cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c0p090f
title: Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip

description: Elucidating the genetic basis of fitness-related traits is a major goal of
 molecular ecology. Traits subject to sexual selection are particularly
 interesting, as non-random mate choice should deplete genetic variation
 and thereby their evolutionary benefits. We examined the genetic basis of
 three sexually selected morphometric traits in bighorn sheep (Ovis
 canadensis): horn length, horn base circumference, and body mass. These
 traits are of specific concern in bighorn sheep as artificial selection
 through trophy hunting opposes sexual selection. Specifically, horn size
 determines trophy status and, in most North American jurisdictions, if an
 individual can be legally harvested. Using between 7,994–9,552 phenotypic
 measures from the long-term individual-based study at Ram Mountain
 (Alberta, Canada), we first showed that all three traits are heritable (h2
 = 0.15–0.23). We then conducted a genome-wide association study (GWAS)
 utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine
 Infinium® HD SNP BeadChip. We found suggestive association for body mass
 at a single locus (OAR9_91647990). The absence of strong associations with
 SNPs suggests that the traits are likely polygenic. These results
 represent a step forward for characterizing the genetic architecture of
 fitness related traits in sexually dimorphic ungulates.
description: Miller_et_al_Animals_with_phenos_transposedPLINK tped file for individuals used in GWAS analysesMiller_et_al_Animals_with_phenos_transposedPLINK tfam file for individuals used in GWAS analysesMiller_et_al_Base_Circ_Typed_IDs_Only_No_DupesPhenotype file with only 1 measure per individual for setting "base model" in RepeatABELMiller_et_al_Base_Circ_Typed_IDs_OnlyRepeated measures of horn base circumference for sheep used in GWAS analysesMiller_et_al_Length_Typed_IDs_OnlyRepeated measures of horn length for sheep used in GWAS analysesMiller_et_al_Mass_Typed_IDs_OnlyRepeated measures of body mass for sheep used in GWAS analysesMiller_et_al_RepeatABLE_GWAS_ScriptR script for conducting GWAS analyses with the RepeatABLE package
DOI: 10.34740/kaggle/dsv/14638568
title: 🌍💰Global Millionaire Migration & Wealth Dataset
DOI: 10.5061/dryad.4kt079g
title: Data from: RRapid global spread of wRi-like Wolbachia across multiple Drosophila

description: Maternally transmitted Wolbachia, Spiroplasma and Cardinium bacteria are
 common in insects, but their interspecific spread is poorly understood.
 Endosymbionts can spread rapidly within host species by manipulating host
 reproduction, as typified by the global spread of wRi Wolbachia observed
 in Drosophila simulans. However, because Wolbachia cannot survive outside
 host cells, spread between distantly related host species requires
 horizontal transfers that are presumably rare. Here we document spread of
 wRi-like Wolbachia among eight highly diverged Drosophila hosts (10–50
 million years) over only about 14,000 years (5,000–27,000). Comparing 110
 wRi-like genomes, we find ≤0.02% divergence from the wRi variant that
 spread rapidly through California populations of D. simulans. The hosts
 include both globally invasive species, D. simulans, D. suzukii and D.
 ananassae , and narrowly distributed Australian endemics, D. anomalata and
 D. pandora. Phylogenetic analyses that include mtDNA genomes indicate
 introgressive transfer of wRi-like Wolbachia between closely related
 species D. ananassa e , D. anomalata and D. pandora , but no horizontal
 transmission within species. Our analyses suggest D. ananassae as the
 Wolbachia source for the recent wRi invasion of D. simulans, and D.
 suzukii as the source of Wolbachia in its sister species D. subpulchrella
 . Although six of these wRi-like variants cause strong cytoplasmic
 incompatibility, two cause no detectable reproductive effects, indicating
 that pervasive mutualistic effects complement the reproductive
 manipulations for which Wolbachia are best known. “Super spreader”
 variants like wRi may be particularly useful for controlling insect pests
 and vector-borne diseases with Wolbachia transinfections.
description: Data from: Rapid global
 spread of wRi-like Wolbachia across multiple DrosophilaThis data archive
 contains the scripts and sequence data used for the phylogenetic analyses
 in the accompanying manuscript (Turelli et al., in press). A detailed
 description of the contents is provided in the README.txt
 file.dryad_package.tar.gz
DOI: 10.5061/dryad.v142481
title: Data from: Development of the Combined Assessment of Risk Encountered in Surgery (CARES) surgical risk calculator for prediction of post-surgical mortality and need for intensive care unit admission risk – a single-centre retrospective study

description: [No abstract entered]
description: CARES risk model
 datasetRetrospective cohort of
 90785 patients who underwent surgery in Singapore General Hospital between
 2012-2016Risk model and elderly dataset
 without cts nes unique cases and new death dates combined no NRIC new
 attempt reorg.xlsx
DOI: 10.5061/dryad.tn60810
title: Data from: The impact of bacteriophages on phyllosphere bacterial abundance and composition

description: Interactions between bacteria and bacteriophage viruses (phages) are known
 to influence pathogen growth and virulence, microbial diversity, and even
 biogeochemical cycling. Lytic phages in particular infect and lyse their
 host cells, and can therefore have significant effects on cell densities
 as well as competitive dynamics within microbial communities. Despite the
 known impacts of lytic phages on the ecology and evolution of bacteria in
 free-living communities, little is known about the role of lytic phages in
 host-associated microbiomes. We set out to characterize the impact of
 phages in the tomato phyllosphere, i.e., the bacteria associated with
 above-ground plant tissues, by transferring microbial communities from
 field-grown tomato plants to juvenile plants grown under mostly sterile
 conditions in either the presence or absence of their associated phage
 community. In three separate experiments, we found that the presence of
 phages affects overall bacterial abundance during colonization of new host
 plants. Furthermore, bacterial community analysis using 16S rRNA amplicon
 sequencing shows that phages significantly alter the relative abundance of
 dominant community members and can influence both within- and among-host
 diversity. These results underscore the importance of lytic phages in
 host-associated microbiomes and are relevant to microbiome transplantation
 approaches, as they suggest transferring non-bacterial components of the
 microbiome among hosts is likely to have a strong impact on growth of both
 the resident and donor microbiota.
description: Table
 S4OTU
 Table from 16S rRNA sequencing: raw numbersTable
 S5OTU
 Table from 16S rRNA sequencing: contaminants removed, rarified to 8,000
 reads/sampleTable
 S6OTU
 Table from 16S rRNA sequencing: contaminants removed, rarified to 500
 reads/sampleddPCR
 DataddPCR data from Figures
 1, 2, 3, S1
DOI: 10.34810/data2003
title: Meteorological data, OpenFOAM files and processed data of: Influence of terrain roughness on numerical simulations of sea-breezes

description: The dataset contains meteorological data, OpenFOAM files, and processed data from the paper titled: "Influence of terrain roughness on numerical simulations of sea breezes".
The dataset is structured into two main folders: "Observational data" and "Numerical simulations".
The folder "Observational data" includes all the observational data shown in the paper, i.e., wind speed and temperature collected at a meteorological station during the week from January 31 to February 6, 2024.
The folder "Numerical simulations" (separated in 3 parts) contains all the numerical cases presented in the paper. This folder is organized into several subfolders that follow the structure of the paper: "MeshValidation", "TimeStepValidation", "SeaLengthStudy", "HeightStudy", and "RoughnessEffectStudy".
Each case includes the necessary "0", "system" and "constant" folders required for running all the cases in OpenFOAM. Additionally, .txt files containing post-processed data computed at 2 km from the sea ("data_at2km_FromSea") are provided for each case.
description: Other funding agency:&gt;

Funding agency: RES, BSC in MareNostrum5<br>
Project number: IM-2024-2-0013 
 Funding agency: RES, BSC in MareNostrum5<br>
Project number: IM-2024-2-0014
DOI: 10.5061/dryad.271nf43
title: Data from: Demographic compensation does not rescue populations at a trailing range edge

description: Species' geographic ranges and climatic niches are likely to be
 increasingly mismatched due to rapid climate change. If a species'
 range and niche are out of equilibrium, then population performance should
 decrease from high-latitude "leading" range edges, where
 populations are expanding into recently ameliorated habitats, to
 low-latitude "trailing" range edges, where populations are
 contracting from newly unsuitable areas. Demographic compensation is a
 phenomenon whereby declines in some vital rates are offset by increases in
 others across time or space. In theory, demographic compensation could
 increase the range of environments over which populations can succeed and
 forestall range contraction at trailing edges. An outstanding question is
 whether range limits and range contractions reflect inadequate demographic
 compensation across environmental gradients, causing population declines
 at range edges. We collected demographic data from 32 populations of the
 scarlet monkeyflower (Erythranthe cardinalis) spanning 11˚ latitude in
 western North America and used integral projection models to evaluate
 population dynamics and assess demographic compensation across the
 species' range. During the 5-year study period, which included
 multiple years of severe drought and warming, population growth rates
 decreased from north to south, consistent with leading-trailing dynamics.
 Southern populations at the trailing range edge declined due to reduced
 survival, growth, and recruitment, despite compensatory increases in
 reproduction and faster life history characteristics. These results
 suggest that demographic compensation may only delay population collapse
 without the return of more favorable conditions or the contribution of
 other buffering mechanisms such as evolutionary rescue.
description: Erythranthe (Mimulus)
 cardinalis demography dataRange-wide demographic
 data for 32 populations of Erythranthe (Mimulus) cardinalis from
 2010-2014. Please see README file for details.Mcard_demog_data_2010-2013.csvAnnual climate data for each study population from 1951-2014Annual climate data for each Erythranthe (Mimulus) cardinalis study population from 1951-2014. Data were obtained from ClimateWNA version 5.41 (Wang T, Hamann A, Spittlehouse DL, Murdock TQ; 2012; "ClimateWNA - High-resolution spatial climate data for western North America," J Appl Meteorol Climatol 51:16-29). ID1: Population, MAT: Mean annual temperature, MAP: Mean annual precipitation.DemoSitesWeather_ClimateWNAOutput_1951-2014YT.csvR scripts for Sheth & Angert PNAS 2018R scripts to reproduce all analyses in Sheth & Angert (2018). Run scripts in order from "01_" to "12_". Scripts in "temporal_demog_compensation_TableS7_FigS7" folder were used to run analyses of temporal demographic compensation for populations from the southern range edge (see SI Appendix for more details).Sheth_Angert_PNAS_2018_Rscripts.zip
DOI: 10.5061/dryad.br73qg2
title: Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)

description: Premise of the study: Nuclear microsatellite markers were developed for
 population genetic analysis of the threatened palaeoendemic conifer
 Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results:
 Fifteen variable loci were identified showing 1 to 13 alleles per
 population with seven loci displaying over four alleles in all populations
 and the average number of alleles per locus ranging from 4.8 to 5.93 per
 population. The observed heterozygosity per locus varied from 0.00 to 0.91
 and overall heterozygosity was markedly consistent between populations
 (from 0.54 to 0.57). All loci also amplified in the endangered congener P.
 fitzgeraldii but only five of the loci had more than one allele.
 Conclusions: These 15 loci are the first microsatellite markers developed
 in the genus Pherosphaera. These loci will be useful for investigating the
 species' extant genetic diversity and structure, the impact of past
 environmental change and the significance of asexual reproduction.
description: Pherosphaera hookeriana
 EST contigsThis data consists of
 33,066 contigs (N50 = 1,728 bp) constructed by de novo assembly from an
 RNA-seq data set of Pherosphaera hookeriana. The P. hookeriana RNA-seq
 data consisted of 43,176,890 pair-end reads of 100 bp length. The contigs
 were used to develop 15 EST nuclear microsatellite
 loci.
DOI: 10.5061/dryad.n4b49kq
title: Data from: Forgone care among middle aged and elderly with chronic diseases in China: evidence from the China Health and Retirement Longitudinal Study Baseline Survey

description: Objective: In general, published studies analyze healthcare utilization,
 rather than foregone care, among different population groups. The
 assessment of forgone care as an aspect of healthcare system performance
 is important because it indicates the gap between perceived need and
 actual utilization of healthcare services. This study focused on a
 specific vulnerable group, middle-aged and elderly people with chronic
 diseases, and evaluated the prevalence of foregone care and associated
 factors among this population in China. Methods: Data were obtained from a
 nationally representative household survey of middle-aged and elderly
 individuals (≥45 years), the China Health and Retirement Longitudinal
 Study (CHARLS), which was conducted by the National School of Development
 of Peking University in 2013. Descriptive statistics were used to analyze
 sample characteristics and the prevalence of foregone care. Andersen’s
 healthcare utilization and binary logistic models were used to evaluate
 the determinants of foregone care among middle-aged and elderly
 individuals with chronic diseases. Results: The prevalence of foregone
 outpatient and inpatient care among middle-aged and elderly people were
 10.21% and 6.84%, respectively, whereas the prevalence of foregone care
 for physical examinations was relatively high (57.88%). Predisposing
 factors, including age, marital status, employment, education, and family
 size, significantly affected foregone care in this population. Regarding
 enabling factors, individuals in the highest income group reported less
 foregone inpatient care or physical examinations compared with those in
 the lowest income group. Social healthcare insurance could significantly
 reduce foregone care in outpatient and inpatient situations; however,
 these schemes (except for Urban Employee Medical Insurance) did not appear
 to have a significant impact on foregone care involving physical
 examinations. Conclusion: In China, policymakers may need to further
 adjust healthcare policies, such as health insurance schemes, and improve
 the hierarchical medical system, to promote reduction in foregone care and
 effective utilization of health services.
description: CHARLES
 dataDATA.dta
DOI: 10.15468/dl.8uravm
title: Occurrence Download

description: A dataset listing the 3468 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "DatasetKey is one of (Artportalen, SHARK - National environmental monitoring of Harbour seal in Sweden since 1988, iNaturalist Research-grade Observations, SHARK - Phyto- and Microzooplankton Data Collected by Imaging FlowCytobots (IFCB) in Swedish and Adjacent Waters, SLU Aqua Institute of Coastal Research Database for Coastal Fish - KUL)",
 "Geometry POLYGON((11.00055 57.54731,11.0429 57.36595,11.0754 57.3245,11.85952 57.41656,11.96849 57.49504,11.94213 57.53308,11.92359 57.55302,11.78671 57.56044,11.52015 57.59311,11.00055 57.54731))",
 "HasGeospatialIssue is false",
 "Year 2000-2026"
 ]
}

 The dataset's 3468 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001516-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bn7p2f5
title: Data from: Private land conservation has landscape-scale benefits for wildlife in agroecosystems

description: Private lands contain much of the world's biodiversity. Conservation
 of private land, especially agricultural land, is urgent yet challenging
 because of the diverse priorities of landowners. Local effects of farmland
 conservation programmes have been evaluated thoroughly, but
 population-level response to these programmes may depend on effects that
 extend beyond targeted land parcels. We investigated the landscape-scale
 effects of a grassland conservation initiative, the Conservation Reserve
 Enhancement Program (CREP), on a socially and economically important
 gamebird, the Northern Bobwhite (Colinus virginianus). Barriers to
 assessing population-level response to conservation include determining
 the spatial scale at which a species responds to environmental change (the
 scale of effect) and untangling density-dependent processes. We performed
 point counts over 6 years at 247 sites with similar local CREP density but
 varying landscape-scale CREP density. We used an open-population distance
 sampling model to evaluate population response to landscape-level CREP
 density and to forecast population densities under differing re-enrollment
 scenarios. Our model included kernel smoothing techniques to estimate
 scale of effect and an estimator of the strength of density dependence.
 Density dependence moderated the effectiveness of the CREP, but overall
 populations responded positively to increasing landscape-scale CREP
 density. We estimated that at least 5% of the landscape needs to be in
 CREP to meet population density goals of 0.25 bobwhite/ha. Conservatively,
 we recommend 10% of the landscape to be in CREP. Our percent cover
 recommendations are based on a distance-weighted average of CREP around
 focal sites. Landscape-scale effects diminished with distance. For
 example, assuming all else is equal, a CREP field 3000 m away had 88% less
 of an effect on local abundance than a field 1000 m away. Fields farther
 than 5000 m away had no effect on local abundance. Synthesis and
 applications. Our study underscores the importance of a landscape-scale
 approach to farmland conservation. Benefits of these programmes can extend
 beyond the local scale, but their importance to local populations
 diminishes with distance. Estimating the relationship between increasing
 distance and the utility of conservation land to local populations could
 provide land managers a practical framework in which to target land
 enrollment to maximize biodiversity outcomes.
description: JAPPL-2017-01144_DataIncluded is the data that went in to each of our models described in the manuscript. Included in data are: counts of bobwhite, aggregated densities of conservation fields without specific spatial information (i.e., no x y coordinates), and distance sampling metrics needed to run the model.
DOI: 10.5061/dryad.84fc873
title: Data from: Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae).

description: Premise of the study: Recent estimates of crown ages for cycad genera
 (Late Miocene) challenge us to consider what processes have produced the
 extant diversity of this ancient group in such relatively little time.
 Pleistocene climate change has driven major shifts in species
 distributions in Mexico and may have led to speciation in the genus Dioon
 by forcing populations to migrate up in elevation thereby becoming
 separated by topography. Methods: We inferred orthologs from
 transcriptomes of five species and sequenced these in 42 individuals
 representing all Dioon species. From these data and published plastid
 sequences we inferred dated species trees and lineage-specific
 diversification rates. Key results: 84 nuclear orthologs and plastid data
 confirm four major clades within Dioon, all of Pleistocene age. Gene tree
 analysis, divergence dates, and an increase in diversification rate
 support very recent and rapid divergence of extant taxa. Conclusions: This
 study confirms the Pleistocene age of Dioon species and implicates
 Pleistocene climate change and established topography in lineage spitting.
 These results add to our understanding of the cycads as evolutionarily
 dynamic lineages, not relicts or evolutionary dead ends. We also find that
 well-supported secondary calibration points can be reliable in the absence
 of fossils. Our hypothesis of lineage splitting mediated by habitat shifts
 may be applicable to other taxa that are restricted to elevation specific
 ecotones.
description: BEAST xml
 filesBEAST_xml_files.zipSupermatrices for plastid and nuclear locisupermatrices.zipMCC gene treesmcc.gene.trees.zip
DOI: 10.5061/dryad.8hv88m0
title: Data from: Community composition and diversity of Neotropical root-associated fungi in common and rare trees

description: Interactions between plants and root-associated fungi can affect the
 assembly, diversity, and relative abundances of tropical plant species.
 Host-symbiont compatibility and some degree of host specificity are
 prerequisites for these processes to occur, and these prerequisites may
 vary with host abundance. However, direct assessments of whether
 specificity of root-associated fungi varies with host abundance are
 lacking. Here, in a diverse tropical forest in Los Tuxtlas, Mexico, we
 couple DNA metabarcoding with a sampling design that controls for host
 phylogeny, plant age, and habitat variation, to characterize fungal
 communities associated with the roots of three confamilial pairs of host
 species that exhibit contrasting (high and low) relative abundances. We
 uncovered a functionally and phylogenetically diverse fungal community
 composed of 1,038 OTUs (operational taxonomic units with 97% genetic
 similarity), only 14 of which exhibited host specificity. Host species was
 a significant predictor of fungal community composition only for the
 subset of OTUs composed of putatively pathogenic fungi. We found no
 significant difference in the number of specialists associating with
 common versus rare trees, but we found that host abundance was negatively
 correlated to the diversity of root fungal communities. This latter result
 was significant for symbiotrophs (mostly arbuscular mycorrhizal fungi),
 and to a lesser extent for pathotrophs (mostly plant pathogens). Thus,
 root fungal communities differ between common and rare trees, which may
 impact the strength of conspecific negative density-dependence. Further
 studies from other tropical sites and host lineages are warranted, given
 the role of root-associated fungi in biodiversity maintenance.
description: S1Supplementary data file
 1: OTU by sample table matrix. Each sample represents an individual root
 tip. Negative controls are included.S2Supplementary data file
 S2: Taxonomic information of each fungal OTU assigned by
 FUNGuild.S3Supplementary data file
 S3: Sample metadata