creator: Elvira Morote creator: Marc Kochzius creator: Eva Garcia-Vazquez uri: https://doi.org/10.7717/peerj.2438 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ardura et al. title: Monte Carlo simulation of OLS and linear mixed model inference of phenotypic effects on gene expression link: https://peerj.com/articles/2575 last-modified: 2016-10-11 description: BackgroundSelf-contained tests estimate and test the association between a phenotype and mean expression level in a gene set defined a priori. Many self-contained gene set analysis methods have been developed but the performance of these methods for phenotypes that are continuous rather than discrete and with multiple nuisance covariates has not been well studied. Here, I use Monte Carlo simulation to evaluate the performance of both novel and previously published (and readily available via R) methods for inferring effects of a continuous predictor on mean expression in the presence of nuisance covariates. The motivating data are a high-profile dataset which was used to show opposing effects of hedonic and eudaimonic well-being (or happiness) on the mean expression level of a set of genes that has been correlated with social adversity (the CTRA gene set). The original analysis of these data used a linear model (GLS) of fixed effects with correlated error to infer effects of Hedonia and Eudaimonia on mean CTRA expression.MethodsThe standardized effects of Hedonia and Eudaimonia on CTRA gene set expression estimated by GLS were compared to estimates using multivariate (OLS) linear models and generalized estimating equation (GEE) models. The OLS estimates were tested using O’Brien’s OLS test, Anderson’s permutation ${r}_{F}^{2}$rF2-test, two permutation F-tests (including GlobalAncova), and a rotation z-test (Roast). The GEE estimates were tested using a Wald test with robust standard errors. The performance (Type I, II, S, and M errors) of all tests was investigated using a Monte Carlo simulation of data explicitly modeled on the re-analyzed dataset.ResultsGLS estimates are inconsistent between data sets, and, in each dataset, at least one coefficient is large and highly statistically significant. By contrast, effects estimated by OLS or GEE are very small, especially relative to the standard errors. Bootstrap and permutation GLS distributions suggest that the GLS results in downward biased standard errors and inflated coefficients. The Monte Carlo simulation of error rates shows highly inflated Type I error from the GLS test and slightly inflated Type I error from the GEE test. By contrast, Type I error for all OLS tests are at the nominal level. The permutation F-tests have ∼1.9X the power of the other OLS tests. This increased power comes at a cost of high sign error (∼10%) if tested on small effects.DiscussionThe apparently replicated pattern of well-being effects on gene expression is most parsimoniously explained as “correlated noise” due to the geometry of multiple regression. The GLS for fixed effects with correlated error, or any linear mixed model for estimating fixed effects in designs with many repeated measures or outcomes, should be used cautiously because of the inflated Type I and M error. By contrast, all OLS tests perform well, and the permutation F-tests have superior performance, including moderate power for very small effects. creator: Jeffrey A. Walker uri: https://doi.org/10.7717/peerj.2575 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Walker title: Boundary curves of individual items in the distribution of total depressive symptom scores approximate an exponential pattern in a general population link: https://peerj.com/articles/2566 last-modified: 2016-10-11 description: BackgroundPreviously, we proposed a model for ordinal scale scoring in which individual thresholds for each item constitute a distribution by each item. This lead us to hypothesize that the boundary curves of each depressive symptom score in the distribution of total depressive symptom scores follow a common mathematical model, which is expressed as the product of the frequency of the total depressive symptom scores and the probability of the cumulative distribution function of each item threshold. To verify this hypothesis, we investigated the boundary curves of the distribution of total depressive symptom scores in a general population.MethodsData collected from 21,040 subjects who had completed the Center for Epidemiologic Studies Depression Scale (CES-D) questionnaire as part of a national Japanese survey were analyzed. The CES-D consists of 20 items (16 negative items and four positive items). The boundary curves of adjacent item scores in the distribution of total depressive symptom scores for the 16 negative items were analyzed using log-normal scales and curve fitting.ResultsThe boundary curves of adjacent item scores for a given symptom approximated a common linear pattern on a log normal scale. Curve fitting showed that an exponential fit had a markedly higher coefficient of determination than either linear or quadratic fits. With negative affect items, the gap between the total score curve and boundary curve continuously increased with increasing total depressive symptom scores on a log-normal scale, whereas the boundary curves of positive affect items, which are not considered manifest variables of the latent trait, did not exhibit such increases in this gap.DiscussionThe results of the present study support the hypothesis that the boundary curves of each depressive symptom score in the distribution of total depressive symptom scores commonly follow the predicted mathematical model, which was verified to approximate an exponential mathematical pattern. creator: Shinichiro Tomitaka creator: Yohei Kawasaki creator: Kazuki Ide creator: Maiko Akutagawa creator: Hiroshi Yamada creator: Toshiaki A. Furukawa creator: Yutaka Ono uri: https://doi.org/10.7717/peerj.2566 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Tomitaka et al. title: Form and function of long-range vocalizations in a Neotropical fossorial rodent: the Anillaco Tuco-Tuco (Ctenomys sp.) link: https://peerj.com/articles/2559 last-modified: 2016-10-11 description: The underground environment poses particular communication challenges for subterranean rodents. Some loud and low-pitched acoustic signals that can travel long distances are appropriate for long-range underground communication and have been suggested to be territorial signals. Long-range vocalizations (LRVs) are important in long-distance communication in Ctenomys tuco-tucos. We characterized the LRV of the Anillaco Tuco-Tuco (Ctenomys sp.) using recordings from free-living individuals and described the behavioral context in which this vocalization was produced during laboratory staged encounters between individuals of both sexes. Long-range calls of Anillaco tuco-tucos are low-frequency, broad-band, loud, and long sounds composed by the repetition of two syllable types: series (formed by notes and soft-notes) and individual notes. All vocalizations were initiated with series, but not all had individual notes. Males were heavier than females and gave significantly lower-pitched vocalizations, but acoustic features were independent of body mass in males. The pronounced variation among individuals in the arrangement and number of syllables and the existence of three types of series (dyads, triads, and tetrads), created a diverse collection of syntactic patterns in vocalizations that would provide the opportunity to encode multiple types of information. The existence of complex syntactic patterns and the description of soft-notes represent new aspects of the vocal communication of Ctenomys. Long-distance vocalizations by Anillaco Tuco-Tucos appear to be territorial signals used mostly in male-male interactions. First, emission of LRVs resulted in de-escalation or space-keeping in male-male and male-female encounters in laboratory experiments. Second, these vocalizations were produced most frequently (in the field and in the lab) by males in our study population. Third, males produced LRVs with greater frequency during male-male encounters compared to male-female encounters. Finally, males appear to have larger home ranges that were more spatially segregated than those of females, suggesting that males may have greater need for long-distance signals that advertise their presence. Due to their apparent rarity, the function and acoustic features of LRV in female tuco-tucos remain inadequately known. creator: Juan Pablo Amaya creator: Juan I. Areta creator: Veronica S. Valentinuzzi creator: Emmanuel Zufiaurre uri: https://doi.org/10.7717/peerj.2559 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Amaya et al. title: Effect of orthodontic debonding and residual adhesive removal on 3D enamel microroughness link: https://peerj.com/articles/2558 last-modified: 2016-10-11 description: BackgroundTermination of fixed orthodontic treatment is associated with bracket debonding and residual adhesive removal. These procedures increase enamel roughness to a degree that should depend on the tool used. Enamel roughening may be associated with bacterial retention and staining. However, a very limited data exists on the alteration of 3D enamel roughness resulting from the use of different tools for orthodontic clean-up.Aims1. To perform a precise assessment of 3D enamel surface roughness resulting from residual adhesive removal following orthodontic debonding molar tubes.2. To compare enamel surfaces resulting from the use of tungsten carbide bur, a one-step polisher and finisher and Adhesive Residue Remover.Material and MethodsBuccal surfaces of forty-five extracted human third molars were analysed using a confocal laser microscope at the magnification of 1080× and 3D roughness parameters were calculated. After 20 s etching, molar tubes were bonded, the teeth were stored in 0.9% saline solution for 24 hours and debonded. Residual adhesive was removed using in fifteen specimen each: a twelve-fluted tungsten carbide bur, a one-step finisher and polisher and Adhesive Residue Remover. Then, surface roughness analysis was repeated. Data normality was assessed using Shapiro–Wilk test. Analysis of variance (ANOVA) was used to compare between variables of normal distribution and for the latter—Kruskal-Wallis test.ResultsSa (arithmetical mean height) was significantly different between the groups (p = 0, 01326); the smoothest and most repeatable surfaces were achieved using Adhesive Residue Remover. Similarly, Sq (root mean square height of the scale-limited surface) had the lowest and most homogenous values for Adhesive Residue Remover (p = 0, 01108). Sz (maximum height of the scale-limited surface) was statistically different between the groups (p = 0, 0327), however no statistically significant differences were found concerning Ssk (skewness of the scale-limited surface).DiscussionConfocal laser microscopy allowed 3D surface analysis of enamel surface, avoiding the limitations of contact profilometry. Tungsten carbide burs are the most popular adhesive removing tools, however, the results of the present study indicate, that a one step polisher and finisher as well as Adhesive Residue Remover are less detrimental to the enamel. This is in agreement with a recent study based on direct 3D scanning enamel surface. It proved, that a one-step finisher and polisher as well as Adhesive Residue Remover are characterized by a similar effectiveness in removing residual remnants as tungsten carbide bur, but they remove significantly less enamel.ConclusionOrthodontic debonding and removal of adhesive remnants increases enamel roughness. The smoothest surfaces were achieved using Adhesive Residue Remover, and the roughest using tungsten carbide bur. creator: Joanna Janiszewska-Olszowska creator: Robert Tomkowski creator: Katarzyna Tandecka creator: Piotr Stepien creator: Tomasz Szatkiewicz creator: Katarzyna Sporniak-Tutak creator: Katarzyna Grocholewicz uri: https://doi.org/10.7717/peerj.2558 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Janiszewska-Olszowska et al. title: Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA link: https://peerj.com/articles/2528 last-modified: 2016-10-11 description: Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater than X kb” as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions. creator: Daniel G. Mulcahy creator: Kenneth S. Macdonald creator: Seán G. Brady creator: Christopher Meyer creator: Katharine B. Barker creator: Jonathan Coddington uri: https://doi.org/10.7717/peerj.2528 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Controlled-release of Bacillus thurigiensis formulations encapsulated in light-resistant colloidosomal microcapsules for the management of lepidopteran pests of Brassica crops link: https://peerj.com/articles/2524 last-modified: 2016-10-11 description: Bacillus thuringiensis (B. t.) based formulations have been widely used to control lepidopteran pests in agriculture and forestry. One of their weaknesses is their short residual activity when sprayed in the field. Using Pickering emulsions, mixtures of spores and crystals from three B. t. serovars were successfully encapsulated in colloïdosomal microparticles (50 μm) using innocuous chemicals (acrylic particles, sunflower oil, iron oxide nanoparticles, ethanol and water). A pH trigger mechanism was incorporated within the particles so that B. t. release occurred only at pH > 8.5 which corresponds to the midgut pH of the target pests. Laboratory assays performed on Trichoplusia ni (T. ni) larvae demonstrated that the microencapsulation process did not impair B. t. bioactivity. The best formulations were field-tested on three key lepidopteran pests that attack Brassica crops, i.e., the imported cabbageworm, the cabbage looper and the diamondback moth. After 12 days, the mean number of larvae was significantly lower in microencapsulated formulations than in a commercial B. t. formulation, and the effect of microencapsulated formulations was comparable to a chemical pesticide (lambda-cyhalothrin). Therefore, colloïdosomal microcapsule formulations successfully extend the bioactivity of B. t. for the management of lepidopteran pests of Brassica crops. creator: Oumar Bashir creator: Jerome P. Claverie creator: Pierre Lemoyne creator: Charles Vincent uri: https://doi.org/10.7717/peerj.2524 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bashir et al. title: Comparative functional characterization of novel non-syndromic GJB2 gene variant p.Gly45Arg and lethal syndromic variant p.Gly45Glu link: https://peerj.com/articles/2494 last-modified: 2016-10-11 description: We characterized a novel GJB2 missense variant, c.133G>A, p.Gly45Arg, and compared it with the only other variant at the same amino acid position of the connexin 26 protein (Cx26) reported to date: c.134G>A, p.Gly45Glu. Whereas both variants are associated with hearing loss and are dominantly inherited, p.Gly45Glu has been implicated in the rare fatal keratitis-ichthyosis-deafness (KID) syndrome, which results in cutaneous infections and septicemia with premature demise in the first year of life. In contrast, p.Gly45Arg appears to be non-syndromic. Subcellular localization experiments in transiently co-transfected HeLa cells demonstrated that Cx26-WT (wild-type) and p.Gly45Arg form gap junctions, whereas Cx26-WT with p.Gly45Glu protein does not. The substitution of a nonpolar amino acid glycine in wildtype Cx26 at position 45 with a negatively charged glutamic acid (acidic) has previously been shown to interfere with Ca2+ regulation of hemichannel gating and to inhibit the formation of gap junctions, resulting in cell death. The novel variant p.Gly45Arg, however, changes this glycine to a positively charged arginine (basic), resulting in the formation of dysfunctional gap junctions that selectively affect the permeation of negatively charged inositol 1,4,5-trisphosphate (IP3) and contribute to hearing loss. Cx26 p.Gly45Arg transfected cells, unlike cells transfected with p.Gly45Glu, thrived at physiologic Ca2+ concentrations, suggesting that Ca2+ regulation of hemichannel gating is unaffected in Cx26 p.Gly45Arg transfected cells. Thus, the two oppositely charged amino acids that replace the highly conserved uncharged glycine in p.Gly45Glu and p.Gly45Arg, respectively, produce strikingly different effects on the structure and function of the Cx26 protein. creator: Juan Rodriguez-Paris creator: Jörg Waldhaus creator: Jeenal A. Gordhandas creator: Lynn Pique creator: Iris Schrijver uri: https://doi.org/10.7717/peerj.2494 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rodriguez-Paris et al. title: Phylogenetic relationships and evolutionary history of the greater horseshoe bat, Rhinolophus ferrumequinum, in Northeast Asia link: https://peerj.com/articles/2472 last-modified: 2016-10-11 description: The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations. creator: Tong Liu creator: Keping Sun creator: Yung Chul Park creator: Jiang Feng uri: https://doi.org/10.7717/peerj.2472 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Liu et al. title: Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses link: https://peerj.com/articles/2463 last-modified: 2016-10-11 description: Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians. creator: Mei Fang Lin creator: Wen Hwa Chou creator: Marcelo V. Kitahara creator: Chao Lun Allen Chen creator: David John Miller creator: Sylvain Forêt uri: https://doi.org/10.7717/peerj.2463 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lin et al. title: Ecomorphological analysis of the astragalo-calcaneal complex in rodents and inferences of locomotor behaviours in extinct rodent species link: https://peerj.com/articles/2393 last-modified: 2016-10-11 description: Studies linking postcranial morphology with locomotion in mammals are common. However, such studies are mostly restricted to caviomorphs in rodents. We present here data from various families, belonging to the three main groups of rodents (Sciuroidea, Myodonta, and Ctenohystrica). The aim of this study is to define morphological indicators for the astragalus and calcaneus, which allow for inferences to be made about the locomotor behaviours in rodents. Several specimens were dissected and described to bridge the myology of the leg with the morphology of the bones of interest. Osteological characters were described, compared, mechanically interpreted, and correlated with a “functional sequence” comprising six categories linked to the lifestyle and locomotion (jumping, cursorial, generalist, fossorial, climber and semi-aquatic). Some character states are typical of some of these categories, especially arboreal climbers, fossorial and “cursorial-jumping” taxa. Such reliable characters might be used to infer locomotor behaviours in extinct species. Linear discriminant analyses (LDAs) were used on a wider sample of species and show that astragalar and calcaneal characters can be used to discriminate the categories among extant species whereas a posteriori inferences on extinct species should be examined with caution. creator: Samuel Ginot creator: Lionel Hautier creator: Laurent Marivaux creator: Monique Vianey-Liaud uri: https://doi.org/10.7717/peerj.2393 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ginot et al. title: Associations between different components of fitness and fatness with academic performance in Chilean youths link: https://peerj.com/articles/2560 last-modified: 2016-10-06 description: ObjectivesTo analyze the associations between different components of fitness and fatness with academic performance, adjusting the analysis by sex, age, socio-economic status, region and school type in a Chilean sample.MethodsData of fitness, fatness and academic performance was obtained from the Chilean System for the Assessment of Educational Quality test for eighth grade in 2011 and includes a sample of 18,746 subjects (49% females). Partial correlations adjusted by confounders were done to explore association between fitness and fatness components, and between the academic scores. Three unadjusted and adjusted linear regression models were done in order to analyze the associations of variables.ResultsFatness has a negative association with academic performance when Body Mass Index (BMI) and Waist to Height Ratio (WHR) are assessed independently. When BMI and WHR are assessed jointly and adjusted by cofounders, WHR is more associated with academic performance than BMI, and only the association of WHR is positive. For fitness components, strength was the variable most associated with the academic performance. Cardiorespiratory capacity was not associated with academic performance if fatness and other fitness components are included in the model.ConclusionsFitness and fatness are associated with academic performance. WHR and strength are more related with academic performance than BMI and cardiorespiratory capacity. creator: Pedro R. Olivares creator: Javier García-Rubio uri: https://doi.org/10.7717/peerj.2560 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Olivares and García-Rubio title: Histology and gametogenesis in Heleobia piscium (Cochliopidae) from the Multiple Use Reserve “Isla Martín García,” Buenos Aires, Argentina link: https://peerj.com/articles/2548 last-modified: 2016-10-06 description: Heleobia piscium (d’Orbigny, 1835), a member of the Cochliopidae family found only in South America, is distributed from Entre Ríos, Delta del Paraná, and the littoral of the Río de la Plata down as far as to Punta Indio (Buenos Aires), the southernmost limit of the snail’s geographical distribution. To date, little information is available regarding the reproductive cycle of species within this family either in Argentina or throughout South America. The present work analyzed the histology of the reproductive system of the gonochoric species H. piscium and determined the stages oogenesis and spermatogenesis under natural conditions. Specimens of H. piscium were collected in the Multiple-Use Natural Reserve Isla Martín García, located in the Upper Río de la Plata estuary to the south of the mouth of the Uruguay River. The gametogenic cycle in both sexes was found to consist of the following stages: early maturation, maturation, and evacuation. The maturation period was found to extend from January to October and evacuation of the gametes to start in November and end in February (summer in the Southern Hemisphere). The results indicated the H. piscium exhibit a reproductive cycle without a resting period. creator: Stella Maris Martin creator: Ana C. Díaz uri: https://doi.org/10.7717/peerj.2548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Martin and Díaz title: Higher central fat and poor self-body image in short-stature overweight/obese women living in Brazilian shantytowns link: https://peerj.com/articles/2547 last-modified: 2016-10-06 description: BackgroundShort stature in adult life, a possible consequence of poor perinatal conditions, is associated with higher risk of mortality and social disabilities. We aimed to determine whether low-income, overweight/obese, short-stature (SS) women show alterations in body composition, self-body-image perception, and biochemical profile compared to their non-short (NS) counterparts.MethodsA cross-sectional study was conducted with women living in shantytowns and mother or relatives to undernourished children treated in a center for recuperation and nutritional education. Inclusion criteria were: (1) age, 19–45 years; (2) stature < 152.3 cm or > 158.7 cm; and (3) body mass index > 25 kg/m2. Socioeconomic, anthropometric, biochemical, and body image data were collected. We analyzed 56 SS and 57 NS women.ResultsThe SS group showed a higher waist-to-height ratio (WHtR) (mean: 0.63; standard deviation: 0.06 for SS and mean: 0.60; standard deviation: 0.07 for the NS group; p = 0.02), and, in the adjusted analysis, showed lower fat-free mass (Estimated Marginal Mean for the SS group: 45.7 kg 95% confidence intervals (CI) (45.2–46.2) and for the NS group: 46.9 kg 95% CI (46.4–47.4); p < 0.01) and higher fat mass (Estimated Marginal Mean for the SS group: 32.5 95% CI (31.9–33.0) and for the NS group: 31.4 kg 95% CI (30.9–31.9); p < 0.01). Body mass index was a better predictor of current self-body-image perception for NS women. The SS coefficient values were β = 0.141, SE = 0.059, and R2-Nagelkerke = 0.107, and the NS coefficients values were β = 0.307, SE = 0.058, and R2-Nagelkerke = 0.491 (Z = 2.006; p < 0.05). Considering the obese subgroup, six out of 32 (18.8%) SS women and 14 out of 33 (42.4%) NS women perceived themselves as obese (χ2 = 4.27; p = 0.03). This difference remained significant even after adjustment by age, schooling, and number of children (p = 0.04). Only the total thyroxin showed significant differences between groups, lower in SS women (p = 0.04).DiscussionOverweight/obese, low-income SS women have more central adiposity and impaired self-body image perception, and the body mass index is a weaker predictor of it, compared to NS women. Misperception about body size may be linked with an overestimation of health and underestimation of risk, which may lead to a lower utilization of the health care system and inadequate physician counseling. These features may account, at least partially, for the higher mortality risk seen in SS adults. creator: Nassib Bezerra Bueno creator: Telma Toledo Florêncio creator: Fabiana Albuquerque Cavalcante creator: Isabela Lopes Lins creator: Ana Grotti Clemente creator: Ana Lydia Sawaya uri: https://doi.org/10.7717/peerj.2547 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Bueno et al. title: Occurrence of Blastocystis sp. in water catchments at Malay villages and Aboriginal settlement during wet and dry seasons in Peninsular Malaysia link: https://peerj.com/articles/2541 last-modified: 2016-10-06 description: In the tropics, there are too few studies on isolation of Blastocystis sp. subtypes from water sources; in addition, there is also an absence of reported studies on the occurrence of Blastocystis sp. subtypes in water during different seasons. Therefore, this study was aimed to determine the occurrence of Blastocystis sp. subtypes in river water and other water sources that drained aboriginal vicinity of highly endemic intestinal parasitic infections during wet and dry seasons. Water samples were collected from six sampling points of Sungai Krau (K1–K6) and a point at Sungai Lompat (K7) and other water sources around the aboriginal villages. The water samples were collected during both seasons, wet and dry seasons. Filtration of the water samples were carried out using a flatbed membrane filtration system. The extracted DNA from concentrated water sediment was subjected to single round polymerase chain reaction and positive PCR products were subjected to sequencing. All samples were also subjected to filtration and cultured on membrane lactose glucuronide agar for the detection of faecal coliforms. During wet season, Blastocystis sp. ST1, ST2 and ST3 were detected in river water samples. Blastocystis sp. ST3 occurrence was sustained in the river water samples during dry season. However Blastocystis sp. ST1 and ST2 were absent during dry season. Water samples collected from various water sources showed contaminations of Blastocystis sp. ST1, ST2, ST3 and ST4, during wet season and Blastocystis sp. ST1, ST3, ST8 and ST10 during dry season. Water collected from all river sampling points during both seasons showed growth of Escherichia coli and Enterobacter aerogenes, indicating faecal contamination. In this study, Blastocystis sp. ST3 is suggested as the most robust and resistant subtype able to survive in any adverse environmental condition. Restriction and control of human and animal faecal contaminations to the river and other water sources shall prevent the transmission of Blastocystis sp. to humans and animals in this aboriginal community. creator: Samseh Abdullah Noradilah creator: Ii Li Lee creator: Tengku Shahrul Anuar creator: Fatmah Md Salleh creator: Siti Nor Azreen Abdul Manap creator: Noor Shazleen Husnie Mohd Mohtar creator: Syed Muhamad Azrul creator: Wan Omar Abdullah creator: Norhayati Moktar uri: https://doi.org/10.7717/peerj.2541 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Noradilah et al. title: Expediting evidence synthesis for healthcare decision-making: exploring attitudes and perceptions towards rapid reviews using Q methodology link: https://peerj.com/articles/2522 last-modified: 2016-10-06 description: BackgroundRapid reviews expedite the knowledge synthesis process with the goal of providing timely information to healthcare decision-makers who want to use evidence-informed policy and practice approaches. A range of opinions and viewpoints on rapid reviews is thought to exist; however, no research to date has formally captured these views. This paper aims to explore evidence producer and knowledge user attitudes and perceptions towards rapid reviews.MethodsA Q methodology study was conducted to identify central viewpoints about rapid reviews based on a broad topic discourse. Participants rank-ordered 50 text statements and explained their Q-sort in free-text comments. Individual Q-sorts were analysed using Q-Assessor (statistical method: factor analysis with varimax rotation). Factors, or salient viewpoints on rapid reviews, were identified, interpreted and described.ResultsAnalysis of the 11 individual Q sorts identified three prominent viewpoints: Factor A cautions against the use of study design labels to make judgements. Factor B maintains that rapid reviews should be the exception and not the rule. Factor C focuses on the practical needs of the end-user over the review process.ConclusionResults show that there are opposing viewpoints on rapid reviews, yet some unity exists. The three factors described offer insight into how and why various stakeholders act as they do and what issues may need to be resolved before increase uptake of the evidence from rapid reviews can be realized in healthcare decision-making environments. creator: Shannon E. Kelly creator: David Moher creator: Tammy J. Clifford uri: https://doi.org/10.7717/peerj.2522 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kelly et al. title: Positive effect of dietary lutein and cholesterol on the undirected song activity of an opportunistic breeder link: https://peerj.com/articles/2512 last-modified: 2016-10-06 description: Song is a sexually selected trait that is thought to be an honest signal of the health condition of an individual in many bird species. For species that breed opportunistically, the quantity of food may be a determinant of singing activity. However, it is not yet known whether the quality of food plays an important role in this respect. The aim of the present study was to experimentally investigate the role of two calorie-free nutrients (lutein and cholesterol) in determining the expression of a sexually selected behavior (song rate) and other behaviors (locomotor activity, self-maintenance activity, eating and resting) in male zebra finches (Taeniopygia guttata). We predicted that males supplemented with lutein and cholesterol would sing at higher rates than controls because both lutein and cholesterol have important health-related physiological functions in birds and birdsong mirrors individual condition. To control for testosterone secretion that may upregulate birdsong, birds were exposed to a decreasing photoperiod. Our results showed that control males down-regulated testosterone in response to a decreasing photoperiod, while birds treated with lutein or cholesterol maintained a constant singing activity. Both lutein- and cholesterol-supplemented groups sang more than control groups by the end of the experiment, indicating that the quality of food can affect undirected song irrespective of circulating testosterone concentrations. None of the other measured behaviors were affected by the treatment, suggesting that, when individuals have full availability of food, sexually selected song traits are more sensitive to the effect of food quality than other behavioral traits. Overall the results support our prediction that undirected song produced by male zebra finches signals access to high-quality food. creator: Stefania Casagrande creator: Rianne Pinxten creator: Erika Zaid creator: Marcel Eens uri: https://doi.org/10.7717/peerj.2512 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Casagrande et al. title: Exploring the socio-emotional factors associated with subjective well-being in the unemployed link: https://peerj.com/articles/2506 last-modified: 2016-10-06 description: In this study, we examined the relations between dimensions of Perceived Emotional Intelligence (PEI) and classic constructs, such as social support, on depression, stress, and subjective well-being indicators (life satisfaction and happiness). The study also sought to determine whether PEI dimensions accounted for a significant portion of the variance beyond that of classic constructs in the study of depression, stress, and well-being outcomes in a sample of 442 unemployed subjects. Results indicated that social support and all PEI dimensions are found to be significant and negatively related to depression and stress, and these variables were also found to be significant and positively associated with life satisfaction and happiness. Additionally, results using regression analysis indicated that PEI, and specifically use of emotions and regulation of emotions, explain a significant amount of the variance of all outcomes after controlling for socio-demographics and social support dimensions. Finally, theoretical and practical implications of these constructs and their relation with psychological adjustment and well-being in unemployed people are discussed. creator: M. Pilar Berrios creator: Natalio Extremera creator: M. Pilar Nieto-Flores uri: https://doi.org/10.7717/peerj.2506 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Berrios et al. title: Effects of elevated CO2 on predator avoidance behaviour by reef fishes is not altered by experimental test water link: https://peerj.com/articles/2501 last-modified: 2016-10-06 description: Pioneering studies into the effects of elevated CO2 on the behaviour of reef fishes often tested high-CO2 reared fish using control water in the test arena. While subsequent studies using rearing treatment water (control or high CO2) in the test arena have confirmed the effects of high CO2 on a range of reef fish behaviours, a further investigation into the use of different test water in the experimental arena is warranted. Here, we used a fully factorial design to test the effect of rearing treatment water (control or high CO2) and experimental test water (control or high CO2) on antipredator responses of larval reef fishes. We tested antipredator behaviour in larval clownfish Amphiprion percula and ambon damselfish Pomacentrus amboinensis, two species that have been used in previous high CO2 experiments. Specifically, we tested if: (1) using control or high CO2 water in a two channel flume influenced the response of larval clownfish to predator odour; and (2) using control or high CO2 water in the test arena influenced the escape response of larval damselfish to a startle stimulus. Finally, (3) because the effects of high CO2 on fish behaviour appear to be caused by altered function of the GABA-A neurotransmitter we tested if antipredator behaviours were restored in clownfish treated with a GABA antagonist (gabazine) in high CO2 water. Larval clownfish reared from hatching in control water (496 µatm) strongly avoided predator cue whereas larval clownfish reared from hatching in high CO2 (1,022 µatm) were attracted to the predator cue, as has been reported in previous studies. There was no effect on fish responses of using either control or high CO2 water in the flume. Larval damselfish reared for four days in high CO2 (1,051 µatm) exhibited a slower response to a startle stimulus and slower escape speed compared with fish reared in control conditions (464 µatm). There was no effect of test water on escape responses. Treatment of high-CO2 reared clownfish with 4 mg l−1 gabazine in high CO2 seawater restored the normal response to predator odour, as has been previously reported with fish tested in control water. Our results show that using control water in the experimental trials did not influence the results of previous studies on antipredator behaviour of reef fishes and also supports the results of novel experiments conducted in natural reef habitat at ambient CO2 levels. creator: Philip L. Munday creator: Megan J. Welch creator: Bridie J.M. Allan creator: Sue-Ann Watson creator: Shannon J. McMahon creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.2501 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Munday et al. title: Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment link: https://peerj.com/articles/2498 last-modified: 2016-10-06 description: Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea. creator: Ana C. Henriques creator: Rui M.S. Azevedo creator: Paolo De Marco uri: https://doi.org/10.7717/peerj.2498 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Henriques et al. title: Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions link: https://peerj.com/articles/2405 last-modified: 2016-10-06 description: Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks. creator: Alberto Muñoz creator: Xavier Santos creator: Ángel M. Felicísimo uri: https://doi.org/10.7717/peerj.2405 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Muñoz et al. title: Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator link: https://peerj.com/articles/2555 last-modified: 2016-10-05 description: BackgroundTalitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species.MethodsWe harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq.ResultsWe identified a comprehensive suite of circadian clock gene homologues in T. saltator including the ‘core’ clock genes period (Talper), cryptochrome 2 (Talcry2), timeless (Taltim), clock (Talclk), and bmal1 (Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period in Talper and Talbmal1. Of the clock-related genes, casein kinase IIβ (TalckIIβ), ebony (Talebony), jetlag (Taljetlag), pigment dispensing hormone (Talpdh), protein phosphatase 1 (Talpp1), shaggy (Talshaggy), sirt1 (Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression.DiscussionWe report the sequences of principle genes that comprise the circadian clock of T. saltator and highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data contribute to the growing inventory of described comparative clocks. Expression profiling of the identified clock genes illuminates tantalising targets for experimental manipulation to elucidate the molecular and cellular control of clock-driven phenotypes in this crustacean. creator: Joseph F. O’Grady creator: Laura S. Hoelters creator: Martin T. Swain creator: David C. Wilcockson uri: https://doi.org/10.7717/peerj.2555 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 O’Grady et al. title: Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda) link: https://peerj.com/articles/2549 last-modified: 2016-10-05 description: We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated. creator: Séverine Fourdrilis creator: Patrick Mardulyn creator: Olivier J. Hardy creator: Kurt Jordaens creator: António Manuel de Frias Martins creator: Thierry Backeljau uri: https://doi.org/10.7717/peerj.2549 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fourdrilis et al. title: The ethnobotany of psychoactive plant use: a phylogenetic perspective link: https://peerj.com/articles/2546 last-modified: 2016-10-05 description: Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg), Papaveraceae (opium poppy), Cactaceae (peyote), Convolvulaceae (morning glory), Solanaceae (tobacco), Lamiaceae (mints), Apocynaceae (dogbane) have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence). However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants suggests multiple ethnobotanical origins and widespread human dependence on these plants, motivating pharmacological investigation into their potential as modern therapeutics for various neurological disorders. creator: Nashmiah Aid Alrashedy creator: Jeanmaire Molina uri: https://doi.org/10.7717/peerj.2546 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Alrashedy and Molina title: A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense) link: https://peerj.com/articles/2520 last-modified: 2016-10-05 description: BackgroundUnderstanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients.MethodsTo better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions.ResultsWe obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation.DiscussionThe current study provides the first broad transcriptome from M. australiense using next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans. creator: Azam Moshtaghi creator: Md. Lifat Rahi creator: Viet Tuan Nguyen creator: Peter B. Mather creator: David A. Hurwood uri: https://doi.org/10.7717/peerj.2520 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moshtaghi et al. title: Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms link: https://peerj.com/articles/2519 last-modified: 2016-10-05 description: BackgroundPlant extracts mixture (PEM) and its individual constituent plant extracts(Psidium sp., Mangifera sp., Mentha sp.) are known to have an anti-adhering effect towards oral bacteria in the single-species biofilm. To date, the adhering ability of the early and late plaque colonisers (Streptococcus sanguinis and Streptococcus mutans) to PEM-treated experimental pellicle have not been investigated in dual-species biofilms.MethodsFresh leaves of these plants were used in the preparation of the respective aqueous extract decoctions. The minimum inhibitory concentration (MIC) of the extracts towards S. sanguinis ATCC BAA-1455 and S. mutans ATCC 25175 was determined using a two-fold serial microdilution method. The sum of fractional inhibitory concentration (ΣFIC) index of PEM and its constituent plant extracts was calculated using the MIC values of the plants. The minimum bactericidal concentration (MBC) of the plant extracts was also determined. The anti-adherence effect of the plant extracts (individually and mixed) was carried out by developing simulated S. sanguinis and S. mutans respectively in single- and dual-species of biofilms in the Nordini’s Artificial Mouth (NAM) model system in which the experimental pellicle was pretreated with the plant extract before bacterial inoculation. The bacterial population in the respective biofilms was quantified using ten-fold serial dilutions method and expressed as colony forming unit per ml (CFU/ml). The bacterial population was also viewed using Scanning Electron Microscope (SEM). All experiments were done in triplicate.ResultsThe PEM compared with its respective constituent plants showed the lowest MIC towards S. sanguinis (3.81 mg/ml) and S. mutans (1.91 mg/ml) and exhibited a synergistic effect. The Psidium sp. (15.24 mg/ml) and, PEM and Psidium sp. (30.48 mg/ml) showed the lowest MBC towards S. sanguinis and S. mutans respectively. The anti-adherence effect of the PEM and its respective constituent plants (except Psidium sp.) was different for the two bacteria in the single-species biofilm. In the dual-species biofilms, PEM demonstrated similar anti-adherence effect towards S. sanguinis and S. mutans. The proportions of the bacterial population viewed under SEM appeared to be in agreement with the quantified population.DiscussionThe combination of the active constituents of the individual plant extracts in PEM may contribute to its low MIC giving rise to the synergistic effect. The different anti-adherence effect towards S. sanguinis and S. mutans in both single- and dual-species biofilms could be due to the different proportion of the active constituents of the extracts and the interaction between different bacteria. The better adhering ability of S. sanguinis towards the PEM-treated pellicle when present together with S. mutans in the dual-species biofilms may suggest the potential of PEM in controlling the balance between the early and late colonisers in biofilms. creator: Zaleha Shafiei creator: Zubaidah Haji Abdul Rahim creator: Koshy Philip creator: Nalina Thurairajah uri: https://doi.org/10.7717/peerj.2519 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shafiei et al. title: Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae link: https://peerj.com/articles/2507 last-modified: 2016-10-05 description: BackgroundThe rice receptor kinase XA21 confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization.MethodsTo determine if the predicted NLS is required for XA21-mediated immunity in planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP).ResultsUbi-XA21nls-GFP plants displayed slightly longer lesion lengths, higher Xoobacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi-XA21-GFP control plants. However, the Ubi-XA21nls-GFP plants express lower levels of protein than that observed in Ubi-XA21-GFP.DiscussionThese results demonstrate that the predicted NLS is not required for XA21-mediated immunity. creator: Tong Wei creator: Tsung-Chi Chen creator: Yuen Ting Ho creator: Pamela C. Ronald uri: https://doi.org/10.7717/peerj.2507 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wei et al. title: The effect of CO2 enrichment on net photosynthesis of the red alga Furcellaria lumbricalis in a brackish water environment link: https://peerj.com/articles/2505 last-modified: 2016-10-05 description: Anthropogenic carbon dioxide (CO2) emissions to the atmosphere are causing reduction in the global ocean pH, also known as ocean acidification. This change alters the equilibrium of different forms of dissolved inorganic carbon in seawater that macroalgae use for their photosynthesis. In the Baltic Sea, benthic macroalgae live in a highly variable environment caused by seasonality and rapid changes in meteorological conditions. The effect of increasing water CO2 concentration on the net photosynthesis of the red macroalgae Furcellaria lumbricalis (Hudson) Lamouroux was tested in short-term mesocosm experiments conducted in Kõiguste Bay (N Gulf of Riga) in June–July 2012 and 2013. Separate mesocosms were maintained at different pCO2 levels: ca. 2,000, ca. 1,000 and ca. 200 µatm. In parallel, different environmental factors were measured such as nutrients, light and water temperature. Thus, the current study also investigated whether elevated pCO2 and different environmental factors exerted interactive effects on the photosynthetic rate of F. lumbricalis. In addition, laboratory experiments were carried out to determine the optimal temperature for photosynthesis of F. lumbricalis. The results of our field experiments demonstrated that elevated pCO2 levels may remarkably enhance the photosynthetic rate of F. lumbricalis. However, the magnitude of this effect is altered by different environmental factors, mainly by changes in water temperature. creator: Liina Pajusalu creator: Georg Martin creator: Tiina Paalme creator: Arno Põllumäe uri: https://doi.org/10.7717/peerj.2505 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pajusalu et al. title: A new hynobiid-like salamander (Amphibia, Urodela) from Inner Mongolia, China, provides a rare case study of developmental features in an Early Cretaceous fossil urodele link: https://peerj.com/articles/2499 last-modified: 2016-10-05 description: A new fossil salamander, Nuominerpeton aquilonaris (gen. et sp. nov.), is named and described based on specimens from the Lower Cretaceous Guanghua Formation of Inner Mongolia, China. The new discovery documents a far northern occurrence of Early Cretaceous salamanders in China, extending the geographic distribution for the Mesozoic fossil record of the group from the Jehol area (40th–45th parallel north) to near the 49th parallel north. The new salamander is characterized by having the orbitosphenoid semicircular in shape; coracoid plate of the scapulocoracoid greatly expanded with a convex ventral and posterior border; ossification of two centralia in carpus and tarsus; and first digit being about half the length of the second digit in both manus and pes. The new salamander appears to be closely related to hynobiids, although this inferred relationship awaits confirmation by research in progress by us on a morphological and molecular combined analysis of cryptobranchoid relationships. Comparison of adult with larval and postmetamorphic juvenile specimens provides insights into developmental patterns of cranial and postcranial skeletons in this fossil species, especially resorption of the palatine and anterior portions of the palatopterygoid in the palate and the coronoid in the mandible during metamorphosis, and postmetamorphic ossification of the mesopodium in both manus and pes. Thus, this study provides a rare case study of developmental features in a Mesozoic salamander. creator: Jia Jia creator: Ke-Qin Gao uri: https://doi.org/10.7717/peerj.2499 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jia and Gao title: Prevention of necrotizing enterocolitis with probiotics: a systematic review and meta-analysis link: https://peerj.com/articles/2429 last-modified: 2016-10-05 description: ContextNecrotizing enterocolitis (NEC) is the most frequent gastrointestinal emergency in neonates. The microbiome of the preterm gut may regulate the integrity of the intestinal mucosa. Probiotics may positively contribute to mucosal integrity, potentially reducing the risk of NEC in neonates.ObjectiveTo perform an updated systematic review and meta-analysis on the efficacy and safety of probiotics for the prevention of NEC in premature infants.Data SourcesStructured searches were performed in: Medline, Embase, and the Cochrane Central Register of Controlled Trials (all via Ovid, from 2013 to January 2015). Clinical trial registries and electronically available conference materials were also searched. An updated search was conducted June 3, 2016.Study SelectionRandomized trials including infants less than 37 weeks gestational age or less than 2,500 g on probiotic vs. standard therapy.Data ExtractionData extraction of the newly-identified trials with a double check of the previously-identified trials was performed using a standardized data collection tool.ResultsThirteen additional trials (n = 5,033) were found. The incidence of severe NEC (RR 0.53 95% CI [0.42–0.66]) and all-cause mortality (RR 0.79 95% CI [0.68–0.93]) were reduced. No difference was shown in culture-proven sepsis RR 0.88 95% CI [0.77–1.00].LimitationsHeterogeneity of organisms and dosing regimens studied prevent a species-specific treatment recommendation from being made.ConclusionsPreterm infants benefit from probiotics to prevent severe NEC and death. creator: Sonja C. Sawh creator: Santosh Deshpande creator: Sandy Jansen creator: Christopher J. Reynaert creator: Philip M. Jones uri: https://doi.org/10.7717/peerj.2429 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sawh et al. title: A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago link: https://peerj.com/articles/2475 last-modified: 2016-10-04 description: Although the existence of coral-reef habitats at depths to 165 m in tropical regions has been known for decades, the richness, diversity, and ecological importance of mesophotic coral ecosystems (MCEs) has only recently become widely acknowledged. During an interdisciplinary effort spanning more than two decades, we characterized the most expansive MCEs ever recorded, with vast macroalgal communities and areas of 100% coral cover between depths of 50–90 m extending for tens of km2 in the Hawaiian Archipelago. We used a variety of sensors and techniques to establish geophysical characteristics. Biodiversity patterns were established from visual and video observations and collected specimens obtained from submersible, remotely operated vehicles and mixed-gas SCUBA and rebreather dives. Population dynamics based on age, growth and fecundity estimates of selected fish species were obtained from laser-videogrammetry, specimens, and otolith preparations. Trophic dynamics were determined using carbon and nitrogen stable isotopic analyses on more than 750 reef fishes. MCEs are associated with clear water and suitable substrate. In comparison to shallow reefs in the Hawaiian Archipelago, inhabitants of MCEs have lower total diversity, harbor new and unique species, and have higher rates of endemism in fishes. Fish species present in shallow and mesophotic depths have similar population and trophic (except benthic invertivores) structures and high genetic connectivity with lower fecundity at mesophotic depths. MCEs in Hawai‘i are widespread but associated with specific geophysical characteristics. High genetic, ecological and trophic connectivity establish the potential for MCEs to serve as refugia for some species, but our results question the premise that MCEs are more resilient than shallow reefs. We found that endemism within MCEs increases with depth, and our results do not support suggestions of a global faunal break at 60 m. Our findings enhance the scientific foundations for conservation and management of MCEs, and provide a template for future interdisciplinary research on MCEs worldwide. creator: Richard L. Pyle creator: Raymond Boland creator: Holly Bolick creator: Brian W. Bowen creator: Christina J. Bradley creator: Corinne Kane creator: Randall K. Kosaki creator: Ross Langston creator: Ken Longenecker creator: Anthony Montgomery creator: Frank A. Parrish creator: Brian N. Popp creator: John Rooney creator: Celia M. Smith creator: Daniel Wagner creator: Heather L. Spalding uri: https://doi.org/10.7717/peerj.2475 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pyle et al. title: Age, growth, and natural mortality of schoolmaster (Lutjanus apodus) from the southeastern United States link: https://peerj.com/articles/2543 last-modified: 2016-10-04 description: Ages of schoolmaster (n = 136) from the southeastern Florida coast from 1981–2015 were determined using sectioned sagittal otoliths. Opaque zones were annular, forming March–July (peaking in May–June). Schoolmaster ranged in age from 1–42 years; the largest fish measured 505 mm total length (TL) and was 19 years old. The oldest fish measured 440 mm TL. Estimated body size relationships for schoolmaster were: W = 9.26 × 10−6TL3.11 (n = 256, r2 = 0.95); W = 2.13 × 10−5FL2.99 (n = 161, r2 = 0.95); TL = 1.03 FL + 10.36 (n = 143, r2 = 0.99); and FL = 0.96 TL − 8.41 (n = 143, r2 = 0.99), where W = whole weight in g, FL = fork length in mm, and TL in mm. The fitted von Bertalanffy growth equation was: Lt = 482 (1 − e−0.12(t+2.79)) (n = 136). Based on published life history relationships, a point estimate of natural mortality for schoolmaster was M = 0.10, while age-specific estimates of M ranged from 1.57–0.18 for ages 1–42. creator: Jennifer C. Potts creator: Michael L. Burton creator: Amanda R. Myers uri: https://doi.org/10.7717/peerj.2543 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae) link: https://peerj.com/articles/2534 last-modified: 2016-10-04 description: Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system. creator: Wanwipa Vongsangnak creator: Pramote Chumnanpuen creator: Ajaraporn Sriboonlert uri: https://doi.org/10.7717/peerj.2534 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Vongsangnak et al. title: Did the 1918 influenza cause the twentieth century cardiovascular mortality epidemic in the United States? link: https://peerj.com/articles/2531 last-modified: 2016-10-04 description: During most of the twentieth century, cardiovascular mortality increased in the United States while other causes of death declined. By 1958, the age-standardized death rate (ASDR) for cardiovascular causes for females was 1.84 times that for all other causes, combined (and, for males, 1.79×). Although contemporary observers believed that cardiovascular mortality would remain high, the late 1950s and early 1960s turned out to be the peak of a roughly 70-year epidemic. By 1988 for females (1986 for males), a spectacular decline had occurred, wherein the ASDR for cardiovascular causes was less than that for other causes combined. We discuss this phenomenon from a demographic point of view. We also test a hypothesis from the literature, that the 1918 influenza pandemic caused the cardiovascular mortality epidemic; we fail to find support. creator: Steven Tate creator: Jamie J. Namkung creator: Andrew Noymer uri: https://doi.org/10.7717/peerj.2531 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tate et al. title: Transcriptome response to elevated atmospheric CO2 concentration in the Formosan subterranean termite, Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) link: https://peerj.com/articles/2527 last-modified: 2016-10-04 description: BackgroundCarbon dioxide (CO2) is a pervasive chemical stimulus that plays a critical role in insect life, eliciting behavioral and physiological responses across different species. High CO2 concentration is a major feature of termite nests, which may be used as a cue for locating their nests. Termites also survive under an elevated CO2 concentration. However, the mechanism by which elevated CO2 concentration influences gene expression in termites is poorly understood.MethodsTo gain a better understanding of the molecular basis involved in the adaptation to CO2 concentration, a transcriptome of Coptotermes formosanus Shiraki was constructed to assemble the reference genes, followed by comparative transcriptomic analyses across different CO2 concentration (0.04%, 0.4%, 4% and 40%) treatments.Results(1) Based on a high throughput sequencing platform, we obtained approximately 20 GB of clean data and revealed 189,421 unigenes, with a mean length and an N50 length of 629 bp and 974 bp, respectively. (2) The transcriptomic response of C. formosanus to elevated CO2 levels presented discontinuous changes. Comparative analysis of the transcriptomes revealed 2,936 genes regulated among 0.04%, 0.4%, 4% and 40% CO2 concentration treatments, 909 genes derived from termites and 2,027 from gut symbionts. Genes derived from termites appears selectively activated under 4% CO2 level. In 40% CO2 level, most of the down-regulated genes were derived from symbionts. (3) Through similarity searches to data from other species, a number of protein sequences putatively involved in chemosensory reception were identified and characterized in C. formosanus, including odorant receptors, gustatory receptors, ionotropic receptors, odorant binding proteins, and chemosensory proteins.DiscussionWe found that most genes associated with carbohydrate metabolism, energy metabolism, and genetic information processing were regulated under different CO2 concentrations. Results suggested that termites adapt to ∼4% CO2 level and their gut symbionts may be killed under high CO2 level. We anticipate that our findings provide insights into the transcriptome dynamics of CO2 responses in termites and form the basis to gain a better understanding of regulatory networks. creator: Wenjing Wu creator: Zhiqiang Li creator: Shijun Zhang creator: Yunling Ke creator: Yahui Hou uri: https://doi.org/10.7717/peerj.2527 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wu et al. title: Geographical and altitudinal distribution of Brachycephalus (Anura: Brachycephalidae) endemic to the Brazilian Atlantic Rainforest link: https://peerj.com/articles/2490 last-modified: 2016-10-04 description: Mountains of the Brazilian Atlantic Forest can act as islands of cold and wet climate, leading to the isolation and speciation of species with low dispersal capacity, such as the toadlet species of the genus Brachycephalus. This genus is composed primarily by diurnal species, with miniaturized body sizes (<2.5 cm), inhabiting microhabitats in the leaf litter of montane forests. Still, little is known about the geographical distribution, altitudinal range, and ecological limits of most Brachycephalus species. In this study, we review the available data on the geographical and altitudinal distribution of Brachycephalus based on occurrence records compiled from literature and museums, both for the genus as a whole and separately for the three recently proposed groups of species (ephippium, didactylus, and pernix). The final ensemble dataset comprised 333 records, 120 localities, 28 described species, and six undescribed ones. Species were recorded in six relief units, the richest of which being the Serra do Mar, with 30 species. When the Serra do Mar is subdivided into three subunits, Northern, Central and Southern Serra do Mar, the number of species increase from north to the south, with records of six, nine, and 16 species, respectively. We were able to estimate the extent of occurrence of nearly half of the described species, and the resulting estimates indicate that many of them show remarkably small ranges, some of which less than 50 ha. Brachycephalus species are present from sea level to roughly 1,900 m a.s.l., with the highest richness being found between 751 and 1,000 m a.s.l. (21 spp.). The species with the broadest altitudinal range were B. didactylus (1,075 m) and Brachycephalus sp. 1 (1,035 m), both in the didactylus group, and B. ephippium (1,050 m), of the ephippium group. The broadest altitudinal amplitude for species of the pernix group was recorded for B. brunneus (535 m). The lowest altitudinal records for the pernix group were at 845 m a.s.l. in the state of Paraná and at 455 m a.s.l. in the state of Santa Catarina. The altitudinal occurrence in the pernixspecies group seems to decrease southward. Syntopy between species is also reviewed. creator: Marcos R. Bornschein creator: Carina R. Firkowski creator: Ricardo Belmonte-Lopes creator: Leandro Corrêa creator: Luiz F. Ribeiro creator: Sérgio A.A. Morato creator: Reuber L. Antoniazzi-Jr. creator: Bianca L. Reinert creator: Andreas L.S. Meyer creator: Felipe A. Cini creator: Marcio R. Pie uri: https://doi.org/10.7717/peerj.2490 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bornschein et al. title: Performance of maximum likelihood mixture models to estimate nursery habitat contributions to fish stocks: a case study on sea bream Sparus aurata link: https://peerj.com/articles/2415 last-modified: 2016-10-04 description: BackgroundMixture models (MM) can be used to describe mixed stocks considering three sets of parameters: the total number of contributing sources, their chemical baseline signatures and their mixing proportions. When all nursery sources have been previously identified and sampled for juvenile fish to produce baseline nursery-signatures, mixing proportions are the only unknown set of parameters to be estimated from the mixed-stock data. Otherwise, the number of sources, as well as some/all nursery-signatures may need to be also estimated from the mixed-stock data. Our goal was to assess bias and uncertainty in these MM parameters when estimated using unconditional maximum likelihood approaches (ML-MM), under several incomplete sampling and nursery-signature separation scenarios.MethodsWe used a comprehensive dataset containing otolith elemental signatures of 301 juvenile Sparus aurata, sampled in three contrasting years (2008, 2010, 2011), from four distinct nursery habitats. (Mediterranean lagoons) Artificial nursery-source and mixed-stock datasets were produced considering: five different sampling scenarios where 0–4 lagoons were excluded from the nursery-source dataset and six nursery-signature separation scenarios that simulated data separated 0.5, 1.5, 2.5, 3.5, 4.5 and 5.5 standard deviations among nursery-signature centroids. Bias (BI) and uncertainty (SE) were computed to assess reliability for each of the three sets of MM parameters.ResultsBoth bias and uncertainty in mixing proportion estimates were low (BI ≤ 0.14, SE ≤ 0.06) when all nursery-sources were sampled but exhibited large variability among cohorts and increased with the number of non-sampled sources up to BI = 0.24 and SE = 0.11. Bias and variability in baseline signature estimates also increased with the number of non-sampled sources, but tended to be less biased, and more uncertain than mixing proportion ones, across all sampling scenarios (BI < 0.13, SE < 0.29). Increasing separation among nursery signatures improved reliability of mixing proportion estimates, but lead to non-linear responses in baseline signature parameters. Low uncertainty, but a consistent underestimation bias affected the estimated number of nursery sources, across all incomplete sampling scenarios.DiscussionML-MM produced reliable estimates of mixing proportions and nursery-signatures under an important range of incomplete sampling and nursery-signature separation scenarios. This method failed, however, in estimating the true number of nursery sources, reflecting a pervasive issue affecting mixture models, within and beyond the ML framework. Large differences in bias and uncertainty found among cohorts were linked to differences in separation of chemical signatures among nursery habitats. Simulation approaches, such as those presented here, could be useful to evaluate sensitivity of MM results to separation and variability in nursery-signatures for other species, habitats or cohorts. creator: Edwin J. Niklitschek creator: Audrey M. Darnaude uri: https://doi.org/10.7717/peerj.2415 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Niklitschek & Darnaude