title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1907 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: New material and revision of Melanorosaurus thabanensis, a basal sauropodomorph from the Upper Triassic of Lesotho link: https://peerj.com/articles/1639 last-modified: 2016-02-01 description: Melanorosaurus is a genus of basal sauropodomorph that currently includes two species from Southern Africa. In this paper, we redescribe the holotype femur of Melanorosaurus thabanensis from the Elliot Formation of Lesotho, as well as associated remains. The stratigraphic position of this taxon is reviewed, and it is clear that it comes from the Lower Elliot Formation being, therefore, Late Triassic in age, and not Early Jurassic as originally described. The knowledge of the anatomy of the basal sauropodomorph of Thabana Morena is enhanced by the description of six new skeletal elements from the type locality. The femur and the ilium from Thabana Morena are diagnostic and characterized by unusual proportions. The first phylogenetic analysis including both this specimen and Melanorosaurus is conducted. This analysis leads to the conclusion that the femur described in the original publication of Melanorosaurus thabanensis can no longer be referred to Melanorosaurus. For these reasons, we hereby create Meroktenos gen. nov. to encompass Meroktenos thabanensis comb. nov. creator: Claire Peyre de Fabrègues creator: Ronan Allain uri: https://doi.org/10.7717/peerj.1639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peyre de Fabrègues and Allain title: Exploration of the “larval pool”: development and ground-truthing of a larval transport model off leeward Hawai‘i link: https://peerj.com/articles/1636 last-modified: 2016-02-01 description: Most adult reef fish show site fidelity thus dispersal is limited to the mobile larval stage of the fish, and effective management of such species requires an understanding of the patterns of larval dispersal. In this study, we assess larval reef fish distributions in the waters west of the Big Island of Hawai‘i using both in situ and model data. Catches from Cobb midwater trawls off west Hawai‘i show that reef fish larvae are most numerous in offshore waters deeper than 3,000 m and consist largely of pre-settlement Pomacanthids, Acanthurids and Chaetodontids. Utilizing a Lagrangian larval dispersal model, we were able to replicate the observed shore fish distributions from the trawl data and we identified the 100 m depth strata as the most likely depth of occupancy. Additionally, our model showed that for larval shore fish with a pelagic larval duration longer than 40 days there was no significant change in settlement success in our model. By creating a general additive model (GAM) incorporating lunar phase and angle we were able to explain 67.5% of the variance between modeled and in situ Acanthurid abundances. We took steps towards creating a predictive larval distribution model that will greatly aid in understanding the spatiotemporal nature of the larval pool in west Hawai‘i, and the dispersal of larvae throughout the Hawaiian archipelago. creator: Johanna L.K. Wren creator: Donald R. Kobayashi uri: https://doi.org/10.7717/peerj.1636 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wren and Kobayashi title: Estimating and comparing microbial diversity in the presence of sequencing errors link: https://peerj.com/articles/1634 last-modified: 2016-02-01 description: Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. creator: Chun-Huo Chiu creator: Anne Chao uri: https://doi.org/10.7717/peerj.1634 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Chiu & Chao title: Climate envelope predictions indicate an enlarged suitable wintering distribution for Great Bustards (Otis tarda dybowskii) in China for the 21st century link: https://peerj.com/articles/1630 last-modified: 2016-02-01 description: The rapidly changing climate makes humans realize that there is a critical need to incorporate climate change adaptation into conservation planning. Whether the wintering habitats of Great Bustards (Otis tarda dybowskii), a globally endangered migratory subspecies whose population is approximately 1,500–2,200 individuals in China, would be still suitable in a changing climate environment, and where this could be found, is an important protection issue. In this study, we selected the most suitable species distribution model for bustards using climate envelopes from four machine learning models, combining two modelling approaches (TreeNet and Random Forest) with two sets of variables (correlated variables removed or not). We used common evaluation methods area under the receiver operating characteristic curves (AUC) and the True Skill Statistic (TSS) as well as independent test data to identify the most suitable model. As often found elsewhere, we found Random Forest with all environmental variables outperformed in all assessment methods. When we projected the best model to the latest IPCC-CMIP5 climate scenarios (Representative Concentration Pathways (RCPs) 2.6, 4.5 and 8.5 in three Global Circulation Models (GCMs)), and averaged the project results of the three models, we found that suitable wintering habitats in the current bustard distribution would increase during the 21st century. The Northeast Plain and the south of North China were projected to become two major wintering areas for bustards. However, the models suggest that some currently suitable habitats will experience a reduction, such as Dongting Lake and Poyang Lake in the Middle and Lower Yangtze River Basin. Although our results suggested that suitable habitats in China would widen with climate change, greater efforts should be undertaken to assess and mitigate unstudied human disturbance, such as pollution, hunting, agricultural development, infrastructure construction, habitat fragmentation, and oil and mine exploitation. All of these are negatively and intensely linked with global change. creator: Chunrong Mi creator: Huettmann Falk creator: Yumin Guo uri: https://doi.org/10.7717/peerj.1630 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mi et al. title: New insights on Prestosuchus chiniquensis Huene, 1942 (Pseudosuchia, Loricata) based on new specimens from the “Tree Sanga” Outcrop, Chiniquá Region, Rio Grande do Sul, Brazil link: https://peerj.com/articles/1622 last-modified: 2016-02-01 description: The ‘rauisuchians’ are a group of Triassic pseudosuchian archosaurs that displayed a near global distribution. Their problematic taxonomic resolution comes from the fact that most taxa are represented only by a few and/or mostly incomplete specimens. In the last few decades, renewed interest in early archosaur evolution has helped to clarify some of these problems, but further studies on the taxonomic and paleobiological aspects are still needed. In the present work, we describe new material attributed to the ‘rauisuchian’ taxon Prestosuchus chiniquensis, of the Dinodontosaurus Assemblage Zone, Middle Triassic (Ladinian) of the Santa Maria Supersequence of southern Brazil, based on a comparative osteologic analysis. Additionally, we present well supported evidence that these represent juvenile forms, due to differences in osteological features (i.e., a subnarial fenestra) that when compared to previously described specimens can be attributed to ontogeny and indicate variation within a single taxon of a problematic but important osteological structure in the study of ‘rauisuchians.’ creator: Marcel B. Lacerda creator: Bianca M. Mastrantonio creator: Daniel C. Fortier creator: Cesar L. Schultz uri: https://doi.org/10.7717/peerj.1622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Lacerda et al. title: Phylogenetic and morphologic evidence confirm the presence of a new montane cloud forest associated bird species in Mexico, the Mountain Elaenia (Elaenia frantzii; Aves: Passeriformes: Tyrannidae) link: https://peerj.com/articles/1598 last-modified: 2016-02-01 description: Here we provide evidence to support an extension of the recognized distributional range of the Mountain Elaenia (Elaenia frantzii) to include southern Mexico. We collected two specimens in breeding condition in northwestern Sierra Norte de Chiapas, Mexico. Morphologic and genetic evidence support their identity as Elaenia frantzii. We compared environmental parameters of records across the entire geographic range of the species to those at the northern Chiapas survey site and found no climatic differences among localities. creator: Zachary R. Hanna creator: Marco F. Ortiz-Ramírez creator: César A. Ríos-Muñoz creator: Héctor Cayetano-Rosas creator: Rauri C. K. Bowie creator: Adolfo G. Navarro-Sigüenza uri: https://doi.org/10.7717/peerj.1598 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hanna et al. title: Unequal contribution of native South African phylogeographic lineages to the invasion of the African clawed frog, Xenopus laevis, in Europe link: https://peerj.com/articles/1659 last-modified: 2016-02-01 description: Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis) populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population. creator: Charlotte De Busschere creator: Julien Courant creator: Anthony Herrel creator: Rui Rebelo creator: Dennis Rödder creator: G. John Measey creator: Thierry Backeljau uri: https://doi.org/10.7717/peerj.1659 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 De Busschere et al. title: Deficiencies of effectiveness of intervention studies in veterinary medicine: a cross-sectional survey of ten leading veterinary and medical journals link: https://peerj.com/articles/1649 last-modified: 2016-01-28 description: The validity of studies that assess the effectiveness of an intervention (EoI) depends on variables such as the type of study design, the quality of their methodology, and the participants enrolled. Five leading veterinary journals and 5 leading human medical journals were hand-searched for EoI studies for the year 2013. We assessed (1) the prevalence of randomized controlled trials (RCTs) among EoI studies, (2) the type of participants enrolled, and (3) the methodological quality of the selected studies. Of 1707 eligible articles, 590 were EoI articles and 435 RCTs. Random allocation to the intervention was performed in 52% (114/219; 95%CI:45.2–58.8%) of veterinary EoI articles, against 87% (321/371; 82.5–89.7%) of human EoI articles (adjusted OR:9.2; 3.4–24.8). Veterinary RCTs were smaller (median: 26 animals versus 465 humans) and less likely to enroll real patients, compared with human RCTs (OR:331; 45–2441). Only 2% of the veterinary RCTs, versus 77% of the human RCTs, reported power calculations, primary outcomes, random sequence generation, allocation concealment and estimation methods. Currently, internal and external validity of veterinary EoI studies is limited compared to human medical ones. To address these issues, veterinary interventional research needs to improve its methodology, increase the number of published RCTs and enroll real clinical patients. creator: Nicola Di Girolamo creator: Reint Meursinge Reynders uri: https://doi.org/10.7717/peerj.1649 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Di Girolamo & Meursinge Reynders title: AMAS: a fast tool for alignment manipulation and computing of summary statistics link: https://peerj.com/articles/1660 last-modified: 2016-01-28 description: The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python’s core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License. creator: Marek L. Borowiec uri: https://doi.org/10.7717/peerj.1660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Borowiec title: An analysis of structural relationship among achievement motive on social participation, purpose in life, and role expectations among community dwelling elderly attending day services link: https://peerj.com/articles/1655 last-modified: 2016-01-28 description: Background. Achievement motive is defined as the intention to achieve one’s goals. Achievement motive is assumed to promote clients to choices and actions toward their valuable goal, so it is an important consideration in rehabilitation.Purpose. The purpose of this study is to demonstrate the structural relationship among achievement motive on purpose in life, social participation, and role expectation of community-dwelling elderly people.Methods. Participants were community-dwelling elderly people in day-service centers. A total of 281 participants (male: 127, female: 154) answered the self-administered questionnaire in cross-sectional research. The questionnaire was comprised of demographic data and scales that evaluated achievement motive, social participation, purpose in life, and role expectation. We studied the structural relationship established by our hypothesized model via a structural equation modeling approach.Results. We checked the standardized path coefficients and the modification indices; the modified model’s statistics were a good fit: CFI = 0.984, TLI = 0.983, RMSEA = 0.050, 90% CI [0.044–0.055]. Achievement motive had a significantly direct effect on purpose in life (direct effect = 0.445, p value < 0.001), a significantly indirect effect on purpose in life via social participation or role expectation (indirect effect = 0.170, p value < 0.001) and a total effect on purpose in life (total effect = 0.615).Discussion. This result suggests that enhancing the intention to achieve one’s goals enables participants to feel a spirit of challenge with a purpose and a sense of fulfillment in their daily lives. creator: Nobuyuki Sano creator: Makoto Kyougoku uri: https://doi.org/10.7717/peerj.1655 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sano and Kyougoku