Find research datasets worth reusing

Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking

Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbour joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.

Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.

opencc-zeroNov 2019View details →

Data from: A new mound-building biota from the lower Carboniferous of Alabama

A small (1.2 m) columnar carbonate mound in shaley strata equivalent to the Hartselle Sandstone (lower Serpukhovian) near Woodville in northeastern Alabama was built by a consortium of species unlike those of other Carboniferous mounds in the southeastern United States. The mound contains a new problematic microencruster, Aphralysia anfracta n. sp., along with encrusting bryozoans (Fistulipora M'Coy, 1849), nonskeletal microbes, and other microencrusters, including Aphralysia capriorae Mamet and Roux 1975, in a carbonate mud matrix. Mound cavities are filled with three generations of carbonate and siliciclastic sediment. Other biotic constituents of the mound include oncoids, sponges (including Pileospongia Rigby et al., 1979), gastropods, crinoids, a tabulate coral, and coenobionts, including coccoid calcimicrobes. The mound biota, especially the microencrusters, is dramatically different from those of other Serpukhovian mounds that have been described from Alabama (made by various consortia of rugose corals, fenestrate bryozoa, crinoids, sponges, and nonskeletal microbes). Indeed, the Woodville mound extends the range of the lower Carboniferous encruster Aphralysia to North America.

opencc-zeroDec 2016View details →

Data from: A new promising phylogenetic marker to study the diversity of fungal communities: the Glycoside Hydrolase 63 gene

In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.

opencc-zeroDec 2018View details →

Data from: Temporal variation in the vocal behaviour of southern right whales in the Auckland Islands, New Zealand

Autonomous recorders are frequently utilised for examining vocal behaviour of animals, and are particularly effective in remote habitats. Southern right whales are known to have an extensive acoustic repertoire. A recorder was moored at the isolated sub-Antarctic Auckland Islands for a year to examine whether the acoustic behaviour of southern right whales differed seasonally and throughout the day at their main calving ground in New Zealand. Recordings were made in each month except June, and vocalisations were audible in all months with recordings except January. A total of 35,487 calls were detected, of which upcalls were the most common (11,623). Call rate peaked in August (288±5.9 [SE] calls/hour) and July (194±8.3). Vocal behaviour varied diurnally with highest call rates detected at dusk and night, consistent with the concept that upcalls function primarily as contact calls. Zero-inflated model results confirmed that seasonal variation was the most important factor for explaining differences in vocal behaviour. An automated detector designed to expedite the analysis process for North Atlantic right whales correctly identified 80% of upcalls, although false detections were frequent, particularly when call rates were low. This study is the first to attempt year-round monitoring of southern right whale presence in New Zealand.

opencc-zeroDec 2011View details →

Data from: IKey+: a new single-access key generation web service

Single-access keys are a major tool for biologists who need to identify specimens. The construction process of these keys is particularly complex (especially if the input dataset is large) so having an automatic single-access key generation tool is essential. As part of the European project ViBRANT, our aim was to develop such a tool as a web service, thus allowing end-users to integrate it directly into their workflow. IKey+generates single-access keys on demand, for single users or research institutions. It receives user input data (using the standard SDD format), accepts several key-generation parameters (affecting the key topology and representation), and supports several output formats. IKey+ is freely available (sources and binary packages) at www.identificationkey.fr. Furthermore, it is deployed on our server and can be queried (for testing purposes) via a simple web client also available at www.identificationkey.fr. Finally a client plugin will be integrated to the Scratchpads biodiversity networking tool (scratchpads.eu).

Data from: Bridging the gap: parkour athletes provide new insights into locomotion energetics of arboreal apes

The tree canopy is an energetically challenging environment to traverse. Along with compliant vegetation, gaps in the canopy can prove energetically costly if they force a route-extending detour. Arboreal apes exhibit diverse locomotion strategies, including for gap crossing. Which one they employ in any given scenario may be influenced by the energy costs to do so, which are affected by the details of the immediate environment in combination with their body size. Measuring energetics of arboreal apes is not tractable; thus our knowledge in this area is limited. We devised a novel, custom-made experimental set-up to record the energy expenditure of parkour athletes tree-swaying, jumping and vertical climbing. The latter strategy was vastly more expensive, indicating that when energy economy is the focus arboreal apes will prioritize routes that limit height changes. Whether tree-swaying or jumping was most economical for the athletes depended upon interactions between tree stiffness, the distance to cross, number of tree-sways required and their own mass. Updated analysis of previous interspecific correlations suggests that whether the relative costs to vertical climb are size-invariant across primate species is complicated by details of the climbing context.

opencc-zeroDec 2012View details →

Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here. Results: Phylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing the strong phylogenetic performance of random subsets of data also shown in this study. Phylogenetic results for both the 19-taxon and 44-taxon datasets corroborate previous hypotheses about the placement of Photobacterium and Aliivibrio within Vibrionaceae and also highlight problems with how Photobacterium is delimited and indicate that it likely should be dissolved into Vibrio to produce a phylogenetic taxonomy. The 19-taxon and 44-taxon trees based on the large chromosome are congruent for the majority of taxa that are present in both datasets. Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies. Conclusions: The phylogenetic analyses presented here represent the most comprehensive genome-level phylogenetic analyses in terms of taxa and data. Based on the availability of genome data for many bacterial species on GenBank, many other bacterial groups would also be amenable to similar genome-scale phylogenetic analyses even when present in multiple contigs. The result that collinear subsets of data are incongruent with the concatenated dataset and with each other while random data subsets show very little incongruence echoes the result of previous work on Shewanellaceae. The 44-taxon phylogenetic analysis presented here thus represents the future of phylogenomic analyses in scope and complexity.

opencc-zeroDec 2019View details →

Data from: Implementation of new standard operating procedures for geriatric trauma patients with multiple injuries: a single level I trauma centre study

Background The demographic changes towards ageing of the populations in developed countries impose a challenge to trauma centres, as geriatric trauma patients require specific diagnostic and therapeutic procedures. This study investigated whether the integration of new standard operating procedures (SOPs) for the resuscitation room (ER) has an impact on the clinical course in geriatric patients. The new SOPs were designed for severely injured adult trauma patients, based on the Advanced Trauma Life Support (ATLS) and imply early whole-body computed tomography (CT), damage control surgery, and the use of goal-directed coagulation management. Methods Single-centre cohort study. We included all patients ≥ 65 years of age with an Injury Severity Score (ISS) ≥ 9 who were admitted to our hospital primarily via ER. A historic cohort was compared to a cohort after the implementation of the new SOPs. Results We enrolled 311 patients who met the inclusion criteria between 2000–2006 (group PreSOP) and 2010–2012 (group SOP). There was a significant reduction in the mortality rate after the implementation of the new SOPs (P = .001). This benefit was seen only for severely injured patients (ISS ≥ 16), but not for moderately injured patients (ISS 9–15). There were no differences with regard to infection rates or rate of palliative care. Conclusions We found an association between implementation of new ER SOPs, and a lower mortality rate in severely injured geriatric trauma patients, whereas moderately injured patients did not obtain the same benefit.

opencc-zeroDec 2016View details →

Data from: Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: an application to bats

Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intra-chromosomal length polymorphism across placental mammals, together with 8 polymorphic microsatellite markers, produced high quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and non-reproductive females) and to estimate population sizes. We showed that visual counts represent well adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and non-pregnant females with a few visiting males whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting non-mothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.

Data from: Neural modularity helps organisms evolve to learn new skills without forgetting old

A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks are organized critically affects their learning dynamics. In this paper, we test whether catastrophic forgetting can be reduced by evolving modular neural networks. Modularity intuitively should reduce learning interference between tasks by separating functionality into physically distinct modules in which learning can be selectively turned on or off. Modularity can further improve learning by having a reinforcement learning module separate from sensory processing modules, allowing learning to happen only in response to a positive or negative reward. In this paper, learning takes place via neuromodulation, which allows agents to selectively change the rate of learning for each neural connection based on environmental stimuli (e.g. to alter learning in specific locations based on the task at hand). To produce modularity, we evolve neural networks with a cost for neural connections. We show that this connection cost technique causes modularity, confirming a previous result, and that such sparsely connected, modular networks have higher overall performance because they learn new skills faster while retaining old skills more and because they have a separate reinforcement learning module. Our results suggest (1) that encouraging modularity in neural networks may help us overcome the long-standing barrier of networks that cannot learn new skills without forgetting old ones, and (2) that one benefit of the modularity ubiquitous in the brains of natural animals might be to alleviate the problem of catastrophic forgetting.

opencc-zeroDec 2016View details →

Data from: Taking movement data to new depths: Inferring prey availability and patch profitability from seabird foraging behavior

Detailed information acquired using tracking technology has the potential to provide accurate pictures of the types of movements and behaviors performed by animals. To date, such data have not been widely exploited to provide inferred information about the foraging habitat. We collected data using multiple sensors (GPS, time depth recorders, and accelerometers) from two species of diving seabirds, razorbills (Alca torda, N = 5, from Fair Isle, UK) and common guillemots (Uria aalge, N = 2 from Fair Isle and N = 2 from Colonsay, UK). We used a clustering algorithm to identify pursuit and catching events and the time spent pursuing and catching underwater, which we then used as indicators for inferring prey encounters throughout the water column and responses to changes in prey availability of the areas visited at two levels: individual dives and groups of dives. For each individual dive (N = 661 for guillemots, 6214 for razorbills), we modeled the number of pursuit and catching events, in relation to dive depth, duration, and type of dive performed (benthic vs. pelagic). For groups of dives (N = 58 for guillemots, 156 for razorbills), we modeled the total time spent pursuing and catching in relation to time spent underwater. Razorbills performed only pelagic dives, most likely exploiting prey available at shallow depths as indicated by the vertical distribution of pursuit and catching events. In contrast, guillemots were more flexible in their behavior, switching between benthic and pelagic dives. Capture attempt rates indicated that they were exploiting deep prey aggregations. The study highlights how novel analysis of movement data can give new insights into how animals exploit food patches, offering a unique opportunity to comprehend the behavioral ecology behind different movement patterns and understand how animals might respond to changes in prey distributions.

Data from: Preschool children's vision screening in New Zealand: a retrospective evaluation of referral accuracy

Objectives: To assess the accuracy of preschool vision screening in a large, ethnically diverse, urban population in South Auckland, New Zealand. Design: Retrospective longitudinal study. Methods: B4 School Check vision screening records (n=5572) were compared with hospital eye department data for children referred from screening due to impaired acuity in one or both eyes who attended a referral appointment (n=556). False positive screens were identified by comparing screening data from the eyes that failed screening with hospital data. Estimation of false negative screening rates relied on data from eyes that passed screening. Data were analysed using logistic regression modelling accounting for the high correlation between results for the two eyes of each child. Primary outcome measure: Positive predictive value of the preschool vision screening programme. Results: Screening produced high numbers of false positive referrals, resulting in poor positive predictive value (PPV=31%, 95% CI 26% to 38%). High estimated negative predictive value (NPV=92%, 95% CI 88% to 95%) suggested most children with a vision disorder were identified at screening. Relaxing the referral criteria for acuity from worse than 6/9 to worse than 6/12 improved PPV without adversely affecting NPV. Conclusions: The B4 School Check generated numerous false positive referrals and consequently had a low PPV. There is scope for reducing costs by altering the visual acuity criterion for referral.

Data from: Neotropical wrens learn new duet rules as adults

Although song development in songbirds has been much studied as an analogue of language development in humans, the development of vocal interaction rules has been relatively neglected in both groups. Duetting avian species provide an ideal model to address the acquisition of interaction rules as duet structure involves time and pattern-specific relationships among the vocalizations from different individuals. In this study, we address the development of the most striking properties of duets: the specific answering rules that individuals use to link their own phrase types to those of their partners (duet codes) and precise temporal coordination. By performing two removal experiments in canebrake wrens (Cantorchilus zeledoni), we show that individuals use a fixed phrase repertoire to create new phrase pairings when they acquire a new partner. Furthermore, immediately after pairing, individuals perform duets with poor coordination and poor duet code adherence, but both aspects improve with time. These results indicate that individuals need a learning period to be able to perform well-coordinated duets that follow a consistent duet code. We conclude that both duet coordination and duet code adherence are honest indicators of pair-bond duration.

Data from: A new plant virus discovered by immunocapture of double stranded RNA; assessment of a novel approach for viral metagenomics studies

Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase–polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31–74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.

Data from: A new framework for investigating biotic homogenization and exploring future trajectories: oceanic island plant and bird assemblages as a case study

Studies of biotic homogenization have focused primarily on characterizing changes that have occurred between some past baseline and the present day. In order to understand how homogenization may change in the future, it is important to contextualize the processes driving these changes. Here, we examine empirical patterns of change in taxonomic similarity among oceanic island plant and bird assemblages. We use these empirical cases to unpack dynamic properties of biotic homogenization, thereby elucidating two important factors that have received little attention: 1) initial similarity and 2) the influence of six classes of introduction and extinction events. We use Jaccard's Index to explore the interplay among these factors in determining the changes in similarity that have occurred between human settlement and the present. Specifically, we develop general formulas for changes in similarity resulting from each of the six types of introductions and extinctions, so that the effect of each event type is formulated in terms of initial similarity and species richness. We then apply these insights to project how similarity levels would change in the future if the present patterns of introductions and extinctions continue. We show that the six event types, along with initial similarity, can show dramatically different behavior in different systems, leading to widely variable influences on similarity. Plant and bird biotas have homogenized only slightly to date, but their trajectories of change are highly divergent. Although existing patterns of colonization and extinction might not continue unchanged, if they were to do so then plant assemblages would show little additional change, whereas bird assemblages would become much more strongly homogenized. Our results suggest that moderate changes in similarity observed to date mask the potential for more dramatic changes in the future, and that the interaction among initial similarity and differential introduction and extinction regimes drives these dynamics.

Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.

opencc-zeroJul 2019View details →

Data from: Evolutionary drivers of group foraging: a new framework for investigating variance in food intake and reproduction

A proposed fundamental driver of group living is more reliable, predictable foraging and reproduction, i.e. reduced variance in food intake and reproductive output. However, existing theories on variance reduction in group foraging are simplistic, refer to variance at the level of individuals and groups without linking the two, and do not spell out crucial underlying assumptions. We provide a new, widely applicable framework for identifying when variance reduction conveys fitness benefits of group foraging in a wide range of organisms. We discuss critical limitations of established theories, the Central Limit Theorem and Risk-Sensitive Foraging Theory applied to group foraging, and incorporate them into our framework while addressing the confusion over the levels of variance and identifying previously unaddressed assumptions. Through a field study on colonial spiders, Cyrtophora citricola, we demonstrate the importance of evaluating the level of food sharing as a critical first step, previously overlooked in the literature. We conclude that variance reduction provides selective advantages only under narrow conditions and does not provide a universal benefit to group foraging as previously proposed. Our framework provides an important tool for identifying evolutionary drivers of group foraging and understanding the role of fitness variance in the evolution of group living.

Data from: Dietary habits of polar bears in Foxe Basin, Canada: possible evidence of a trophic regime shift mediated by a new top predator

Polar bear (Ursus maritimus) subpopulations in several areas with seasonal sea ice regimes have shown declines in body condition, reproductive rates, or abundance as a result of declining sea ice habitat. In the Foxe Basin region of Nunavut, Canada, the size of the polar bear subpopulation has remained largely stable over the past 20 years, despite concurrent declines in sea ice habitat. We used fatty acid analysis to examine polar bear feeding habits in Foxe Basin and thus potentially identify ecological factors contributing to population stability. Adipose tissue samples were collected from 103 polar bears harvested during 2010–2012. Polar bear diet composition varied spatially within the region with ringed seal (Pusa hispida) comprising the primary prey in northern and southern Foxe Basin, whereas polar bears in Hudson Strait consumed equal proportions of ringed seal and harp seal (Pagophilus groenlandicus). Walrus (Odobenus rosmarus) consumption was highest in northern Foxe Basin, a trend driven by the ability of adult male bears to capture large-bodied prey. Importantly, bowhead whale (Balaena mysticetus) contributed to polar bear diets in all areas and all age and sex classes. Bowhead carcasses resulting from killer whale (Orcinus orca) predation and subsistence harvest potentially provide an important supplementary food source for polar bears during the ice-free period. Our results suggest that the increasing abundance of killer whales and bowhead whales in the region could be indirectly contributing to improved polar bear foraging success despite declining sea ice habitat. However, this indirect interaction between top predators may be temporary if continued sea ice declines eventually severely limit on-ice feeding opportunities for polar bears.

Data from: New insights on equid locomotor evolution from the lumbar region of fossil horses

The specialization of equid limbs for cursoriality is a classic case of adaptive evolution, but the role of the axial skeleton in this famous transition is not well understood. Extant horses are extremely fast and efficient runners, which use a stiff-backed gallop with reduced bending of the lumbar region relative to other mammals. This study tests the hypothesis that stiff-backed running in horses evolved in response to evolutionary increases in body size by examining lumbar joint shape from a broad sample of fossil equids in a phylogenetic context. Lumbar joint shape scaling suggests that stability of the lumbar region does correlate with size through equid evolution. However, scaling effects were dampened in the posterior lumbar region, near the sacrum, which suggests strong selection for sagittal mobility in association with locomotor-respiratory coupling near the lumbosacral joint. I hypothesize that small-bodied fossil horses may have used a speed-dependent running gait, switching between stiff-backed and flex-backed galloping as speed increased.