cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jq2bvq878
title: Bird abundance data for the period 2002-2014 from the French Breeding Bird Survey (STOC)

description: Abundance data on breeding birds from the French Breeding Bird
 Survey (Suivi Temporel des Oiseaux Communs, STOC), for the period
 2002-2014. The dataset comprises 7,115 bird communities. Only 107 common
 species were included in the study. 
description: This dataset was supplied by the French breeding bird monitoring programme, in which ornithologists identify breeding birds by song or visual contact following a standardized monitoring protocol. Each spring. Briefly, a 2 × 2 km plot consisting of 10-point counts -separated by at least 300 m- is randomly assigned to each volunteer. Volunteers record year after year all birds seen or heard in each of the ten sites during a 5-min period. Point counts are visited at dawn twice within three weeks around mid-May to ensure the detection of both early- and late-breeders. The maximum value of the two censuses is retained for each species as yearly abundance index.
DOI: 10.5061/dryad.kh189323p
title: Geography of artiodactyl locomotor morphology as an environmental predictor

description: Aim: We investigate locomotor function in artiodactyls, represented by
 calcaneal gear ratio, as it relates to multiple environments. Using an
 ecometrics approach, we develop a trait-environment model to investigate
 ecosystem level changes through time and to reconstruct past environments.
 We apply the trait-environment model to a case study of six sites in Kenya
 to evaluate changes over the past 100 years. Location: Global. Methods:
 Locomotor morphology was represented by calcaneal gear ratios measured as
 the overall length of a calcaneum divided by length of its in-lever, i.e.
 calcaneal tuber. We collected calcaneal gear ratio measurements from
 skeletal specimens of 157 artiodactyl species in museum collections and
 used species’ spatial distributions to determine the composition of 47,420
 communities globally. For 21,827 communities with three or more species of
 artiodactyls, we used maximum likelihood to model ecometric relationships
 between community-level locomotor morphology and five environmental
 variables, including mean annual temperature, annual precipitation,
 elevation, vegetation cover, and ecoregion province. Results: Community
 mean gear ratios range from 1.43 to 1.56 (µ = 1.50). Mean gear ratios are
 highest in the tropical regions and lowest in the mid-latitudes. Variance
 in mean calcaneal gear ratio is related to ecoregion division (68.6%),
 vegetation cover (63.5%), and precipitation (60.7%). In a case study of
 Kenyan sites, we demonstrate habitat homogenization patterns that match
 mammal community turnover patterns. Main conclusions: With this ecometric
 framework, fossils of artiodactyl postcrania can be used to assist in
 interpreting past ecoregion, vegetation cover, and precipitation for a
 more comprehensive understanding of paleoenvironment. These relationships
 between functional traits and environment will enable better models of
 biotic responses for conservation of functional diversity under changing
 environments.
DOI: 10.5061/dryad.kd51c5b3z
title: A new species of bridled darter endemic to the Etowah River system in Georgia (Percidae: Etheostomatinae: Percina)

description: Percina freemanorum, the Etowah Bridled Darter, is described as a new
 species endemic to the Etowah River system in Georgia, specifically in
 Long Swamp Creek, Amicalola Creek, and the upper portion of the Etowah
 River. The earliest collection records for Percina freemanorum date to
 1948 and in 2007 the species was delimited as populations of Percina
 kusha. Our investigation into the systematics of Percina kusha is
 motivated by the uncertain status of populations in the Coosawattee River
 system and observed morphological disparity in several meristic traits
 between populations in the Conasauga and Etowah River systems. Our
 analyses of morphological divergence, nuclear genotypes, and mtDNA
 haplotype networks confirm the distinctiveness of Percina freemanorum.
 Morphologically, Percina freemanorum is distinguished from Percina kusha
 through lower average numbers of lateral line scales (65.4 vs. 72.3); rows
 of transverse scales (18.0 vs. 21.4); scales around the caudal peduncle
 (22.1 vs. 24.9); and modally more pectoral fin rays (14 vs. 13). The two
 species are not reciprocally monophyletic in phylogenetic analysis of
 mtDNA sequences, but the two species do not share mtDNA haplotypes.
 Analysis of up to 158,000 RADseq loci resolve each of the two species as
 reciprocally monophyletic and genomic clustering analysis of single
 nucleotide polymorphisms identifies two genetic clusters that correspond
 to the morphologically delimited Percina freemanorum and Percina kusha.
DOI: 10.5061/dryad.vhhmgqnrh
title: Socioeconomic disparities in subway use and COVID-19 outcomes in New York City

description: Using data from New York City, we found that there was an estimated 28-day
 lag between the onset of reduced subway use and the end of the exponential
 growth period of SARS-CoV-2 within New York City boroughs. We also
 conducted a cross-sectional analysis of the associations between human
 mobility (i.e., subway ridership), sociodemographic factors, and COVID-19
 incidence as of April 26, 2020. Areas with lower median income, a greater
 percentage of individuals who identify as non-white and/or
 Hispanic/Latino, a greater percentage of essential workers, and a greater
 percentage of healthcare essential workers had greater mobility during the
 pandemic. When adjusted for the percent of essential workers, these
 associations do not remain, suggesting essential work drives human
 movement in these areas. Increased mobility and all sociodemographic
 variables (except percent older than 75 years old and percent of
 healthcare essential workers) was associated with a higher rate of
 COVID-19 cases per 100k, when adjusted for testing effort. Our study
 demonstrates that the most socially disadvantaged are not only at an
 increased risk for COVID-19 infection, but lack the privilege to fully
 engage in social distancing interventions.
description: Original Data Sources: 1. Weekly Metropolitan
 Transportation Authority (MTA) New York City transit subway data are
 publicly availably (Link:
 https://data.ny.gov/Transportation/Fare-Card-History-for-Metropolitan-Transportation-/v7qc-gwpn). 2. New York City Department of Health and Mental Hygiene COVID-19 data are available openly (Link: https://github.com/nychealth/coronavirus-data).
description: There are five data sets: 1. Cross-sectional
 NYC mobility and COVID-19 data (ZCTA-level)
 2. Longitudinal NYC COVID-19 data (Borough-level)
 3. Longitudinal NYC mobility data (ZCTA and
 borough-level) 4. Geographic coordinates for NYC
 (ZCTA-level) 5. Regression output for Figure 4
 (ZCTA-level)
DOI: 10.5061/dryad.wpzgmsbjw
title: Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

description: The interactions between transposable elements (TEs) and their hosts
 constitute one of the most profound co-evolutionary processes found in
 nature. The population dynamics of TEs depends on factors specific to each
 TE families, such as the rate of transposition and insertional preference,
 the demographic history of the host and the genomic landscape. How these
 factors interact has yet to be investigated holistically. Here we are
 addressing this question in the green anole ( Anolis carolinensis ) whose
 genome contains an extraordinary diversity of TEs (including non-LTR
 retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We
 observe a positive correlation between recombination rate and TEs
 frequencies and densities for LINEs, SINEs and DNA transposons. For these
 elements, there was a clear impact of demography on TE frequency and
 abundance, with a loss of polymorphic elements and skewed frequency
 spectra in recently expanded populations. On the other hand, some
 LTR-retrotransposons displayed patterns consistent with a very recent
 phase of intense amplification. To determine how demography, genomic
 features and intrinsic properties of TEs interact we ran simulations using
 SLiM3. We determined that i) short TE insertions are not strongly
 counter-selected, but long ones are, ii) neutral demographic processes,
 linked selection and preferential insertion may explain positive
 correlations between average TE frequency and recombination, iii) TE
 insertions are unlikely to have been massively recruited in recent
 adaptation. We demonstrate that deterministic and stochastic processes
 have different effects on categories of TEs and that a combination of
 empirical analyses and simulations can disentangle these mechanisms.
description: TEs were called using MELT (https://melt.igs.umaryland.edu/), using the consensus sequences found in the file TE_consensus_for_MELT.fasta. Information about TE counts, lengths, and densities were extracted from the VCF files using VCFTools and BEDTOOLs. A file with the average effective recombination rate divided by nucleotide diversity in 1Mb windows is also provided. Because the effective recombination rate depends on the effective population size, it is directly correlated to local reduction of diversity due to linked selection. Thus, a low value may be due to either low diversity due to linked selection or to reduced recombination (r). Since nucleotide diversity is an estimator of 4Nm,with m the mutation rate and N the local effective population size, this statistic can be seen as the ratio between r and the mutation rate m.
description: VCF files contain TE genotypes without missing data for the 29
 individuals included in the study. The
 file Correspondance_individuals_VCF_clades.txt details to which genetic
 cluster/species each individual belongs.
DOI: 10.5061/dryad.wdbrv15m9
title: The dataset of five chloroplast regions used in: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: Two new species, reinstatement of Cyathea bonii, and their phylogenetic positions

description: Gymnosphaera represents a minor lineage within the scaly tree-fern family
 Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution
 area of Gymnosphaera. However, the species diversity of Gymnosphaera is
 currently incompletely known in mainland Asia due to lacking critical
 revision. Here we present new findings of species diversity and their
 relationships with mainland Asian Gymnosphaera based on field surveys, the
 examination of herbarium collections, and phylogenetic analyses of
 sequences of multiple chloroplast and nuclear regions. Two new species, G.
 saxicola from southwestern Yunnan and G. bachmaensis from central Vietnam
 are established. Traditionally recognized G. podophylla is revealed to be
 a complex, from which G. bonii is reinstated as a distinct species. Our
 phylogenetic analyses identified four clades within Gymnosphaera in
 mainland Asia: G. denticulata clade, G. gigantea clade, G. podophylla
 clade, and G. salletii clade. The new species G. saxicola, which is
 special for its saxicolous habitat, was resolved as a sister to G.
 austroyunnanensis in the G. salletii clade. The newly discovered G.
 bachmaensis, which is characterized especially by the spathulate frond,
 was positioned in the G. podophylla clade, being sister to G. bonii. The
 mountainous region from south-central Vietnam northwards to western Yunnan
 is a diverse center of Gymnosphaera and more species of this group are
 probably to be discovered there.
DOI: 10.5061/dryad.gtht76hjp
title: Species responses to changing precipitation depends on trait plasticity rather than trait means and intraspecific variation

description: 1. Trait-based approaches are key to develop mechanistic understanding of
 differences in plant species performance under environmental change. While
 mean trait values have been widely used to link functional traits to
 species performance, the contribution of intraspecific trait variation and
 trait plasticity remains unclear. Moreover, environmentally induced
 changes in species biomass is caused by changes in the number of
 individuals and individual growth rate, both of which should be influenced
 by trait differences and plasticity. Our goal in this study is to use
 trait-based information to explain species performance via changes in
 species abundance and individual weight. 2. We measured the mean,
 intraspecific variation and plasticity of nine aboveground plant traits,
 and a further three mean root traits of ten common species in a
 precipitation manipulation experiment in semiarid grassland. We used this
 trait information to explain differences in the responses of species
 biomass, abundance and mean individual weight to changing precipitation.
 Species responses were calculated as the normalized slopes of the
 regressions between species biomass, abundance and individual weight with
 the manipulated precipitation amount. 3. We found strong differences in
 species responses to changing precipitation for species biomass, abundance
 and mean individual weight. Reduced precipitation decreased biomass,
 abundance and mean individual weight for some species, but increased them
 for others. Biomass and mean individual weight of species with
 resource-acquisitive traits, such as shallow rooted species, showed
 stronger positive responses to changing precipitation compared to
 resource-conservative traits, like those with deep roots. For aboveground
 traits, trait plasticity was the strongest predictor of species responses
 compared to mean traits and intraspecific trait variation. In addition,
 trait plasticity regulated changes in species biomass more via changes in
 species abundance than mean individual weight. 4. These results indicate
 that trait plasticity is a key driver for determining species specific
 responses to changing precipitation and needs more consideration for
 understanding and predicting ecosystem structure and functioning in future
 climate scenarios.
DOI: 10.15468/dl.92mrc2
title: Occurrence Download

description: A dataset containing 49221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cocos nucifera"
 ]
}

 The dataset includes 49221 records from 475 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002546-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dfn2z34zq
title: Relative influence of wild prey and livestock abundance on carnivore caused livestock predation

description: Conservation conflict over livestock depredation is one of the key drivers
 of large mammalian carnivore declines worldwide. Mitigating this conflict
 requires strategies informed by reliable knowledge of factors influencing
 livestock depredation. Wild prey and livestock abundance are critical
 factors influencing the extent of livestock depredation. We compared
 whether the extent of livestock predation by snow leopards Panthera uncia
 differed in relation to densities of wild prey, livestock and snow
 leopards at two sites in Shey Phoksundo National Park, Nepal. We used
 camera trap-based spatially explicit capture-recapture models to estimate
 snow leopard density; double-observer surveys to estimate the density of
 their main prey species, the blue sheep Pseudois nayaur; and
 interview-based household surveys to estimate livestock population and
 number of livestock killed by snow leopards. The proportion of livestock
 lost per household was seven times higher in Upper Dolpa, the site which
 had higher snow leopard density (2.51 snow leopards per 100 km2) and
 higher livestock density (17.21 livestock per km2) compared to Lower Dolpa
 (1.21 snow leopards per 100 km2; 4.5 livestock per km2). The wild prey
 density was similar across the two sites (1.81 and 1.57 animals per km2 in
 Upper and Lower Dolpa, respectively). Our results suggest that livestock
 depredation level may largely be determined by the abundances of the snow
 leopards and livestock and predation levels on livestock can vary even at
 similar levels of wild prey density.  In large parts of the snow
 leopard range, livestock production is indispensable to local livelihoods
 and livestock population is expected to increase to meet the demand of
 cashmere. Hence, we recommend that any efforts to increase livestock
 populations or conservation initiatives aimed at recovering or increasing
 snow leopard population be accompanied by better herding practices (e.g.,
 predator-proof corrals) to protect livestock from snow leopard.
description: This is the final processed data set used for the analysis. The
 snow leopard density is obtained using spatial capture recapture analysis
 of camera trap data. The density of snow loepard's prey species blue
 sheep was based on double observer surveys. Livestock holding size and
 livestock number killed by snow leopard was obtained through
 interview-based household surveys.  
description: The data uploaded here is the final data set used for analysis.
 The raw data is not included here. The rows and columns in the data set
 are self explanatory. Anyone interested to replicate the analysis can
 reach out to corresponding author for the raw data set.<br>
DOI: 10.5061/dryad.gf1vhhmmp
title: Climate vulnerability assessment of the Espeletia complex on Páramo sky islands in the northern Andes

description: Some of the largest impacts of climate change are expected in the
 environmentally heterogeneous and species rich high mountain ecosystems.
 Among those, the Neotropical alpine grassland above the tree line (c.
 2,800 m), known as Páramo, is the fastest evolving biodiversity hotspot on
 earth, and one of the most threatened. Yet, predicting climate responses
 of typically slow-growing, long-lived plant linages in this unique high
 mountain ecosystem remains challenging. Here we coupled climate
 sensitivity modeling and adaptive potential inferences to efficiently
 assess climate vulnerability of Espeletia, Páramo’s most iconic,
 predominant and rapidly evolving plant complex. In order to estimate
 climate sensitivity, we first modeled the distribution of 28 Espeletia
 taxa under a niche conservatism scenario using altitude and five current
 (1970-2000) and future (2050 RCP 8.5) bioclimatic variables across 36
 different Páramo complexes in the northern Andes (49 % of the world’s
 Páramo area). As an alternative to range shifts via migration, we also
 computed the adaptive capacity of these Páramo complexes by considering
 three enhancing factors of the biodiversity’s adaptive potential as well
 as three environmental limiting factors of the populations’ plastic
 response. These predictors showed that diverse Páramos in the Eastern
 Cordillera were more vulnerable likely because the counteracting effects
 of the adaptive potential (r = -0.93 ± 0.01) were not sufficient to buffer
 higher distribution losses (r = 0.39 ± 0.01). Agriculture (r = -0.48 ±
 0.01), mining (r = -0.36 ± 0.01), and rural population density (r = -0.23
 ± 0.01) also weakened the adaptive capacity. These results speak for a
 limited persistence via migration in the short-term responses of Espeletia
 to climate change, even though the past population dynamics in concert
 with glacial cycling is indicative of a predominant role of range shifts.
 Furthermore, changing climate, together with a general inability to adapt,
 may eventually constrain the rapid diversification in the Espeletia
 complex. Our integrative modeling illustrates how future climate may
 impact plant populations in a mega diverse and highly threatened ecosystem
 such as the Páramo, and encourages carrying out similar estimates in
 diverse plant complexes across other high mountain and island-like
 ecosystems.
DOI: 10.5061/dryad.d51c5b01b
title: The importance of the Mexican taxa of Asteraceae on the family phylogeny

description: Asteraceae is the largest plant family in México with about 417 genera and
 3,113 species, more than 60% of them endemic. Phylogenetic relationships
 at subfamily and tribal levels have been previously resolved employing
 both nuclear and plastid molecular markers. However, Asteraceae species
 native to Mexico have been underrepresented in such phylogenies. To tackle
 this issue, the taxon sampling of this study included 90 Asteraceae
 species native to México, four species from the Caribbean, 119 previously
 sequenced species, and six outgroups. With this sampling, all the
 Asteraceae subfamilies and all of the tribes recognized to date are
 represented. The analyzed data set consisted of eleven chloroplast markers
 (atpB, matK, ndhC, ndhD, ndhF, ndhI, ndhJ, ndhK, rbcL, trnL-trnF,
 23S-trnA). We present two phylogenetic reconstructions obtained by maximum
 likelihood and pseudocoalescent methods. Besides, we present a
 time-calibrated phylogeny, used to infer the best configuration of
 diversification rate shifts. Our results show that Mexican species are
 distributed mainly in the subfamily Asteroideae (80 species), followed by
 Cichorioideae (6 species), Carduoideae (2 species), and Mutisioideae (2
 species). Four net diversification rate shifts were found: One near the
 base of the tree and four within Asteroideae subfamily. Our extended
 sampling of the family with the representation of native species to Mexico
 allowed us to identify important events in the evolutionary history of the
 family.
DOI: 10.15468/dl.4gm9du
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caragana sukiensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 26 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002547-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.73n5tb2v9
title: How to build a dinosaur: musculoskeletal modelling and simulation of locomotor biomechanics in extinct animals

description: The intersection of paleontology and biomechanics can be reciprocally
 illuminating, helping to improve paleobiological knowledge of extinct
 species and furthering our understanding of the generality of
 biomechanical principles derived from study of extant species. However,
 working with data gleaned primarily from the fossil record has its
 challenges. Building on decades of prior research, we outline and
 critically discuss a complete workflow for biomechanical analysis of
 extinct species, using locomotor biomechanics in the Triassic theropod
 dinosaur Coelophysis as a case study. We progress from the digital capture
 of fossil bone morphology to creating rigged skeletal models, to
 reconstructing musculature and soft tissue volumes, to the development of
 computational musculoskeletal models, and finally to the execution of
 biomechanical simulations. Using a three-dimensional musculoskeletal model
 comprising 33 muscles, a static inverse simulation of the mid-stance of
 running shows that Coelophysis probably used more upright (extended)
 hindlimb postures, and was likely capable of withstanding a vertical
 ground reaction force of magnitude more than 2.5 times body weight. We
 identify muscle force-generating capacity as a key source of uncertainty
 in the simulations, highlighting the need for more refined methods of
 estimating intrinsic muscle parameters such as fibre length. Our approach
 emphasizes the explicit application of quantitative techniques and
 physics-based principles, which helps maximize results robustness and
 reproducibility. Although we focus on one specific taxon and question,
 many of the techniques and philosophies explored here have much generality
 to them, so they can be applied in biomechanical investigation of other
 extinct organisms.
description: All files and their usage are described in the main supplementary
 text document.