title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1785 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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.