title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1786 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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.