cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qr20n
title: Data from: Gene expression, chromosome heterogeneity and the fast-X effect in mammals

description: The higher rate of non-synonymous over synonymous substitutions (dN/dS) of
 the X chromosome compared with autosomes is often interpreted as a
 consequence of X hemizygosity. However, other factors, such as gene
 expression, are also known to vary between X and autosomes. Analysing 4800
 orthologues in six mammals, we found that gene expression levels,
 associated with GC content, fully account for the variation in dN/dS
 between X and autosomes with no detectable effect of hemizygosity. We also
 report an extensive variance in dN/dS and gene expression between
 autosomes.
description: Table_S1 -
 DatasetsDatasets used in the
 main statistical analyses of the study. Details of column headings : gene
 : Ensembl accession number (human); Species; labs : Species+Chromosome;
 chrMark : X or Autosomes; chr : Chromosome number; dN : Number of
 nonsynonymous substitutions; dS: Number of synonymous substitutions , dNdS
 : ratio of dN/dS; RPKM : Expression level in Reads Per Kilobase per
 Million sequenced Reads; Tau : Expression specificity, GC3 : GC content of
 the third codon positionTable_S1.csvAlignmentsAlignments were obtained from ORTHOMAM v6 (http://www.orthomam.univ-montp2.fr/) and then cleaned using Gblocks (see materials and methods for details). Alignment names correspond to Ensembl accession number and match the datasets (Table_S1).omm_DNA_fasta.36tax_CDS.gblocks.zip
DOI: 10.5061/dryad.ct5q3
title: Data from: Genetic differentiation but no reduction in genetic diversity at the northern range edge of two species with different dispersal modes

description: Theory predicts that genetic variation should be reduced at range margins,
 but empirical support is equivocal. Here, we used genotyping-by-sequencing
 technology to investigate genetic variation in central and marginal
 populations of two species in the marine gastropod genus Crepidula. These
 two species have different development and dispersal types, and might
 therefore show different spatial patterns of genetic variation. Both
 allelic richness and the proportion of private alleles were highest in the
 most central populations of both species, and lower at the margin. The
 species with low dispersal, C. convexa, showed high degrees of structure
 throughout the range that conform to the pattern found in previous studies
 using other molecular markers. The northernmost populations of the
 high-dispersing species, C. fornicata, are distinct from more central
 populations, though this species has been previously observed to have
 little genetic structure over much of its range. Although genetic
 diversity was significantly lower at the range margin, the absolute
 reduction in diversity observed with these genome-wide markers was slight,
 and it is not yet known if there are functional consequences for these
 marginal populations.
description: mergedSNPsSampling coordinates and site codesThis file lists all sampling sites, with their associated GPS coordinates. It gives the letter and number abbreviations for the main text and all analysis files.bayescan_input_fornicataInput file for Bayescan for Crepidula fornicata.bayescan_input_convexaInput file for Bayescan with Crepidula convexa data.bayescan_output_fornicataOutput from Bayescan analysis from Crepidula fornicata.bayescan_output_convexaOutput from Bayescan analysis for Crepidula convexapairwise_distance_matricesMatrices of pairwise genetic (Fst) and geographic (in kilometers) distances for populations of Crepidula fornicata and C. convexa.input_hierfstat_fornicataThis file is the input file for Hierfstat for Crepidula fornicata. It was used for both Hierfstat and Adegenet analyses.input_hierfstat_convexaThis file was used as input for the Hierfstat package in R, and downstream analyses in Adegenet, for Crepidula convexa.filtered_SNPs_convexaFiltered SNP dataset for Crepidula convexa. Filtering was done as described in the main text. SNPs are reported using the IUPAC codes.filtered_SNPs_fornicataFiltered SNP dataset for Crepidula fornicata. Filtering was done as described in the main manuscript text. SNPs are reported using IUPAC codes.
DOI: 10.5061/dryad.n821p
title: Data from: Cyclic bouts of extreme bradycardia counteract the highmetabolism of frugivorous bats

description: Active flight requires the ability to efficiently fuel bursts of costly
 locomotion while maximizing energy conservation during non-flying times.
 We took a multi-faceted approach to estimate how fruit-eating bats
 (Uroderma bilobatum) manage a high-energy lifestyle fueled primarily by
 fig juice. Miniaturized heart rate telemetry shows that they use a novel,
 cyclic, bradycardic state that reduces daily energetic expenditure by 10%
 and counteracts heart rates as high as 900 bpm during flight. Uroderma
 bilobatum support flight with some of the fastest metabolic incorporation
 rates and dynamic circulating cortisol in vertebrates. These bats will
 exchange fat reserves within 24 hr, meaning that they must survive on the
 food of the day and are at daily risk of starvation. Energetic flexibly in
 U. bilobatum highlights the fundamental role of ecological pressures on
 integrative energetic networks and the still poorly understood energetic
 strategies of animals in the tropics.
description: Data Uroderma heart
 ratesHeart rates and
 calculated energetic expenditure of free-ranging tent-making bats
 (Uroderma bilobatum) in Gamboa, Panama.Data Uroderma
 respirometryEnergy consumption,
 heart rate, body temperature, and ambient temperature of tent-making bats
 (Uroderma bilobatum) measured in open-flow
 respirometry.Data Uroderma
 breathCarbon stable isotope
 enrichment of tent-making bats (Uroderma bilobatum) that were fed figs or
 agave nectar to measure metabolic incorporation rates and fat
 turnover.Data Uroderma
 cortisolCortisol dynamics of
 female and male tent-making bats (Uroderma bilobatum) sampled at baseline
 and after 1 hour of restraint.
DOI: 10.5061/dryad.jh5h4
title: Data from: Trunk orientation causes asymmetries in leg function in small bird terrestrial locomotion

description: In contrast to the upright trunk in humans, trunk orientation in most
 birds is almost horizontal (pronograde). It is conceivable that the
 orientation of the heavy trunk strongly influences the dynamics of bipedal
 terrestrial locomotion. Here we analyze for the first time the effects of
 a pronograde trunk orientation on leg function and stability during
 bipedal locomotion. For this, we first inferred the leg function and trunk
 control strategy applied by a generalized small bird during terrestrial
 locomotion by analyzing synchronously recorded kinematic (3D x-ray
 videography) and kinetic (3D force measurement) quail locomotion data.
 Then, by simulating quail gaits using a simplistic bio-inspired numerical
 model which made use of parameters obtained in in vivo experiments with
 real quail, we show that the observed asymmetric leg function (reflected
 in left-skewed ground reaction force and touchdown lift-off limb
 asymmetry) is necessary for pronograde steady-state locomotion. In
 addition, steady-state locomotion becomes stable for specific
 morphological parameters. For quail-like parameters, the most common
 stable solution is grounded running, a gait preferred by the quail and
 most of the other small birds. We hypothesize that stability of bipedal
 locomotion is a functional demand that, depending on trunk orientation,
 constrains basic hind limb morphology and function.
description: kinematic_and_kinetic_data.mat files
DOI: 10.5061/dryad.n3c2f
title: Data from: Disentangling woodland caribou movements in response to clearcuts and roads across temporal scales

description: Although prey species typically respond to the most limiting factors at
 coarse spatiotemporal scales while addressing biological requirements at
 finer scales, such behaviour may become challenging for species inhabiting
 human altered landscapes. We investigated how woodland caribou, a
 threatened species inhabiting North-American boreal forests, modified
 their fine-scale movements when confronted with forest management features
 (i.e. clearcuts and roads). We used GPS telemetry data collected between
 2004 and 2010 on 49 female caribou in a managed area in Québec, Canada.
 Movements were studied using a use – availability design contrasting
 observed steps (i.e. line connecting two consecutive locations) with
 random steps (i.e. proxy of immediate habitat availability). Although
 caribou mostly avoided disturbances, individuals nonetheless modulated
 their fine-scale response to disturbances on a daily and annual basis,
 potentially compromising between risk avoidance in periods of higher
 vulnerability (i.e. calving, early and late winter) during the day and
 foraging activities in periods of higher energy requirements (i.e. spring,
 summer and rut) during dusk/dawn and at night. The local context in which
 females moved was shown to influence their decision to cross clearcut
 edges and roads. Indeed, although females typically avoided crossing
 clearcut edges and roads at low densities, crossing rates were found to
 rapidly increase in greater disturbance densities. In some instance,
 however, females were less likely to cross edges and roads as densities
 increased. Females may then be trapped and forced to use disturbed
 habitats, known to be associated with higher predation risk. We believe
 that further increases in anthropogenic disturbances could exacerbate such
 behavioural responses and ultimately lead to population level
 consequences.
description: Beauchesne Jaeger and
 St-Laurent_PLoS ONE datasetsCharacteristics of
 observed and random steps of female Woodland caribou inhabiting a highly
 disturbed landscape in eastern Canada.Beauchesne et al_datasets PLoS
 ONE.zip
DOI: 10.5061/dryad.81pq863
title: Data from: Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers

description: The Neotropical region represents one of the greatest biodiversity
 hotspots on earth. Despite its unparalleled biodiversity, regional
 comparative phylogeographic studies are still scarce, with most focusing
 on model clades (e.g., birds) and typically examining a handful of loci.
 Here, we apply a genome-wide comparative phylogeographic approach to test
 hypotheses of co-diversification of freshwater fishes in the trans-Andean
 region. Using target capture methods, we examined exon data for over 1,000
 loci combined with complete mitochondrial genomes to study the
 phylogeographic history of five primary fish species (&gt;150
 individuals) collected from eight major river basins in Northwestern South
 America and Lower Central America. To assess their patterns of genetic
 structure, we inferred genealogical concordance taking into account all
 major aspects of phylogeography (within loci, across multiple genes,
 across species, and among biogeographic provinces). Based on
 phylogeographic concordance factors, we tested four a priori biogeographic
 hypotheses, finding support for three of them and uncovering a novel,
 unexpected pattern of co-diversification. The four emerging inter-riverine
 patterns are: (i) Tuira + Atrato, (ii) Ranchería + Catatumbo, (iii)
 Magdalena system, and (iv) Sinú + Atrato. These patterns are interpreted
 as shared responses to the complex uplifting and orogenic processes that
 modified or sundered watersheds, allowing co-diversification and
 speciation over geological time. We also find evidence of cryptic
 speciation in one of the species examined and instances of mitochondrial
 introgression in others. These results help further our knowledge of the
 historical geographic factors shaping the outstanding biodiversity of the
 Neotropics.
description: Dryad
 RepositoryThis is a compressed zip
 file containing all the datasets used in this study, grouped by analysis
 (1.master reference FASTA file, 2. alignments of exon loci and
 mitochondrial DNA, 3. BPP input files by species, and 4. SNPs used in
 SNAPP, STRUCTURE and SVDquartets) and the inferred
 trees.README
DOI: 10.5061/dryad.v22n5
title: Data from: The influence of landscape on gene flow in the eastern massasauga rattlesnake (Sistrurus c. catenatus): insight from computer simulations

description: Understanding how gene flow shapes contemporary population structure
 requires the explicit consideration of landscape composition and
 configuration. New landscape genetic approaches allow us to link such
 heterogeneity to gene flow within and among populations. However, the
 attribution of cause is difficult when landscape features are spatially
 correlated, or when genetic patterns reflect past events. We use spatial
 Bayesian clustering and landscape resistance analysis to identify the
 landscape features that influence gene flow across two regional
 populations of the eastern massasauga rattlesnake, Sistrurus c. catenatus.
 Based on spatially explicit simulations, we inferred how habitat
 distribution modulates gene flow and attempted to disentangle the effects
 of spatially confounded landscape features. We found genetic clustering
 across one regional landscape but not the other, and also local
 differences in the effect of landscape on gene flow. Beyond the effects of
 isolation-by-distance, water bodies appear to underlie genetic
 differentiation among individuals in one regional population. Significant
 effects of roads were additionally detected locally, but these effects are
 possibly confounded with the signal of water bodies. In contrast, we found
 no signal of isolation-by-distance or landscape effects on genetic
 structure in the other regional population. Our simulations imply that
 these local differences have arisen as a result of differences in
 population density or tendencies for juvenile rather than adult dispersal.
 Importantly, our simulations also demonstrate that the ability to detect
 the consequences of contemporary anthropogenic landscape features (e.g.
 roads) on gene flow may be compromised when long-standing natural features
 (e.g. water bodies) co-exist on the landscape.
description: Microsatellite data and
 population designationsgenotypes.csv provides
 genotypes for 12 nuclear microsatellite markers described in the main text
 Abbreviations: Bruce Peninsula, BP; Lyal, Lyal Island; NPS, North of Parry
 Sound; SPS, South of Parry Sound; Georgian Bay Islands (Beausoleil
 Island), GBI; -9 indicates non-amplified product Please contact
 michelle.dileo@gmail.com with any questions about this
 dataset.genotypes.csvCircuitscape Input FilesThis .zip includes two folders of Circuitscape input files: BP for the Bruce Peninsula, and EGB for eastern Georgian Bay. Res_x files are the resistance surfaces used to calculate pairwise resistances in Circuitscape and correspond to the models described in Table 1 of the main text. Please contact michelle.dileo@gmail.com for focal points input files.CDPOP Input FilesThis .zip includes CDPOP 1.0 input files for Simulation Set 1 (implementation of a road onto an otherwise neutral landscape) and Simulation Set 2 (simulations across our empirical landscape south of Parry Sound). The full set of parameters is described in the main text.
DOI: 10.5061/dryad.nq68420
title: Data from: Grizzly bear response to spatio-temporal variability in human recreational activity.

description: 1. Outdoor recreation on trail networks is a growing form of disturbance
 for wildlife. However, few studies have examined behavioural responses by
 large carnivores to motorised and non-motorised recreational activity-- a
 knowledge gap that has implications for the success of human access
 management aimed at improving habitat quality for wildlife. 2. We used an
 integrated step-selection analysis of grizzly bear (Ursus arctos)
 radiotelemetry data and a spatio-temporal model of motorised and
 non-motorised human recreational activity to examine the effect of human
 recreational activity along trails on both habitat selection and movement
 behaviour of individual bears. Grizzly bears were captured and
 radiocollared in the west-central Alberta Rocky Mountains and Foothills,
 and trail cameras were deployed on trails to obtain data on human
 recreational activity. 3. We found that models including data on
 recreational activity outperformed trail-proximity models when
 interactions with movement covariates were included. Responses were highly
 variable among individuals, and across classes; males, females and females
 with cubs. 4. Male and solitary female grizzly bears increased avoidance
 of trails with a high probability of motorised activity, as well as
 displaying increased movement rates in response to motorised recreation.
 Females with cubs did not increase avoidance, however they had the largest
 response with higher movement rates. In contrast, for all classes
 selection for proximity to trail increased when probability of
 non-motorised activity was high, and the effect on movement was dampened
 relative to the motorised response. 5. Synthesis and applications. By
 combining selection and movement into a unified modelling framework, we
 show that bears alter selection and movement behaviour in response to
 trails and recreation, and that such responses are determined by the type
 of recreational activity. Reduced selection and increased movement in
 proximity to motorised trails could affect bears’ ability to exploit
 foraging opportunities in these areas. Future access management actions
 for grizzly bear recovery should consider frequency and type of linear
 feature use by humans rather than solely relying on thresholds relating to
 feature densities.
description: R code and data for
 iSSAIncludes grizzly bear
 covariate data and grizzly bear sex and reproductive status data, along
 with R code for running iSSA and beta coefficient bootstrap
 procedureData_and_Rcode.zip
DOI: 10.5061/dryad.fh592
title: Data from: A phylogenomic approach based on PCR target enrichment and high throughput sequencing: resolving the diversity within the South American species of Bartsia l. (Orobanchaceae)

description: Advances in high-throughput sequencing (HTS) have allowed researchers to
 obtain large amounts of biological sequence information at speeds and
 costs unimaginable only a decade ago. Phylogenetics, and the study of
 evolution in general, is quickly migrating towards using HTS to generate
 larger and more complex molecular datasets. In this paper, we present a
 method that utilizes microfluidic PCR and HTS to generate large amounts of
 sequence data suitable for phylogenetic analyses. The approach uses the
 Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two
 sets of PCR primers to simultaneously amplify 48 target regions across 48
 samples, incorporating sample-specific barcodes and HTS adapters (2,304
 unique amplicons per Access Array). The final product is a pooled set of
 amplicons ready to be sequenced, and thus, there is no need to construct
 separate, costly genomic libraries for each sample. Further, we present a
 bioinformatics pipeline to process the raw HTS reads to either generate
 consensus sequences (with or without ambiguities) for every locus in every
 sample or—more importantly—recover the separate alleles from heterozygous
 target regions in each sample. This is important because it adds allelic
 information that is well suited for coalescent-based phylogenetic analyses
 that are becoming very common in conservation and evolutionary biology. To
 test our approach and bioinformatics pipeline, we sequenced 576 samples
 across 96 target regions belonging to the South American clade of the
 genus Bartsia L. in the plant family Orobanchaceae. After sequencing
 cleanup and alignment, the experiment resulted in ~25,300bp across 486
 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp
 for 363 samples for a set of primers targeting regions in the nuclear
 genome. Finally, we constructed a combined concatenated matrix from all 96
 primer combinations, resulting in a combined aligned length of ~40,500bp
 for 349 samples.
description: Data from Uribe-Convers
 et al - A targeted subgenomic approach for phylogenomics based on
 microfluidic PCR and high throughput sequencing
DOI: 10.5061/dryad.dg237
title: Data from: Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees

description: There is significant and often heritable variation in cognition and its
 underlying neural mechanisms, yet specific genetic contributions to such
 variation are not well characterized. Black-capped chickadees present a
 good model to investigate the genetic basis of cognition because they
 exhibit tremendous climate-related variation in memory, hippocampal
 morphology and neurogenesis rates throughout the North American continent,
 and these cognitive traits appear to have a heritable basis. We examined
 the hippocampal transcriptome profiles of laboratory-reared chickadees
 from the two most divergent populations to test whether differential gene
 expression in the hippocampus is associated with population differences in
 spatial memory, hippocampal morphology and adult hippocampal neurogenesis
 rates. Using high-resolution mRNA sequencing coupled to a de novo
 transcriptome assembly, we generated 23 295 consensus sequences, which
 predicted 16 206 protein sequences with 13 982 showing high similarity to
 known protein sequences or conserved hypothetical proteins in other
 species. Of these, we identified differential expression in nearly 380
 genes, with 47 genes specifically linked to neurogenesis, apoptosis,
 synaptic function, and learning and memory processes. Many of the other
 differentially expressed genes, however, may be associated with other
 functions. Our study presents the first avian hippocampal transcriptome,
 and it is the first study identifying differential gene expression
 associated with natural variation in cognition and the hippocampus. Our
 results provide additional support to the hypothesis that population
 differences in memory, hippocampal morphology and neurogenesis in
 chickadees have likely resulted from natural selection that appears to act
 on memory and its underlying neural mechanisms.
description: assembled transcript
 sequencesFinal contigs from the
 assembly, minimum 100 bp. The names correspond to the specific transcript
 builds, where contig_id is the contig identifier, for example,
 avdl_parai-20111027|1234. Possibly includes UTRs. Sequences contain IUPAC
 ambiguity codes representing ambiguous bases
 (http://www.bioinformatics.org/sms/iupac.html).predicted protein
 sequencesProtein products
 predicted by ESTScan, minimum 30 aa. Sequence identifiers for these
 predicted products correspond to the associated nucleotide sequence in
 file assembled transcript sequences.txt, and are provided suffixes _0, _1,
 etc., to accommodate multiple predictions.