cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3r85690
title: Data from: The population and landscape genetics of the European badger (Meles meles) in Ireland.

description: The population genetic structure of free-ranging species is expected to
 reflect landscape-level effects. Quantifying the role of these factors and
 their relative contribution often has important implications for wildlife
 management. The population genetics of the European badger (Meles meles)
 have received considerable attention, not least because the species acts
 as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain
 and Ireland. Herein, we detail the most comprehensive population and
 landscape genetic study of the badger in Ireland to date – comprised of
 454 Irish badger samples, genotyped at 14 microsatellite loci. Contrasting
 Bayesian and multivariate clustering methods demonstrated continuous
 clinal variation across the island, with potentially distinct
 differentiation observed in Northern Ireland. Landscape genetic analyses
 identified geographic distance and elevation as the primary drivers of
 genetic differentiation, in keeping with badgers exhibiting high levels of
 philopatry. Other factors hypothesized to affect gene flow, including
 earth worm habitat suitability, land cover type and the River Shannon, had
 little to no detectable effect. By providing a more accurate picture of
 badger population structure and the factors effecting it, these data can
 guide current efforts to manage the species in Ireland and to better
 understand its role in bTB.
description: Supplementary Data 1
 (badger genotypes)Genotypes of 454 Irish
 badgers (Meles meles) at 14 microsatellite loci.Supplementary Data
 1.xlsx
DOI: 10.5061/dryad.4429j
title: Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

description: In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island
 (CUIS), Georgia, USA, from which they had previously been extirpated. They
 were monitored intensively for 3 years immediately post-reintroduction,
 but no estimation of the size or genetic diversity of the population had
 been conducted in over 20 years since reintroduction. We returned to CUIS
 in 2012 to estimate abundance and effective population size of the
 present-day population, as well as to quantify genetic diversity and
 inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated
 from scats to establish genetic profiles to identify individuals. We used
 spatially explicit capture–recapture population estimation to estimate
 abundance. From nine unique genetic profiles, we estimate a population
 size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne)
 of 5–8 breeding individuals. This is consistent with predictions of a
 population viability analysis conducted at the time of reintroduction,
 which estimated the population would average 12–13 bobcats after 10 years.
 We identified several pairs of related bobcats (parent-offspring and full
 siblings), but ~75% of the pairwise comparisons were typical of unrelated
 individuals, and only one individual appeared inbred. Despite the small
 population size and other indications that it has likely experienced a
 genetic bottleneck, levels of genetic diversity in the CUIS bobcat
 population remain high compared to other mammalian carnivores. The
 reintroduction of bobcats to CUIS provides an opportunity to study changes
 in genetic diversity in an insular population without risk to this common
 species. Opportunities for natural immigration to the island are limited;
 therefore, continued monitoring and supplemental bobcat reintroductions
 could be used to evaluate the effect of different management strategies to
 maintain genetic diversity and population viability. The successful
 reintroduction and maintenance of a bobcat population on CUIS illustrates
 the suitability of translocation as a management tool for re-establishing
 felid populations.
description: Data and R code to
 estimate abundanceThis zip folder
 contains: (1) file containing the locations of ID'd individuals on
 Cumberland Island; (2) the locations of transects (x-y of center of each
 200-m segment); (3) shapefiles of island boundary (multiple files); (4) R
 code for spatially explicit capture-recapture population estimation (SECR)
 for abundanceBobcat SECR
 analysis.zipCumberland Island
 GenotypesMicrosatellite genotypes
 of all bobcat scats collected on Cumberland Island (1st spreadsheet tab),
 and summary of genotypes of 9 bobcats that could be individually
 identified (2nd spreadsheet tab). Amplification conditions are described
 in primary manuscript (Diefenbach et al.) and in associated supplementary
 information.
DOI: 10.5281/zenodo.18382840
title: Data and analytical codes for: Ishizawa et al. (2026) Competition-induced metabolic switching governs the interaction network in plant microbiome assembly

description: Data and analytical codes for: Ishizawa et al. (2026) Competition-induced metabolic switching governs the interaction network in plant microbiome assembly
DOI: 10.5281/zenodo.18382841
title: Data and analytical codes for: Ishizawa et al. (2026) Competition-induced metabolic switching governs the interaction network in plant microbiome assembly

description: Data and analytical codes for: Ishizawa et al. (2026) Competition-induced metabolic switching governs the interaction network in plant microbiome assembly
DOI: 10.5061/dryad.q2cs3
title: Data from: Poststroke alterations in heart rate variability during orthostatic challenge

description: Older adults following recovery from ischemic stroke have a higher
 incidence of orthostatic hypotension, syncope, and fall risk, which may be
 related to impaired autonomic responses limiting the ability to maintain
 cerebral blood flow. Thus, we investigated cerebrovascular and
 cardiovascular regulation in 23 adults ≥55 years of age, 10 diagnosed with
 ischemic stroke, and 13 age-matched healthy controls when sitting at rest
 and upon standing to compare differences of autonomic variables at ∼7
 months (218 ± 41 days) poststroke.
description: Blood
 Pressure
DOI: 10.5061/dryad.478kp63
title: Data from: The enemy of my enemy is my friend: native pine marten recovery reverses the decline of the red squirrel by suppressing grey squirrel populations

description: Shared enemies may instigate or modify competitive interactions between
 species. The dis-equilibrium caused by non-native species introductions
 has revealed that the outcome of such indirect interactions can often be
 dramatic. However, studies of enemy mediated competition mostly consider
 the impact of a single enemy, despite species being embedded in complex
 networks of interactions. Here we demonstrate that native red and invasive
 grey squirrels in Britain, two terrestrial species linked by resource and
 disease-mediated apparent competition, are also now linked by a second
 enemy-mediated relationship involving a shared native predator recovering
 from historical persecution, the European pine marten. Through combining
 spatial capture recapture techniques to estimate pine marten density, and
 squirrel site occupancy data, we find that the impact of exposure to
 predation is highly asymmetrical, with non-native grey squirrel occupancy
 strongly negatively affected by exposure to pine martens. In contrast,
 exposure to pine marten predation has an indirect positive effect on red
 squirrel populations. Pine marten predation thus reverses the
 well-documented outcome of resource and apparent competition between red
 and grey squirrels.
description: Pine marten encounter
 histories for use in SCR analysis using oSCR package in
 RData
 collected in the field and processed in lab to obtain genotypes. id= pine
 marten id/genotype, occasion = visit (1-5), trapid = detector name, sex =
 f/m, session = region name, site = name of cluster in which detector was
 locatedSheehy_et_al_Data_S9_enc_ESM.csvPine marten trap locations and operational data for use with oSCR packagePine marten detector data relating to location of detectors and whether they were operational. X = British National Grid easting, Y = British National Grid northing, o1-o5 = whether detector was operational for each session, site = name of cluster which detector belongs to, region = LL (Central Scotland), BO (Borders) or HI (Highlands)Sheehy_et_al_Data_S10_traps_ESM.csvRed squirrel detection histories and covariates for occupancy analysis in UNMARKED R packageDetection/non-detection data site and survey specific covariates for red squirrels. 0=name of cluster which detector belongs to, region = CS (Central Scotland), BO (Borders) and HI (Highlands), X = BNG easting, Y= BNG northing, species = red squirrel, visit1-5 = detection (1) /non detection (0), cover = % of 100m buffer which is forested, bl = % of cover which is broadleaved, gs = portion of feeders within 500m used by grey squirrels, tCov1-tCov5 = hair (feeder only used) or both (feeder and camera used)Sheehy_et_al_Data_S11_detections_red_ESM.csvGrey squirrel detection histories and covariates for use in occupancy analysis using UNMARKED R packageSame as red squirrel detection history file except species = grey squirrelSheehy_et_al_Data_S12_detections_grey_ESM.csv
DOI: 10.5061/dryad.5s07m
title: Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

description: Approximate Bayesian computation (ABC) is rapidly gaining popularity in
 population genetics. One example, msBayes, infers the distribution of
 divergence times among pairs of taxa, allowing phylogeographers to test
 hypotheses about historical causes of diversification in co-distributed
 groups of organisms. Using msBayes, we infer the distribution of
 divergence times among 22 pairs of populations of vertebrates distributed
 across the Philippine Archipelago. Our objective was to test whether
 sea-level oscillations during the Pleistocene caused diversification
 across the islands. To guide interpretation of our results, we perform a
 suite of simulation-based power analyses. Our empirical results strongly
 support a recent simultaneous divergence event for all 22 taxon pairs,
 consistent with the prediction of the Pleistocene-driven diversification
 hypothesis. However, our empirical estimates are sensitive to changes in
 prior distributions, and our simulations reveal low power of the method to
 detect random variation in divergence times and bias toward supporting
 clustered divergences. Our results demonstrate that analyses exploring
 power and prior sensitivity should accompany ABC model-selection
 inferences. The problems we identify are potentially mitigable with
 uniform priors over divergence models (rather than classes of models) and
 more flexible prior distributions on demographic and divergence-time
 parameters.
description: oaks_etal_2012_evolution.tar.gz
DOI: 10.5061/dryad.9p311
title: Data from: Revisiting the cost of carnivory in mammals

description: Predator-prey relationships play a key role in the evolution and ecology
 of carnivores. An understanding of predator-prey relationships and how
 this differs across species and environments provides information on how
 carnivorous strategies have evolved and how they may change in response to
 environmental change. We aim to determine how mammals overcame the
 challenges of living within the marine environment; specifically, how this
 altered predator-prey body mass relationships relative to terrestrial
 mammals. Using predator and prey mass data collected from the literature,
 we applied phylogenetic piecewise regressions to investigate the
 relationship between predator and prey size across carnivorous mammals (51
 terrestrial and 56 marine mammals). We demonstrate that carnivorous
 mammals have four broad dietary groups: small marine carnivores
 (&lt;11,000 kg) and small terrestrial carnivores (&lt;11 kg) feed
 on prey less than 5kg and 2kg, respectively. On average, large marine
 carnivores (&gt;11,000 kg) feed on prey equal to 0.01% of the
 carnivore’s body size, compared to 45% or greater in large terrestrial
 carnivores (&gt;11 kg). We propose that differences in prey
 availability, and the relative ease of processing large prey in the
 terrestrial environment and small prey in marine environment, has led to
 the evolution of these novel foraging behaviours. Our results provide
 important insights into the selection pressures that may have been faced
 by early marine mammals and ultimately led to the evolution of a range of
 feeding strategies and predatory behaviours.
description: Mammalian Predator-Prey
 Body-Mass DataThis data file includes
 data on predator body mass for 107 carnivorous mammals. Associated
 information on prey body mass and daily energetic expenditure are also
 included. All data have been extracted from the literature and the data
 sources have been included. All body mass and energetic data have been
 log10 transformed. Mass data is measured in kilograms. Energetic
 information is in kJ day-1. Each species has been classified by habitat
 type; marine or terrestrial.TuckerDatabaseJEB.xlsx
DOI: 10.5061/dryad.54259
title: Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

description: Environmental degradation may have strong effects on community assembly
 processes. We examined the assembly of bacterial and fungal communities in
 anthropogenically altered and near-pristine streams. Using pyrosequencing
 of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we
 specifically examined if environmental degradation deterministically
 decreases or increases the compositional turnover of bacterial and fungal
 communities. Our results showed that near-pristine streams and
 anthropogenically altered streams supported distinct fungal and bacterial
 communities. The mechanisms assembling these communities were different in
 near-pristine and altered environments. Environmental disturbance
 homogenized bacterial communities, whereas fungal communities were more
 dissimilar in disturbed sites than in near-pristine sites. Compositional
 variation of both bacteria and fungi was related to water chemistry
 variables in disturbed sites, further implying the influence of
 environmental degradation on community assembly. Bacterial and fungal
 communities in near-pristine streams were weakly controlled by
 environmental factors, suggesting that the relative importance of
 niche-based versus neutral processes in assembling microbial communities
 may strongly depend on the spatial scale and local environmental context.
 Our results thus suggest that environmental degradation may strongly
 affect the composition and β-diversity of stream microbial communities
 colonizing leaf litter, and that the direction of the change can be
 different between bacteria and fungi. A better understanding of the
 environmental tolerances of microbes and the mechanisms assembling
 microbial communities in natural environmental settings is needed to
 predict how environmental alteration is likely to affect microbial
 communities.
description: Environmental variables
 and bacterial and fungal OTUsMeasured environmental
 variables for the study sites and occurrences of bacterial and fungal OTUs
 obtained using pyrosequencing. Units for environmental variables are
 provided in column headings. Unit for particle size is explained in a
 separate row below the data.
DOI: 10.5061/dryad.9r06k
title: Data from: Prevalence and factors associated with gonorrhea infection with respect to anatomic distributions among men who have sex with men

description: Introduction: Gonorrhea (GC) infection caused by Neisseria gonorrhoeae has
 been steadily increasing in Thailand over the last decade. Men who have
 sex with men (MSM) are at high risk for gonorrhea infection. Materials and
 methods: In this study, we determined the prevalence of and risk factors
 associated with gonococcal infections by three anatomical sites among MSM.
 We have conducted a cross-sectional analysis of a sexually transmitted
 disease (STD), gonorrhea among MSM attending two STD clinics in Khon Kaen,
 Thailand. We included 358 MSM over 18 years of age. Data were collected
 using self-administered questionnaire. In each participant, an
 oropharyngeal, anorectal, and endourethral swab were tested with culture
 and nucleic acid amplification test (NAAT). However, 267 urine samples
 were tested by both methods. Factors associated with gonorrhea infections
 were assessed using univariate and multivariate logistic regression.
 Results: One hundred and ninety-five out of 358 (54.47%) MSM tested were
 found to be positive for gonorrhea using a porA gene targeted NAAT by
 Real-time PCR with TaqMan probes, but there was no positive result by
 culture. The gonorrheal prevalence for male genital site, anal, and
 oropharyngeal, were 34.73% (95%CI 33.07, 45.08), 29.01% (95%CI 24.61,
 34.33), and 27.93% (95%CI 23.35, 32.89), respectively, while 5.9% (21/355)
 were positive for gonococcal infection in all anatomic sites (oropharynx +
 anus + urethra) of one participant. Previous history of diagnosed STDs was
 a significant factor associated urethral gonorrhea (odds ratio = 3.52,
 95%CI 1.87-6.66, P Value&lt; 0.001). In addition, having more than one
 partner was increased urethral gonorrhea (adjusted odds ratio = 2.26,
 95%CI 1.10-4.68, P Value=0.026). 100% of condom use was found decreasing
 urethral infection (adjusted odds ratio = 0.39, 95%CI 0.15-0.99, P
 Value=0.046). Conclusions: The most common anatomic site of gonorrhea
 infection was male genital site, and the independent risk factors were
 having history of diagnosed STDs and having more than one partner in the
 past 3 months, but 100% condom use was a protective factor of this
 infection.
description: MSM-GC result
 31-8-59
 MSM-GC result 31-8-59.xlsx
DOI: 10.5061/dryad.325vm
title: Data from: The genetic legacy of the 19th century decline of the British polecat: evidence for extensive introgression from feral ferrets

description: In the 19th century, the British polecat suffered a demographic
 contraction, as a consequence of direct persecution, reaching its lowest
 population in the years that preceded the First World War. The polecat is
 now recovering and expanding throughout Britain, but introgressive
 hybridization with feral ferrets has been reported, which could be masking
 the true range of the polecat and introducing domestic genes into the
 species. We used a fragment of the mitochondrial DNA control region and 11
 microsatellite loci to characterize the frequency and extent of
 hybridization and introgression between the two species and assess whether
 the 19th-century decline corresponded to a genetic bottleneck in the
 polecat. The proportion of admixture detected in the wild was high (31%)
 and hybrids were more frequently found outside Wales, suggesting that
 hybridization is more likely to occur along the eastern edge of the
 polecat's range expansion. The patterns observed in the mitochondrial
 and nuclear DNA data show that introgression was mediated by crosses
 between male polecats and female ferrets, whose offspring backcrossed with
 polecats. No first-generation (F1) hybrids were identified, and the broad
 range of observed admixture proportions agrees with a scenario of past
 extensive hybridization between the two species. Using several different
 methods to investigate demographic history, we did not find consistent
 evidence for a genetic bottleneck in the British polecat, a result that
 could be interpreted as a consequence of hybridization with ferrets. Our
 results highlight the importance of the Welsh polecat population for the
 conservation and restoration of the genetic identity of the British
 polecat.
description: Sample
 InformationInformation and results
 (microsatellite data analyses and control region - CR - haplotypes) for
 the samples analysed in the study and respective GenBank Accession Numbers
 for mtDNA data.SampleInformation.xlsxMicrosatellite DatasetMicrosatellite dataset used in the study. Genotypes recovered for 302 samples analysed for 11 microsatellite loci.DataSet_PolecatFerretMicrosatellites.xlsx
DOI: 10.5061/dryad.nq82081
title: Data from: The effects of warming and nitrogen addition on ecosystem respiration in a Tibetan alpine meadow: the significance of winter warming

description: Global warming has become an indisputable fact on the Tibetan Plateau in
 the last decades. Alpine ecosystems are very sensitive to global warming,
 while the impact may depend on the degree of atmospheric nitrogen (N)
 deposition. Previous studies paid more attention on year-round warming,
 while the effects of winter warming was still lacking. In this paper, a
 manipulative experiment consisted of warming and N addition was carried
 out in an alpine meadow since 2010, and three types of warming treatments
 were set up: no-warming (NW), year-round (YW) and winter warming (WW).
 Warming significantly increased air and soil temperature, but decreased
 soil moisture. YW significantly decreased ecosystem respiration (Reco) in
 2012, and WW decreased Reco under no N addition in 2014, while neither YW
 nor WW had significant effects on Reco under N addition, indicating that N
 addition compensated the negative effect of warming on Reco. Annually, YW
 and WW decreased total carbon (C) emissions, and the decrease extent was
 even larger under winter warming. Both YW and WW significantly decreased
 aboveground biomass under no N addition. YW significantly decreased soil
 inorganic N, and WW decreased it in 2013 and 2014 under no N, and WW
 decreased soil microbial biomass C. Structure Equation Modelling showed
 that soil moisture was the most important factors regulating Reco, and
 soil inorganic N content and microbial biomass C can explain 46.6% and
 16.8% variations of Reco. The ﬁndings indicate that soil properties
 changes under warming had substantially effects on ecosystem C efﬂux in
 this alpine meadow. Inhibitory effects of winter warming on ecosystem C
 efflux were mainly attributed to the decline of soil N and soil microbial
 biomass, thus the effects of winter warming on ecosystem C emission are
 not so serious as expected and largely depend on N deposition in this
 semi-arid alpine meadow.
description: Raw data
 file