cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cs947
title: Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)

description: PREMISE OF THE STUDY: Hybridization has played an important role in the
 evolution and ecological adaptation in diploid and polyploid plants.
 Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and
 of great ecological importance. These tetraploids are often taxonomically
 identified as A. tridentata ssp. wyomingensis, or as autotetraploids of
 diploid subspecies tridentata and vaseyana. Few details are available as
 to how these tetraploids are formed or how they are related to diploid
 subspecies. METHODS: We used amplicon sequencing to assess phylogenetic
 relationships among three recognized subspecies: tridentata, vaseyana and
 wyomingensis. DNA sequence data from putative genes were pyrosequenced and
 assembled from 329 samples. Nucleotide diversity and putative haplotypes
 were estimated from the high-read coverage. Phylogenies were constructed
 from Bayesian coalescence and neighbor-net network analyses. KEY RESULTS:
 Analyses support distinct diploid subspecies of tridentata and vaseyana in
 spite of known hybridization in ecotones. Nucleotide diversity estimates
 of populations compared to the total diversity indicate the relationships
 are predominately driven by a small proportion of the amplicons.
 Tetraploids, including subspecies wyomingenesis, are polyphyletic
 occurring within and between diploid subspecies groups. CONCLUSIONS:
 Artemisia tridentata is a species comprised of phylogenetically distinct
 diploid progenitors and a tetraploid complex with varying degrees of
 phylogenetic and morphological affinities to the diploid subspecies. These
 analyses suggest tetraploids are formed locally or regionally from diploid
 tridentata and vaseyana populations via autotetraploidy, followed by
 introgression between tetraploid groups. Understanding the phylogenetic
 versus ecological relationships of A. tridentata subspecies will have
 bearing on how to restore these desert ecosystems.
description: Alignment of Artemisia
 tridentata consensus sequencesConcatenated consensus
 sequence of 25 amplicons from 49 populations including diploid and
 tetraploid populations. Readme file describes the
 populations.Concat_dipl_tetraploid.nex
DOI: 10.5061/dryad.k7k4m
title: Data from: A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

description: Determining the boundaries between species and deciding when to describe
 new species are challenging practices that are particularly difficult in
 groups with high levels of geographic variation. The coast horned lizards
 (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive
 geographic distribution spanning many distinctive ecological regions
 ranging from northern California to the Cape Region of Baja California,
 Mexico, and populations differ substantially with respect to external
 morphology across much of this range. The number of taxa recognized in the
 group has been re-evaluated by herpetologists over 20 times during the
 last 180 years, and typically without the aid of explicit species
 delimitation methods, resulting in a turbulent taxonomy containing
 anywhere from one to seven taxa. In this study, we evaluate taxonomic
 trends through time by ranking 15 of these species delimitation models
 (SDMs) using coalescent analyses of nuclear loci and SNPs in a Bayesian
 model comparison framework. SDMs containing more species were generally
 favored by Bayesian model selection; however, several three-species models
 outperformed some four and five species SDMs, and the top-ranked model,
 which contained five species, outperformed all SDMs containing six
 species. Model performance peaked in the 1950s based on marginal
 likelihoods estimated from nuclear loci and SNPs. Not surprisingly, SDMs
 based on genetic data outperformed morphological taxonomies when using
 genetic data alone to evaluate models. The de novo estimation of
 population structure favors a three-population model that matches the
 currently recognized integrative taxonomy containing three species. We
 discuss why Bayesian model selection might favor models containing more
 species, and why recognizing more than three species might be warranted.
description: SDM_nuclearBEAST XML files containing the final nuclear gene alignments and species delimitation model (SDM) assignments.SDM_SNP.v2SNAPP/BEAST2 XML files for SNP-based species delimitation in coast horned lizards.SDM_snps.tar.gz
DOI: 10.5061/dryad.m2187
title: Data from: Opportunistic data reveal widespread species turnover in Enallagma damselflies at biogeographical scales

description: An information tradeoff exists between systematic presence/absence surveys
 and purely opportunistic (presence-only) records for investigating the
 geography of community structure. Opportunistic species occurrence data
 may be of relatively limited quality, but typically involves numerous
 observations and species. Given the quality-quantity tradeoff, what can
 opportunistic data reveal about spatial patterns in community structure?
 Here we explore opportunistic data in describing geographic patterns of
 species composition, using over 4,600 occurrence records of Enallagma
 damselflies in the United States. We tested phylogenetic scale (genus
 level, Enallagma major clades, Enallagma subclades) and spatial extent
 (U.S. vs. watershed regions), hypothesizing that nonrandom structure is
 more likely at larger spatial extents. We also used three sets of
 systematic presence/absence surveys as a benchmark for validating
 opportunistic presence-only records. Null model analysis of matrix
 coherence and species replacements showed many cases of nonrandom
 structure and widespread species turnover. This outcome was repeated
 across spatial and environmental gradients and community composition
 scenarios. Turnover dominated across the U.S. and two watersheds spanning
 biogeographic boundaries, but random assemblages were prevalent in a third
 watershed with limited longitudinal extent. Turnover also pervaded each
 level of phylogeny. Opportunistic presence-only datasets showed identical
 patterns as systematic presence/absence datasets. These results indicate
 that extensive opportunistic data can be used to detect species turnover,
 especially at geographic scales where range margins are crossed.
description: Species occurrence
 matrix and locality dataThis table summarizes
 the 4608 observation localities and 29 species used for analyses. For each
 locality it gives the species occurrences ("1"), latitude,
 longitude, ordination value for temperature ('Temp'), and
 ordination value for precipitation ('Precip'). Note that
 temperature and precipitation data were unavailable for five observation
 localities. This table also designates the localities found within
 selected watershed regions (ark = Arkansas-White-Red; ca = California; ma
 = Mid Atlantic). The table, along with species information in Table 1 of
 the publication, can be used to reproduce all our analyses and
 results.Dryad.data.xlsx
DOI: 10.5061/dryad.n1m8d
title: Data from: Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range

description: Reductions in body size are increasingly being identified as a response to
 climate warming. Here we present evidence for a case of such body
 shrinkage, potentially due to malnutrition in early life. We show that an
 avian long-distance migrant (red knot, Calidris canutus canutus), which is
 experiencing globally unrivaled warming rates at its high-Arctic breeding
 grounds, produces smaller offspring with shorter bills during summers with
 early snowmelt. This has consequences half a world away at their tropical
 wintering grounds, where shorter-billed individuals have reduced survival
 rates. This is associated with these molluscivores eating fewer deeply
 buried bivalve prey and more shallowly buried seagrass rhizomes. We
 suggest that seasonal migrants can experience reduced fitness at one end
 of their range as a result of a changing climate at the other end.
description: vanGils_Fig2_Arctic_climateThis file contains annual data on high-Arctic climate data (also presented in Table S1).vanGils_Fig2_Polish_biometryThis file contains the biometry measured on juvenile red knots caught in Gdańsk Bay.vanGils_Fig3A_Mauritania_stable_isotopesThis file contains the stable isotope data on 676 juvenile and 1664 adult red knots at their wintering site Banc d'Arguin (Mauritania).vanGils_Fig3B_Mauritania_prey_depthThis file contains the prey depth distributions estimated for the three food types in Mauritania.vanGils_Fig4_resighting_historyThis file contains the resighting history of 690 juvenile and 1691 adult red knot caught in Mauritania.breeding groundspolygon of the breeding grounds of red knots at Taymir Peninsulaarea.longlat.RDataData manipulation high-Arctic climateThis R script handles the data on high-Arctic climate with respect to temperature, NDVI and snow.DataManipulation.R
DOI: 10.15468/dl.kxtq5n
title: Occurrence Download

description: A dataset containing 7440 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Specimen",
 "TaxonKey is one of (Hymenophyllum capillare, Hymenophyllum hirsutum, Hymenophyllum kuhnii, Crepidomanes africanum, Didymoglossum ballardianum, Didymoglossum chamaedrys, Crepidomanes chevalieri, Crepidomanes clarenceanum, Trichomanes crispiforme, Polyphlebium diaphanum, Abrodictyum dregei, Didymoglossum erosum, Crepidomanes fallax, Vandenboschia gigantea, Abrodictyum guineense, Didymoglossum liberiense, Crepidomanes parvulum, Crepidomanes melanotrichum, Crepidomanes mettenii)"
 ]
}

 The dataset includes 7440 records from 219 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000527-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.87486
title: Data from: Characteristics of patients included and enrolled in studies on the prognostic value of serum biomarkers for prediction of post-concussion symptoms following a mild traumatic brain injury: a systematic review

description: Objective: Mild traumatic brain injury (mTBI) has been insufficiently
 researched and its definition remains elusive. Investigators are
 confronted by heterogeneity in patients, mechanism of injury and outcomes.
 Findings are thus often limited in generalizability and clinical
 application. Serum protein biomarkers are increasingly assessed to enhance
 prognostication of outcomes but their translation into clinical practice
 has yet to be achieved. A systematic review was performed to describe the
 adult populations included and enrolled in studies that evaluated the
 prognostic value of protein biomarkers to predict post-concussion symptoms
 following a mTBI. Data sources: Searches of MEDLINE, EMBASE, CENTRAL,
 CINAHL, Web of Science, PsycBITE, and PsycINFO up to October 2016. Data
 selection and extraction: Two reviewers independently screened for
 potentially eligible studies, extracted data and assessed the overall
 quality of evidence by outcome using the Grading of Recommendations
 Assessment, Development and Evaluation approach. Results: A total of
 23,298 citations were obtained from which 166 manuscripts were reviewed.
 Thirty-six cohort studies (2,812 patients) having enrolled between 7 and
 311 patients (median 89) fulfilled our inclusion criteria. Most studies
 excluded patients based on advanced age (n=10 (28%)), neurologic disorders
 (n=20 (56%)), psychiatric disorders (n=17 (47%)), substance abuse
 disorders (n=13 (36%)) or previous TBI (n=10 (28%)). Twenty-one studies
 (58%) used at least two of these exclusion criteria. The pooled mean age
 of included patients was 39.3 (SD 4.6) years old (34 studies). The
 criteria used to define a mTBI were inconsistent. The most frequently
 reported outcome was post-concussion syndrome (PCS) using the Rivermead
 Post-Concussion Symptoms Questionnaire (n=18 (50%)) with follow-ups
 ranging from 7 days to 5 years after the mTBI. Conclusions: Most studies
 have recruited samples that are not representative and generalizable to
 the mTBI population. These exclusion criteria limit the potential use and
 translation of promising serum protein biomarkers to predict
 post-concussion symptoms.
description: BMJ. Supplement -
 eFigure 1 (age)BMJ. Supplement - eTable
 1 (EMBASE Search Strategy)BMJ. Supplement - eTable
 2 (Congress)BMJ. Supplement - eTable
 3 (Prisma Checklist)
DOI: 10.5061/dryad.k7r52
title: Data from: Early reproductive investment, senescence and lifetime reproductive success in female Asian elephants

description: The evolutionary theory of senescence posits that as the probability of
 extrinsic mortality increases with age, selection should favour early-life
 over late-life reproduction. Studies on natural vertebrate populations
 show early reproduction may impair later-life performance, but the
 consequences for lifetime fitness have rarely been determined, and little
 is known of whether similar patterns apply to mammals which typically live
 for several decades. We used a longitudinal dataset on Asian elephants
 (Elephas maximus) to investigate associations between early-life
 reproduction and female age-specific survival, fecundity and offspring
 survival to independence, as well as lifetime breeding success (lifetime
 number of calves produced). Females showed low fecundity following sexual
 maturity, followed by a rapid increase to a peak at age 19 and a
 subsequent decline. High early life reproductive output (before the peak
 of performance) was positively associated with subsequent age-specific
 fecundity and offspring survival, but significantly impaired a
 female's own later-life survival. Despite the negative effects of
 early reproduction on late-life survival, early reproduction is under
 positive selection through a positive association with lifetime breeding
 success. Our results suggest a trade-off between early reproduction and
 later survival which is maintained by strong selection for high early
 fecundity, and thus support the prediction from life history theory that
 high investment in reproductive success in early life is favoured by
 selection through lifetime fitness despite costs to later-life survival.
 That maternal survival in elephants depends on previous reproductive
 investment also has implications for the success of (semi-)captive
 breeding programmes of this endangered species.
description: Hayward et al_Elephant
 senescence_JEB dryad dataContains two dataframes
 in an Excel spreadsheet. The first of these gives age-specific fecundity
 and survival for all female elephants aged &gt;5 years. All abbreviations
 are as described in the main text. These contain data allowing analysis of
 reproduction across life as well as survival and reproduction in later
 life as a function of age and early-life fecundity and the association
 between early-life fecundity and lifetime breeding success. The second
 dataframe contains data on calf survival, which may be used for the
 analysis of age-specific calf survival in later life in relation to
 early-life fecundity.
DOI: 10.5061/dryad.3g2n7dc
title: Data from: Gene signature of the human pancreatic ε-cell

description: The ghrelin producing ε-cell represents the fifth endocrine cell type in
 human pancreatic islets. The abundance of ε-cells in adult pancreas is
 extremely low, which has hampered the investigation on the molecular
 pathways regulating the development and the function of this cell type. In
 this study, we explored the molecular features defining the function of
 pancreatic ε-cells isolated from adult non-diabetic donors using
 single-cell RNA sequencing technology. We focus on transcription factors,
 cell surface receptors and genes involved in metabolic pathways that
 contribute to regulation of cellular function. Furthermore, the genes that
 separate ε-cells from the other islet endocrine cell types are presented.
 This study expands prior knowledge about the genes important for the
 function of the ε-cell during development and provides a resource to
 interrogate the transcriptome of this rare human islet cell type.
description: Supplemental Figure
 1Supplemental Figure
 2Supplemental table
 1Supplemental table
 2Supplemental table
 3Supplemental table
 4Supplemental table
 5
DOI: 10.5061/dryad.74mn5
title: Data from: Asynchronous diversification of snakes in the North American warm deserts

description: Aim: We quantify the degree to which co-distributed snakes across the
 Cochise Filter Barrier (CFB) have a shared history of population
 divergence and estimate the timing of divergence for each taxon pair.
 Location: North America. Methods: A single locus dataset was collected (n
 = 747 individuals) for 12 snake taxon pairs. Phylogeographical structure
 was estimated for each taxon. Redundancy analyses were used to assess the
 importance of geographical distance, climate and putative barriers to gene
 flow in structuring genetic diversity. Hierarchical approximate Bayesian
 computation was used to estimate the magnitude of synchronicity in
 divergence times across a well-documented phylogeographical barrier.
 Lastly, gene divergence and population divergence times were estimated
 using multiple methods. Results: There is substantial phylogeographical
 structure in many of the snake taxa, particularly at the CFB. A model
 containing distance, climate and barriers explained the greatest amount of
 genetic variation in nearly all taxa. When each variable was examined
 separately, climate explained the most variation. The hABC model testing
 indicates that there is overwhelming support for asynchronous
 phylogeographical histories within these co-distributed taxa. Estimated
 divergence times range throughout the Quaternary and Neogene. Main
 Conclusions: We demonstrate that the 12 snake taxon pairs studied here
 have diversified within the desert Southwest forming distinct Sonoran and
 Chihuahuan populations, illustrating the importance of this region in
 driving diversification in North American taxa. Although these groups
 exhibit the same pattern of lineage formation, there is strong support for
 asynchronous diversification and little concordance in divergence time
 estimates.
description: RDA_code_from_Myers_et_al_2016.RR script for RDA analysislampropeltisL. getula fasta filelampropeltis_pointsCollecting localities for L. getula specimensRhinocheilus leconteiRhinocheilus lecontei tree filerhino.trePituophis cateniferPituophis catenifer tree file from Beastpituophis.treArizona elegansA. elegans tree file from Beastarizona.trelampropeltis getulaLamp. getula tree from BeastL_getula_mu.treHypsiglena torquataHypsiglena torquata tree file from Beasthypsi_mu.trethamnophis marcianusthamnophis marcianus tree file from Beastthamnophis.treCrotalus atroxCrotalus atrox tree fileC_atrox.treTrimorphodonTrimorphodon tree file from Beasttrimorphodon.treCrotalus molossusCrot molossus tree file from BeastC_mol.treCrotalus scutulatusCrot scutulatus tree file from BeastC_scut.tremasticophis flagellumMast. flagellum tree file from Beastmasticophis_cfb.treSalvadora hexalepisSal. hexalepis tree file from Beastsalv_hex.tre
DOI: 10.5061/dryad.4nj8t
title: Data from: The correlation between colouration and exploration behaviour varies across hierarchical levels in a wild passerine bird

description: IIn vertebrates, darker individuals are often found to be more active and
 willing to take risks (representing characteristics of a ‘proactive’
 coping style), whereas lighter individuals are instead more cautious and
 less active (representing characteristics of a ‘reactive’ coping style).
 It is thus generally expected that melanin-based colouration and
 proactivity form a suite of positively integrated traits at the
 among-individual level. Here we use a multi-generational pedigree of
 free-living great tits (Parus major) to partition variation in, and the
 correlation between, melanin-based breast stripe (‘tie’) size and
 exploration behaviour (a proxy for coping style) into its among- and
 within-individual components. We show that both traits harbour heritable
 variation. Against predictions, tie size and speed of exploration were
 negatively correlated at the among-individual level due to the combined
 influences of permanent environmental and additive genetic effects. By
 contrast, the two traits were weakly positively correlated within
 individuals (i.e., individuals increasing in tie size after moult tended
 to become more explorative). The patterns of among-individual covariance
 were not caused by correlational selection as we found additive and
 opposite selection pressures acting on the two traits. These findings
 imply that testing hypotheses regarding the existence of a ‘syndrome’ at
 the among-individual level strictly requires variance partitioning to
 avoid inappropriate interpretations as the negative ‘unpartitioned’
 phenotypic correlation between exploration and tie size resulted from
 counteracting effects of within- and among-individual correlations.
 Identifying sources and levels of (co)variation in phenotypic traits is
 thus critical to our understanding of biological patterns and evolutionary
 processes.
description: data quantitative
 genetic analyses Nicolaus et al 2016file containing all the
 data used for the quantitative genetic analyses of exploratory behaviour
 and tie size of the Lauwersmeer great tit populationdata QG Nicolaus et
 al.xlsxphenotypic pedigree
 Nicolaus et al 2016pedigree file of the
 Lauwersmeer great tit populationdata selection analyses
 Nicolaus et al 2016file containing the data
 used for the correlational selection analysesdata selection analyses
 Nicolaus et al.xlsx
DOI: 10.5061/dryad.gt178
title: Data from: Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica

description: Local adaptation is important in evolutionary processes and speciation. We
 used multiple tests to identify several candidate genes that may be
 involved in local adaptation from 1026 loci in 14 natural populations of
 Cryptomeria japonica, the most economically important forestry tree in
 Japan. We also studied the relationships between genotypes and
 environmental variables to obtain information on the selective pressures
 acting on individual populations. Outlier loci were mapped onto a linkage
 map, and the positions of loci associated with specific environmental
 variables are considered. The outlier loci were not randomly distributed
 on the linkage map; linkage group 11 was identified as a genomic island of
 divergence. Three loci in this region were also associated with
 environmental variables such as mean annual temperature, daily maximum
 temperature, maximum snow depth, and so on. Outlier loci identified with
 high significance levels will be essential for conservation purposes and
 for future work on molecular breeding.
description: CJ_geno_1026SNPThe genotype data of 1026 SNPs in 14 populations with 186 individuals.