title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1944 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Were early pterosaurs inept terrestrial locomotors? link: https://peerj.com/articles/1018 last-modified: 2015-06-16 description: Pterodactyloid pterosaurs are widely interpreted as terrestrially competent, erect-limbed quadrupeds, but the terrestrial capabilities of non-pterodactyloids are largely thought to have been poor. This is commonly justified by the absence of a non-pterodactyloid footprint record, suggestions that the expansive uropatagia common to early pterosaurs would restrict hindlimb motion in walking or running, and the presence of sprawling forelimbs in some species. Here, these arguments are re-visited and mostly found problematic. Restriction of limb mobility is not a problem faced by extant animals with extensive fight membranes, including species which routinely utilise terrestrial locomotion. The absence of non-pterodactyloid footprints is not necessarily tied to functional or biomechanical constraints. As with other fully terrestrial clades with poor ichnological records, biases in behaviour, preservation, sampling and interpretation likely contribute to the deficit of early pterosaur ichnites. Suggestions that non-pterodactyloids have slender, mechanically weak limbs are demonstrably countered by the proportionally long and robust limbs of many Triassic and Jurassic species. Novel assessments of pterosaur forelimb anatomies conflict with notions that all non-pterodactyloids were obligated to sprawling forelimb postures. Sprawling forelimbs seem appropriate for species with ventrally-restricted glenoid articulations (seemingly occurring in rhamphorhynchines and campylognathoidids). However, some early pterosaurs, such as Dimorphodon macronyx and wukongopterids, have glenoid arthrologies which are not ventrally restricted, and their distal humeri resemble those of pterodactyloids. It seems fully erect forelimb stances were possible in these pterosaurs, and may be probable given proposed correlation between pterodactyloid-like distal humeral morphology and forces incurred through erect forelimb postures. Further indications of terrestrial habits include antungual sesamoids, which occur in the manus and pes anatomy of many early pterosaur species, and only occur elsewhere in terrestrial reptiles, possibly developing through frequent interactions of large claws with firm substrates. It is argued that characteristics possibly associated with terrestriality are deeply nested within Pterosauria and not restricted to Pterodactyloidea as previously thought, and that pterodactyloid-like levels of terrestrial competency may have been possible in at least some early pterosaurs. creator: Mark P. Witton uri: https://doi.org/10.7717/peerj.1018 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Witton title: Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY link: https://peerj.com/articles/1026 last-modified: 2015-06-16 description: The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited. creator: Abhishek Kumar uri: https://doi.org/10.7717/peerj.1026 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kumar title: GenomePeek—an online tool for prokaryotic genome and metagenome analysis link: https://peerj.com/articles/1025 last-modified: 2015-06-16 description: As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options. creator: Katelyn McNair creator: Robert A. Edwards uri: https://doi.org/10.7717/peerj.1025 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McNair and Edwards title: Is grazing exclusion effective in restoring vegetation in degraded alpine grasslands in Tibet, China? link: https://peerj.com/articles/1020 last-modified: 2015-06-16 description: Overgrazing is considered one of the key disturbance factors that results in alpine grassland degradation in Tibet. Grazing exclusion by fencing has been widely used as an approach to restore degraded grasslands in Tibet since 2004. Is the grazing exclusion management strategy effective for the vegetation restoration of degraded alpine grasslands? Three alpine grassland types were selected in Tibet to investigate the effect of grazing exclusion on plant community structure and biomass. Our results showed that species biodiversity indicators, including the Pielou evenness index, the Shannon–Wiener diversity index, and the Simpson dominance index, did not significantly change under grazing exclusion conditions. In contrast, the total vegetation cover, the mean vegetation height of the community, and the aboveground biomass were significantly higher in the grazing exclusion grasslands than in the free grazed grasslands. These results indicated that grazing exclusion is an effective measure for maintaining community stability and improving aboveground vegetation growth in alpine grasslands. However, the statistical analysis showed that the growing season precipitation (GSP) plays a more important role than grazing exclusion in which influence on vegetation in alpine grasslands. In addition, because the results of the present study come from short term (6–8 years) grazing exclusion, it is still uncertain whether these improvements will be continuable if grazing exclusion is continuously implemented. Therefore, the assessments of the ecological effects of the grazing exclusion management strategy on degraded alpine grasslands in Tibet still need long term continued research. creator: Yan Yan creator: Xuyang Lu uri: https://doi.org/10.7717/peerj.1020 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Yan and Lu title: Influence of sediment characteristics on the composition of soft-sediment intertidal communities in the northern Gulf of Mexico link: https://peerj.com/articles/1014 last-modified: 2015-06-16 description: Benthic infaunal communities are important components of coastal ecosystems. Understanding the relationships between the structure of these communities and characteristics of the habitat in which they live is becoming progressively more important as coastal systems face increasing stress from anthropogenic impacts and changes in climate. To examine how sediment characteristics and infaunal community composition were related along the northern Gulf of Mexico coast, we sampled intertidal infaunal communities at seven sites covering common habitat types at a regional scale. Across 69 samples, the communities clustered into four distinct groups on the basis of faunal composition. Nearly 70% of the variation in the composition of the communities was explained by salinity, median grain size, and total organic content. Our results suggest that at a regional level coarse habitat characteristics are able to explain a large amount of the variation among sites in infaunal community structure. By examining the relationships between infaunal communities and their sedimentary habitats, we take a necessary first step that will allow the exploration of how changes in habitat and community composition influence higher trophic levels and ecosystem scale processes. creator: Kyle E. Coblentz creator: Jessica R. Henkel creator: Bryan J. Sigel creator: Caz M. Taylor uri: https://doi.org/10.7717/peerj.1014 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Coblentz et al. title: Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review link: https://peerj.com/articles/1008 last-modified: 2015-06-16 description: Associations between microorganisms occur extensively throughout Earth’s oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually. creator: Felipe H. Coutinho creator: Pedro M. Meirelles creator: Ana Paula B. Moreira creator: Rodolfo P. Paranhos creator: Bas E. Dutilh creator: Fabiano L. Thompson uri: https://doi.org/10.7717/peerj.1008 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Coutinho et al. title: Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea link: https://peerj.com/articles/997 last-modified: 2015-06-16 description: Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. creator: Dawn B. Goldsmith creator: Rachel J. Parsons creator: Damitu Beyene creator: Peter Salamon creator: Mya Breitbart uri: https://doi.org/10.7717/peerj.997 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Goldsmith et al. title: Modelling Tradescantia fluminensis to assess long term survival link: https://peerj.com/articles/1013 last-modified: 2015-06-11 description: We present a simple Poisson process model for the growth of Tradescantia fluminensis, an invasive plant species that inhibits the regeneration of native forest remnants in New Zealand. The model was parameterised with data derived from field experiments in New Zealand and then verified with independent data. The model gave good predictions which showed that its underlying assumptions are sound. However, this simple model had less predictive power for outputs based on variance suggesting that some assumptions were lacking. Therefore, we extended the model to include higher variability between plants thereby improving its predictions. This high variance model suggests that control measures that promote node death at the base of the plant or restrict the main stem growth rate will be more effective than those that reduce the number of branching events. The extended model forms a good basis for assessing the efficacy of various forms of control of this weed, including the recently-released leaf-feeding tradescantia leaf beetle (Neolema ogloblini). creator: Alex James creator: Sue M. Molloy creator: Agate Ponder-Sutton creator: Michael J. Plank creator: Shona L. Lamoureaux creator: Graeme W. Bourdôt creator: Dave Kelly uri: https://doi.org/10.7717/peerj.1013 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 James et al. title: Non-lethal approach identifies variability of δ15N values in the fin rays of Atlantic Goliath Grouper, Epinephelus itajara link: https://peerj.com/articles/1010 last-modified: 2015-06-11 description: The Atlantic Goliath Grouper, Epinephelus itajara, is critically endangered throughout its range but has begun to show initial signs of recovery in Florida state waters. As the population continues to rebound, researchers face a pressing need to fill the knowledge gaps about this iconic species. Here, we examined the δ15N isotopic records in fin rays collected from Atlantic Goliath Grouper, and related changes of isotopic ratios over time to life history characteristics. Fin-ray analysis was used as a non-lethal technique to sample individuals from two locations at similar latitudes from the west and east coasts of Florida, USA. δ15N data were acquired by mechanically separating the annuli of each fin ray and then analyzing the material in an Irradiance Elemental Analyzer Mass Spectrometer. The δ15N values were consistent among individuals within populations from each coast of Florida, and mirrored the expected changes over the lives of the fish. Overall, differences were found between δ15N values at juvenile life history phases versus adult phases, but the patterns associated with these differences were unique to each coastal group. We demonstrated, for the first time, that δ15N values from fin rays can be used to assess the life histories of Atlantic Goliath Grouper. The non-lethal strategies outlined here can be used to acquire information essential to the management of species of concern, such as those that are threatened or endangered. creator: Orian E. Tzadik creator: Ethan A. Goddard creator: David J. Hollander creator: Christopher C. Koenig creator: Christopher D. Stallings uri: https://doi.org/10.7717/peerj.1010 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Tzadik et al. title: Rotation survival forest for right censored data link: https://peerj.com/articles/1009 last-modified: 2015-06-11 description: Recently, survival ensembles have found more and more applications in biological and medical research when censored time-to-event data are often confronted. In this research, we investigate the plausibility of extending a rotation forest, originally proposed for classification purpose, to survival analysis. Supported by the proper statistical analysis, we show that rotation survival forests are able to outperform the state-of-art survival ensembles on right censored data. We also provide a C-index based variable importance measure for evaluating covariates in censored survival data. creator: Lifeng Zhou creator: Qingsong Xu creator: Hong Wang uri: https://doi.org/10.7717/peerj.1009 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Zhou et al.