title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1936
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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.

title: Uneven distribution of enamel in the tooth crown of a Plains Zebra (Equus quagga)
link: https://peerj.com/articles/1002
last-modified: 2015-06-11
description: Unworn teeth of herbivorous mammals are not immediately functional. They have to be partially worn to expose enamel ridges which can then act as shear-cutting blades to break the food down. We use the Plains Zebra (Equus quagga) as a hypsodont, herbivorous model organism to investigate how initial wear of the tooth crown is controlled by underlying structures. We find that the enamel proportion is smaller at the apical half of the tooth crown in all upper tooth positions and suggest that lower enamel content here could promote early wear. Besides this uneven enamel distribution, we note that the third molar has a higher overall enamel content than any other tooth position. The M3 is thus likely to have a slightly different functional trait in mastication, resisting highest bite forces along the tooth row and maintaining functionality when anterior teeth are already worn down.
creator: Daniela E. Winkler
creator: Thomas M. Kaiser
uri: https://doi.org/10.7717/peerj.1002
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Winkler and Kaiser

title: Musculoskeletal modelling of an ostrich (Struthio camelus) pelvic limb: influence of limb orientation on muscular capacity during locomotion
link: https://peerj.com/articles/1001
last-modified: 2015-06-11
description: We developed a three-dimensional, biomechanical computer model of the 36 major pelvic limb muscle groups in an ostrich (Struthio camelus) to investigate muscle function in this, the largest of extant birds and model organism for many studies of locomotor mechanics, body size, anatomy and evolution. Combined with experimental data, we use this model to test two main hypotheses. We first query whether ostriches use limb orientations (joint angles) that optimize the moment-generating capacities of their muscles during walking or running. Next, we test whether ostriches use limb orientations at mid-stance that keep their extensor muscles near maximal, and flexor muscles near minimal, moment arms. Our two hypotheses relate to the control priorities that a large bipedal animal might evolve under biomechanical constraints to achieve more effective static weight support. We find that ostriches do not use limb orientations to optimize the moment-generating capacities or moment arms of their muscles. We infer that dynamic properties of muscles or tendons might be better candidates for locomotor optimization. Regardless, general principles explaining why species choose particular joint orientations during locomotion are lacking, raising the question of whether such general principles exist or if clades evolve different patterns (e.g., weighting of muscle force–length or force–velocity properties in selecting postures). This leaves theoretical studies of muscle moment arms estimated for extinct animals at an impasse until studies of extant taxa answer these questions. Finally, we compare our model’s results against those of two prior studies of ostrich limb muscle moment arms, finding general agreement for many muscles. Some flexor and extensor muscles exhibit self-stabilization patterns (posture-dependent switches between flexor/extensor action) that ostriches may use to coordinate their locomotion. However, some conspicuous areas of disagreement in our results illustrate some cautionary principles. Importantly, tendon-travel empirical measurements of muscle moment arms must be carefully designed to preserve 3D muscle geometry lest their accuracy suffer relative to that of anatomically realistic models. The dearth of accurate experimental measurements of 3D moment arms of muscles in birds leaves uncertainty regarding the relative accuracy of different modelling or experimental datasets such as in ostriches. Our model, however, provides a comprehensive set of 3D estimates of muscle actions in ostriches for the first time, emphasizing that avian limb mechanics are highly three-dimensional and complex, and how no muscles act purely in the sagittal plane. A comparative synthesis of experiments and models such as ours could provide powerful synthesis into how anatomy, mechanics and control interact during locomotion and how these interactions evolve. Such a framework could remove obstacles impeding the analysis of muscle function in extinct taxa.
creator: John R. Hutchinson
creator: Jeffery W. Rankin
creator: Jonas Rubenson
creator: Kate H. Rosenbluth
creator: Robert A. Siston
creator: Scott L. Delp
uri: https://doi.org/10.7717/peerj.1001
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hutchinson et al.

title: Can endocranial volume be estimated accurately from external skull measurements in great-tailed grackles (Quiscalus mexicanus)?
link: https://peerj.com/articles/1000
last-modified: 2015-06-11
description: There is an increasing need to validate and collect data approximating brain size on individuals in the field to understand what evolutionary factors drive brain size variation within and across species. We investigated whether we could accurately estimate endocranial volume (a proxy for brain size), as measured by computerized tomography (CT) scans, using external skull measurements and/or by filling skulls with beads and pouring them out into a graduated cylinder for male and female great-tailed grackles. We found that while females had higher correlations than males, estimations of endocranial volume from external skull measurements or beads did not tightly correlate with CT volumes. We found no accuracy in the ability of external skull measures to predict CT volumes because the prediction intervals for most data points overlapped extensively. We conclude that we are unable to detect individual differences in endocranial volume using external skull measurements. These results emphasize the importance of validating and explicitly quantifying the predictive accuracy of brain size proxies for each species and each sex.
creator: Corina J. Logan
creator: Christin R. Palmstrom
uri: https://doi.org/10.7717/peerj.1000
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Logan et al.

title: Development of a cognitive bias methodology for measuring low mood in chimpanzees
link: https://peerj.com/articles/998
last-modified: 2015-06-11
description: There is an ethical and scientific need for objective, well-validated measures of low mood in captive chimpanzees. We describe the development of a novel cognitive task designed to measure ‘pessimistic’ bias in judgments of expectation of reward, a cognitive marker of low mood previously validated in a wide range of species, and report training and test data from three common chimpanzees (Pan troglodytes). The chimpanzees were trained on an arbitrary visual discrimination in which lifting a pale grey paper cone was associated with reinforcement with a peanut, whereas lifting a dark grey cone was associated with no reward. The discrimination was trained by sequentially presenting the two cone types until significant differences in latency to touch the cone types emerged, and was confirmed by simultaneously presenting both cone types in choice trials. Subjects were subsequently tested on their latency to touch unrewarded cones of three intermediate shades of grey not previously seen. Pessimism was indicated by the similarity between the latency to touch intermediate cones and the latency to touch the trained, unreinforced, dark grey cones. Three subjects completed training and testing, two adult males and one adult female. All subjects learnt the discrimination (107–240 trials), and retained it during five sessions of testing. There was no evidence that latencies to lift intermediate cones increased over testing, as would have occurred if subjects learnt that these were never rewarded, suggesting that the task could be used for repeated testing of individual animals. There was a significant difference between subjects in their relative latencies to touch intermediate cones (pessimism index) that emerged following the second test session, and was not changed by the addition of further data. The most dominant male subject was least pessimistic, and the female most pessimistic. We argue that the task has the potential to be used to assess longitudinal changes in sub-clinical levels of low mood in chimpanzees, however further work with a larger sample of animals is required to validate this claim.
creator: Melissa Bateson
creator: Daniel Nettle
uri: https://doi.org/10.7717/peerj.998
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bateson and Nettle