cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9c6k203
title: Data from: The effects of stress and glucocorticoids on vocalizations: a test in North American red squirrels

description: Acoustic signaling is an important means by which animals communicate both
 stable and labile characteristics. Although it is widely appreciated that
 vocalizations can convey information on labile state, such as fear and
 aggression, fewer studies have experimentally examined the acoustic
 expression of stress state. The transmission of such public information
 about physiological state could have broad implications, potentially
 influencing the behavior and life history traits of neighbors. North
 American red squirrels (Tamiasciurus hudsonicus) produce vocalizations
 known as rattles that advertise territorial ownership. We examined the
 influence of changes in physiological stress state on rattle acoustic
 structure through the application of a stressor (trapping and handling the
 squirrels) and by provisioning squirrels with exogenous glucocorticoids
 (GCs). We characterized the acoustic structure of rattles emitted by these
 squirrels by measuring rattle duration, mean frequency, and entropy. We
 found evidence that rattles do indeed exhibit a “stress signature.” When
 squirrels were trapped and handled, they produced rattles that were longer
 in duration with a higher frequency and increased entropy. However,
 squirrels that were administered exogenous GCs had similar rattle
 duration, frequency, and entropy as squirrels that were fed control
 treatments and unfed squirrels. Our results indicate that short-term
 stress does affect the acoustic structure of vocalizations, but elevated
 circulating GC levels do not mediate such changes.
description: Capture Stress
 ExperimentThis is the rattle
 acoustic data used in the experiment examining the effects of
 capture-induced stress on rattle acoustic structureGC Rattle
 ExperimentThis is the rattle
 acoustic data used for the experiment assessing the influence of exogenous
 GCs on rattle acoustic structure
DOI: 10.5061/dryad.g860c9s
title: Data from: Female reproduction bears no survival cost in captivity for grey mouse lemurs

description: The survival cost of reproduction has been revealed in many free-ranging
 vertebrates. However, recent studies on captive populations failed to
 detect this cost. Theoretically, this lack of survival/reproduction
 trade-off is expected when resources are not limiting, but these studies
 may have failed to detect the cost, as they may not have fully accounted
 for potential confounding effects, in particular inter-individual
 heterogeneity. Here we investigated the effects of current and past
 reproductive effort on later survival in captive females of a small
 primate, the grey mouse lemur. Survival analyses showed no cost of
 reproduction in females; and the pattern was even in the opposite
 direction: the higher the reproductive effort, the higher the chances of
 survival until the next reproductive event. These conclusions hold even
 while accounting for inter-individual heterogeneity. In agreement with
 aforementioned studies on captive vertebrates, these results remind us
 that reproduction is expected to be traded against body maintenance and
 the survival prospect only when resources are so limiting that they induce
 an allocation trade-off. Thus, the cost of reproduction has a major
 extrinsic component driven by environmental conditions.
description: Data_Microcebus_murinus_CoRData_Microcebus_murinus_CoR.csv contains individuals’ characteristics and reproductive history, and the dates each individual enters and exits each reproductive season, from first reproductive success to death or censoring time, collected on captive female grey mouse lemurs.
DOI: 10.5061/dryad.p353tk1
title: Data from: Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

description: The amount of dispersal that occurs among populations can be limited by
 landscape heterogeneity, which is often due to both natural processes and
 anthropogenic activity leading to habitat loss or fragmentation.
 Understanding how populations are structured and mapping existing
 dispersal corridors among populations is imperative to both determining
 contemporary forces mediating population connectivity, and informing
 proper management of species with fragmented populations. Furthermore, the
 contemporary processes mediating gene flow across heterogeneous landscapes
 on a large scale are understudied, particularly with respect to widespread
 species. This study focuses on a widespread game bird, the Ruffed Grouse
 (Bonasa umbellus), for which we analyzed samples from the western extent
 of the range. Using three types of genetic markers, we uncovered multiple
 factors acting in concert that are responsible for mediating contemporary
 population connectivity in this species. Multiple genetically distinct
 groups were detected; microsatellite markers revealed six groups, and a
 mitochondrial marker revealed four. Many populations of Ruffed Grouse are
 genetically isolated, likely by macrogeographic barriers. Furthermore, the
 addition of landscape genetic methods not only corroborated genetic
 structure results, but also uncovered compelling evidence that dispersal
 resistance created by areas of unsuitable habitat is the most important
 factor mediating population connectivity among the sampled populations.
 This research has important implications for both our study species and
 other inhabitants of the early successional forest habitat preferred by
 Ruffed Grouse. Moreover, it adds to a growing body of evidence that
 isolation by resistance is more prevalent in shaping population structure
 of widespread species than previously thought.
description: Msat_Genotype
 data_DRYAD_Jensen_etal_2019Microsatellite genotypes
 of Ruffed Grouse used in Jensen et al. 2019. Samples from Alberta were
 collected in the field from live birds as well as birds harvested by
 hunters. Samples from other areas (outside Alberta) were provided by the
 following museum collections: University of Alaska Museum, Burke Museum,
 and Field Museum of Natural History. The ReadMe file attached has
 information for both data files.AldolaseB_SNP_genotypes_DRYAD_Jensen_etal_2019Aldolase B SNP data from Ruffed Grouse used in Jensen et al. 2019. Samples from Alberta were collected in the field from live birds as well as birds harvested by hunters. Samples from other areas (outside Alberta) were provided by the following museum collections: University of Alaska Museum, Burke Museum, and Field Museum of Natural History. The ReadMe file attached has information for both data files.
DOI: 10.5061/dryad.77r7b60
title: Data from: Red panda fine-scale habitat selection along a Central Himalayan longitudinal gradient

description: Red panda Ailurus fulgens, an endangered habitat specialist, inhabits a
 narrow distribution range in bamboo abundance forests along mountain
 slopes in the Himalaya and Hengduan Mountains. However, their habitat use
 may be different in places with different longitudinal environmental
 gradients, climatic regimes, and microclimate. This study aimed to
 determine the habitat variables affecting red panda distribution across
 different longitudinal gradients through a multivariate analysis. We
 studied habitat selection patterns along the longitudinal gradient in
 Nepal's Himalaya which is grouped into the eastern, central, and
 western complexes. We collected data on red panda presence and habitat
 variables (e.g., tree richness, canopy cover, bamboo abundance, water
 availability, tree diameter, tree height) by surveys along transects
 throughout the species’ potential range. We used a multimodal inference
 approach with a generalized linear model to test the relative importance
 of environmental variables. Although the study showed that bamboo
 abundance had a major influence, habitat selection was different across
 longitudinal zones. Both canopy cover and species richness were
 unimportant in eastern Nepal, but their influence increased progressively
 toward the west. Conversely, tree height showed a decreasing influence on
 habitat selection from Eastern to Western Nepal. Red panda's habitat
 selection revealed in this study corresponds to the uneven distribution of
 vegetation assemblages and the dry climatic gradient along the
 eastern‐western Himalayas which could be related to a need to conserve
 energy and thermoregulate. This study has further highlighted the need of
 importance of bamboo conservation and site‐specific conservation planning
 to ensure long‐term red panda conservation.
description: RedPandaSurveyDataThis data represents the aggregated environmental variables, eg., tree height, tree DBH, canopy cover, bamboo abundance and tree species richness of red panda presence locations.
DOI: 10.5061/dryad.c9q4gt6
title: Data from: How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna

description: Due to the lack of recombination, asexual organisms are predicted to
 accumulate mutations and show high levels of within-individual allelic
 divergence (heterozygosity) however, empirical evidence for this
 prediction is largely missing. Instead, evidence of genome homogenization
 during asexual reproduction is accumulating. Ameiotic crossover
 recombination is a mechanism that could lead to long genomic stretches of
 loss of heterozygosity (LOH) and unmasking of mutations that have little
 or no effect in heterozygous state. Therefore, LOH might be an important
 force for inducing variation among asexual offspring and may contribute to
 the limited longevity of asexual lineages. To investigate the genetic
 consequences of asexuality, here we used high-throughput sequencing of
 Daphnia magna for assessing the rate of LOH over a single generation of
 asexual reproduction. Comparing parthenogenetic daughters with their
 mothers at several thousand genetic markers generated by Restriction site
 Associated DNA (RAD) sequencing resulted in high LOH rate estimation that
 largely overlapped with our estimates for the error rate. To distinguish
 these two, we Sanger re-sequenced the top 18 candidate RAD-loci for LOH,
 and all of them proved to be false positives. Hence, even though we cannot
 exclude the possibility that short stretches of LOH occur in genomic
 regions not covered by our markers, we conclude that LOH does not occur
 frequently during asexual reproduction in D. magna and ameiotic crossovers
 are very rare or absent. This finding suggests that clonal lineages of D.
 magna will remain genetically homogeneous at least over time periods
 typically relevant for experimental work.
description: Consensus
 sequencesConsensus sequences with
 assigned genotype for each individual. 48 text files in total - for each
 of the four lines, 10 daughter individual files (marked with
 "d") and files for two mother samples (marked with
 "m"). _consensus.txt file structure: contig 3'position
 coverage(sum) haplotype(X-OR-Y)
 diploid_homozygote(N)-OR-diploid_heterozygote(Y)-OR-haploid_low_coverage(L)-OR-hemizygote(H) consensus_sequenceMarkers_offspring_gntpsFour files - table of marker SNPs for each line and their genotype in each daughter. "_markers_offspring_gtps.txt" file structure: contig locus(3'position) base(SNP) mother.gtp d1 d2 d3 d4 d5 d6 d7 d8 d9 d10 "--"(same_as_mother_genotype) OR "LL"(Low_coverage) OR "NN"(missing genotype) OR different baseSanger_fasta_seqsFasta sequences of re-sequenced RAD-markers (Sanger sequencing). First line ("&gt;") denotes the sequenced individual and the primer used. "F" stands for forward and "R" for reverse primerLOH_analysis_pipelinePipeline summary including the code for all steps
DOI: 10.5061/dryad.vj2dj82
title: Data from: Pooled analysis suggests benefit of catheter-based hematoma removal for intracerebral hemorrhage

description: Objective: To develop models of outcome for intracerebral hemorrhage (ICH)
 to identify promising and futile interventions based on their early phase
 results without need for correction for baseline imbalances. Methods: We
 developed a pooled outcome model from the control arms of randomized
 control trials and tested different interventions against the model at
 comparable baseline conditions. Eligible clinical trials and large case
 series were identified from multiple library databases. Models based on
 baseline factors reported in the control arms were tested for the ability
 to predict functional outcome (modified Rankin Scale score) and mortality.
 Interventions were grouped into blood pressure control,
 fibrinolytic-assisted hematoma evacuation, hemostatic medications, and
 neuroprotective agents. Statistical intervals around the model were
 generated at the p = 0.1 level to screen how each trial’s outcome compared
 to expected outcome. Results: Fourteen control arms with 3,386 patients
 were used to develop 7 alternate models for functional outcome. The model
 incorporating baseline NIH Stroke Scale, age, and hematoma volume yielded
 the best fit (adjusted R2 = 0.89). All early phase treatments that
 eventually resulted in negative late phase trials were identified as
 negative by this method. Early phase fibrinolytic-assisted hematoma
 evacuation studies showed the most promise trending toward improved
 functional outcome with no suggestion of an increase in mortality,
 supporting its further study. Conclusions: We successfully developed an
 outcome model for ICH that identified interventions destined to be
 negative while identifying a promising one. Such an approach may assist in
 prioritizing resources prior to multicenter trial.
description: Supplement Mandava
 Santosh Kent_Neurology_align_with_proof
DOI: 10.6084/m9.figshare.31158271
title: <b>Knowledge and attitudes about HPV infection and prevention methods among medical students in Yemen: a cross-sectional study</b>

description: Data to the study about <b>Knowledge and attitudes about HPV infection and prevention methods among medical students in Yemen: a cross-sectional study</b>
DOI: 10.6084/m9.figshare.31158271.v1
title: <b>Knowledge and attitudes about HPV infection and prevention methods among medical students in Yemen: a cross-sectional study</b>

description: Data to the study about <b>Knowledge and attitudes about HPV infection and prevention methods among medical students in Yemen: a cross-sectional study</b>
DOI: 10.5061/dryad.d78b42h
title: Data from: On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Background: Congruent patterns in the distribution of biodiversity between
 regions or habitats suggest that key factors such as climatic and
 topographic variation may predictably shape evolutionary processes. In a
 number of tropical and arid biomes, genetic analyses are revealing deeper
 and more localised lineage diversity in rocky ranges than surrounding
 habitats. Two potential drivers of localised endemism in rocky areas are
 refugial persistence through climatic change, or ecological
 diversification and specialisation. Here we examine how patterns of
 lineage and phenotypic diversity differ across two broad habitat types
 (rocky ranges and open woodlands) in a small radiation of gecko lizards in
 the genus Gehyra (the australis group) from the Australian Monsoonal
 Tropics biome. Results: Using a suite of approaches for delineating
 evolutionarily independent lineages, we find between 26 and 41 putative
 evolutionary units in the australis group (versus eight species currently
 recognised). Rocky ranges are home to a greater number of lineages that
 are also relatively more restricted in distribution, while lineages in
 open woodland habitats are fewer, more widely distributed, and, in one
 case, show evidence of range expansion. We infer at least two shifts out
 of rocky ranges and into surrounding woodlands. Phenotypic divergence
 between rocky ranges specialist and more generalist taxa is detected, but
 no convergent evolutionary regimes linked to ecology are inferred.
 Conclusions: In climatically unstable biomes such as savannahs, rocky
 ranges have functioned as zones of persistence, generators of diversity
 and a source of colonists for surrounding areas. Phenotypic divergence can
 also be linked to the use of differing habitat types, however, the extent
 to which ecological specialisation is a primary driver or secondary
 outcome of localised diversification remains uncertain.
description: Gehyra australis group
 ND2 alignmentMitochondrial ND2
 alignment for the Gehyra australis complex with outgroup, in fasta
 format_Gehyra_australis_group_ND2_alignment.fastaExon-capture alignments for IQ-tree analysisExon-capture 1634 gene super-matrix alignment for IQ-tree analysis of the Gehyra australis complexec_alignments_1634.tar.gzExon-capture alignments for ASTRAL-II analysisExon-capture alignments, reduced subset of 569 loci, used for ASTRAL-II analysis of the Gehyra australis complexec_alignments_569.tar.gz50 loci alignments for StarBEAST2 analysis50 loci alignments for StarBEAST2 analysis of the Gehyra australis complexstarbeast2_australis_alignments_50.zipMorphology raw measurement dataMorphology raw measurement data for the Gehyra australis complexmorphology_australis_complex_data.xlsx
DOI: 10.5061/dryad.mb2d353
title: Data from: How many cubs can a mum nurse? Maternal age and size influence litter size in polar bears

description: Life history theory predicts that females' age and size affect the
 level of maternal investment in current reproduction, balanced against
 future reproductive effort, maintenance and survival. Using long-term (30
 years) individual data on 193 female polar bears (Ursus maritimus), we
 assessed age- and size-specific variation on litter size. Litter size
 varied with maternal age, younger females had higher chances of losing a
 cub during their first months of life. Results suggest an improvement of
 reproductive abilities early in life due to experience with subsequent
 reproductive senescence. Litter size increased with maternal size,
 indicating that size may reflect individual quality. We also found an
 optimum in the probability of having twins, suggesting stabilizing
 selection on female body size. Heterogeneity was observed among the
 largest females, suggesting that large size comes at a cost.
description: polarbear
DOI: 10.5061/dryad.0md816p
title: Data from: Social and ecological factors alter stress physiology of Virunga mountain gorillas (Gorilla beringei beringei)

description: Living in a rapidly changing environment can alter stress physiology at
 the population level, with negative impacts on health, reproductive rates,
 and mortality that may ultimately result in species decline. Small,
 isolated animal populations where genetic diversity is low are at
 particular risks, such as endangered Virunga mountain gorillas (Gorilla
 beringei beringei). Along with climate change‐associated environmental
 shifts that are affecting the entire population, subpopulations of the
 Virunga gorillas have recently experienced extreme changes in their social
 environment. As the growing population moves closer to the forest's
 carrying capacity, the gorillas are coping with rising population density,
 increased frequencies of interactions between social units, and changing
 habitat use (e.g., more overlapping home ranges and routine ranging at
 higher elevations). Using noninvasive monitoring of fecal glucocorticoid
 metabolites (FGM) on 115 habituated Virunga gorillas, we investigated how
 social and ecological variation are related to baseline FGM levels, to
 better understand the adaptive capacity of mountain gorillas and monitor
 potential physiological indicators of population decline risks.
 Generalized linear mixed models revealed elevated mean monthly baseline
 FGM levels in months with higher rainfall and higher mean maximum and
 minimum temperature, suggesting that Virunga gorillas might be sensitive
 to predicted warming and rainfall trends involving longer, warmer dry
 seasons and more concentrated and extreme rainfall occurrences. Exclusive
 use of smaller home range areas was linked to elevated baseline FGM
 levels, which may reflect reduced feeding efficiency and increased travel
 efforts to actively avoid neighboring groups. The potential for additive
 effects of stress‐inducing factors could have short‐ and long‐term impacts
 on the reproduction, health, and ultimately survival of the Virunga
 gorilla population. The ongoing effects of environmental changes and
 population dynamics must be closely monitored and used to develop
 effective long‐term conservation strategies that can help address these
 risk factors.
description: Envir_GrpCharact_Stress_upload_DryadThe file contains the response variable (monthly mean fecal glucocorticoid metabolite levels N=1,094), fixed effects (ecological and social factors), and random effects (groups and gorillas ID) entered in the GLMM as described in the manuscript.
DOI: 10.5061/dryad.3sg4g82
title: Data from: Do scavengers prevent or promote disease transmission? The effect of invertebrate scavenging on Ranavirus transmission

description: 1. Host-parasite interactions are shaped by the broader web of community
 interactions, from interspecific competition to predator-prey dynamics.
 Heterospecific scavengers might also affect parasite transmission from
 infectious carcasses, which can be an important source of infections for
 some wildlife diseases. 2. A robust scavenger community can quickly remove
 carcasses and tissue and thus prevent secondary transmission by necrophagy
 or contact with infectious carcasses. Alternatively, by spreading
 infectious particles and tissues throughout the environment, scavengers
 may increase rates of casual contact with pathogens and thus overall
 transmission. However, there has been little empirical consideration of
 the contrasting roles that scavengers might play in infectious disease
 dynamics. 3. We carried out a series of studies to determine the
 efficiency with which scavenging invertebrates remove carcasses of
 Long-toed Salamander (Ambystoma macrodactylum) larvae and their role in
 the transmission of Frog Virus 3 (Genus: Ranavirus, Family: Iridoviridae)
 from carcasses. We then estimated the functional response of one efficient
 invertebrate scavenger (Family: Dytiscidae) to increasing carcass
 densities in field conditions in order to determine the capacity of
 scavenging invertebrates to consume large amounts of carcass tissue, as
 may be present at high prevalence sites. 4. We found that removal of
 infectious carcasses by scavengers strongly reduced transmission to naïve
 larvae. Scavengers were as effective at reducing transmission from a
 carcass as a physical barrier preventing contact with the carcass. There
 was little evidence that scavenging released sufficient infectious tissues
 into the water column to rival direct contact as a route of infection.
 Moreover, while scavenging rates saturated at increasing carcass
 densities, consistent with a type II functional response, there were
 sufficient densities of dytiscid larvae, not to mention other scavenging
 invertebrates, in a surveyed pond to theoretically prevent transmission
 from carcasses. 5. Our results suggest that at least in systems in which
 conspecific necrophagy is common, the scavenger community can play an
 important role in reducing transmission.
description: Ranavirus Transmission
 DatasetRanavirusTransmissionDataset.csvPond Survey DatasetPondSurveyDataset.csvScavenger Effectiveness Trials DatasetScavengerEffectivenessTrialsDataset.csvFunctional Response DatasetFunctionalResponseDataset.csv