cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jq712
title: Data from: Southern montane populations did not contribute to the recolonization of West Siberian Plain by Siberian larch (Larix sibirica): a range-wide analysis of cytoplasmic markers

description: While many species were confined to southern latitudes during the last
 glaciations, there has lately been mounting evidence that some of the most
 cold-tolerant species were actually able to survive close to the ice
 sheets. The contribution of these higher latitude outposts to the main
 recolonization thrust remains, however, untested. In the present study, we
 use the first range-wide survey of genetic diversity at cytoplasmic
 markers in Siberian larch (Larix sibirica; four mitochondrial (mt) DNA
 loci and five chloroplast (cp) DNA SSR loci) to (i) assess the relative
 contributions of southern and central areas to the current L. sibirica
 distribution range; and (ii) date the last major population expansion in
 both L. sibirica and adjacent Larix species. The geographic distribution
 of cpDNA variation was uninformative, but that of mitotypes clearly
 indicates that the southernmost populations, located in Mongolia and the
 Tien-Shan and Sayan Mountain ranges, had a very limited contribution to
 the current populations of the central and northern parts of the range. It
 also suggests that the contribution of the high latitude cryptic refugia
 was geographically limited and that most of the current West Siberian
 Plain larch populations likely originated in the foothills of the Sayan
 Mountains. Interestingly, the main population expansion detected through
 Approximate Bayesian Computation (ABC) in all four larch species
 investigated here pre-dates the LGM, with a mode in a range of 220 000–1
 340 000 years BP. Hence, L. sibirica, like other major conifer species of
 the boreal forest, was strongly affected by climatic events pre-dating the
 Last Glacial Maximum.
description: DataIndividual by individual
 mtDNA and cpDNA genotype data, locations of studied populations,
 distribution of haplotypes in populations and primary diversity
 estimates.
DOI: 10.5061/dryad.68fn0
title: Data from: The conquering of North America: dated phylogenetic and biogeographic inference of migratory behavior in bee hummingbirds

description: Background: Geographical and temporal patterns of diversification in bee
 hummingbirds (Mellisugini) were assessed with respect to the evolution of
 migration, critical for colonization of North America. We generated a
 dated multilocus phylogeny of the Mellisugini based on a dense sampling
 using Bayesian inference, maximum-likelihood and maximum parsimony
 methods, and reconstructed the ancestral states of distributional areas in
 a Bayesian framework and migratory behavior using maximum parsimony,
 maximum-likelihood and re-rooting methods. Results: All phylogenetic
 analyses confirmed monophyly of the Mellisugini and the inclusion of
 Atthis, Calothorax, Doricha, Eulidia, Mellisuga, Microstilbon, Myrmia,
 Tilmatura, and Thaumastura. Mellisugini consists of two clades: (1) South
 American species (including Tilmatura dupontii), and (2) species
 distributed in North and Central America and the Caribbean islands. The
 second clade consists of four subclades: Mexican (Calothorax, Doricha) and
 Caribbean (Archilochus, Calliphlox, Mellisuga) sheartails, Calypte, and
 Selasphorus (incl. Atthis). Coalescent-based dating places the origin of
 the Mellisugini in the mid-to-late Miocene, with crown ages of most
 subclades in the early Pliocene, and subsequent species splits in the
 Pleistocene. Bee hummingbirds reached western North America by the end of
 the Miocene and the ancestral mellisuginid (bee hummingbirds) was
 reconstructed as sedentary, with four independent gains of migratory
 behavior during the evolution of the Mellisugini. Conclusions: Early
 colonization of North America and subsequent evolution of migration best
 explained biogeographic and diversification patterns within the
 Mellisugini. The repeated evolution of long-distance migration by
 different lineages was critical for the colonization of North America,
 contributing to the radiation of bee hummingbirds. Comparative
 phylogeography is needed to test whether the repeated evolution of
 migration resulted from northward expansion of southern sedentary
 populations.
description: AK1_I5_FileAK1_I5_File: Bee hummingbirds sequences of the adenylate kinase 1 intron 5 (nuDNA).FBG_I7_FileFBG_I7_File: Bee hummingbirds sequences of the fibrinogen beta chain intron (nuDNA).ODC_1_FileODC_1_File: Bee hummingbirds sequences of the ornithine decarboxylase 1 introns 6 and 7 intervening exon (nuDNA).MUSK_I3_FileMUSK_I3_File: Bee hummingbirds sequences of the Z-linked muscle, skeletal, receptor tyrosine kinase intron 3 (nuDNA).ND2_FileND2_File: Bee hummingbirds sequences of nicotinamide dehydrogenase 9 subunit 2 (mtDNA).ND4_FileND4_File: Bee hummingbirds sequences of nicotinamide dehydrogenase subunit 4 (mtDNA).
DOI: 10.5281/zenodo.18265774
title: Simulation files (Cases 0-3) and video files for ApJ Article "A Dynamo Confinement Scenario for the Solar Tachocline and its Implications for Spin-down in the Radiative Spreading Regime"
DOI: 10.5281/zenodo.18265773
title: Simulation files (Cases 0-3) and video files for ApJ Article "A Dynamo Confinement Scenario for the Solar Tachocline and its Implications for Spin-down in the Radiative Spreading Regime"
DOI: 10.5061/dryad.0k8c4
title: Data from: Usage of unscheduled hospital care by homeless individuals in Dublin, Ireland: a cross-sectional study

description: Objectives: Homeless people lack a secure, stable place to live, and
 experience higher rates of serious illness than the housed population.
 Studies, mainly from the US, have reported increased use of unscheduled
 health care by homeless individuals. We compared the use of unscheduled ED
 and inpatient care between housed and homeless hospital patients in a
 high-income European setting. Setting: A large university teaching
 hospital serving the south inner city in Dublin, Ireland. Patient data is
 collected on an electronic patient record within the hospital.
 Participants: We carried out an observational cross-sectional study using
 data on all ED visits (n=47,174) and all unscheduled admissions under the
 general medical take (n=7,031) in 2015. Primary and Secondary Outcome
 Measures: The address field of the hospital’s electronic patient record
 was used to identify patients living in emergency accommodation or rough
 sleeping (hereafter referred to as homeless). Data on demographic details,
 length of stay and diagnoses was extracted. Results: In comparison to
 housed individuals in the hospital catchment area, homeless individuals
 had higher rates of ED attendance (0.16 attendances per person/annum vs
 3.0 attendances per person/annum respectively) and inpatient bed days (0.3
 bed days per person/annum vs 4.4 bed days per person/annum. The rate of
 leaving ED before assessment was higher in homeless individuals (40% of ED
 attendances vs 15% of ED attendances in housed individuals). The mean age
 of homeless medical inpatients was 44.19 (95% CI 42.98-45.40), whereas
 that of housed patients was 61.20 (95% CI 60.72-61.68). Homeless patients
 were more likely to terminate an inpatient admission against medical
 advice (15% of admissions vs 2% of admissions in homeless individuals).
 Conclusion: Homeless patients represent a significant proportion of ED
 attendees and medical inpatients. In contrast to housed patients, the bulk
 of usage of unscheduled care by homeless people occurs in individuals
 younger than 65.
description: MedicalAdmissionsDe-identified data on medical inpatient admissions (age rounded to within 10 years).
DOI: 10.5061/dryad.f448b91
title: Data from: Using museum specimens to track morphological shifts through climate change

description: Museum specimens offer a largely untapped resource for detecting
 morphological shifts in response to climate change. However, morphological
 shifts can be obscured by shifts in phenology or distribution or sampling
 biases. Additionally, interpreting phenotypic shifts requires
 distinguishing whether they result from plastic or genetic changes.
 Previous studies using collections have documented consistent historical
 size changes, but the limited studies of other morphological traits have
 often failed to support, or even test, hypotheses. We explore the
 potential of collections by investigating shifts in the
 functionally-significant coloration of a montane butterfly, Colias meadii,
 over the past 60 years within three North American geographic regions. We
 find declines in ventral wing melanism, which correspond to reduced
 absorption of solar radiation and thus reduced risk of overheating, in two
 regions. However, contrary to expected responses to climate warming, we
 find melanism increases in the most thoroughly sampled region.
 Relationships among temperature, phenology, and morphology vary across
 years and complicate the distinction between plastic and genetic
 responses. Differences in these relationships may account for the
 differing morphological shifts among regions. Our findings highlight the
 promise of using museum specimens to test mechanistic hypotheses for
 shifts in functional traits, which is essential for deciphering
 interacting responses to climate change.
description: ColiasMuseumDataSpecimen Data in csv formatFullDataColiasMuseums_publish.csvspatial_functionsR code for spatial analysis functions. See https://github.com/lbuckley/MuseumTraits for full code.
DOI: 10.5061/dryad.bk583
title: Data from: Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

description: Farmed fish are typically genetically different from wild conspecifics.
 Escapees from fish farms may contribute one-way gene flow from farm to
 wild gene pools, which can depress population productivity, dilute local
 adaptations and disrupt coadapted gene complexes. Here, we reanalyse data
 from two experiments (McGinnity et al., 1997, 2003) where performance of
 Atlantic salmon (Salmo salar) progeny originating from experimental
 crosses between farm and wild parents (in three different cohorts) were
 measured in a natural stream under common garden conditions. Previous
 published analyses focussed on group-level differences but did not account
 for pedigree structure, as we do here using modern mixed-effect models.
 Offspring with one or two farm parents exhibited poorer survival in their
 first and second year of life compared with those with two wild parents
 and these group-level inferences were robust to excluding outlier
 families. Variation in performance among farm, hybrid and wild families
 was generally similar in magnitude. Farm offspring were generally larger
 at all life stages examined than wild offspring, but the differences were
 moderate (5–20%) and similar in magnitude in the wild versus hatchery
 environments. Quantitative genetic analyses conducted using a Bayesian
 framework revealed moderate heritability in juvenile fork length and mass
 and positive genetic correlations (&gt;0.85) between these
 morphological traits. Our study confirms (using more rigorous statistical
 techniques) previous studies showing that offspring of wild fish
 invariably have higher fitness and contributes fresh insights into
 family-level variation in performance of farm, wild and hybrid Atlantic
 salmon families in the wild. It also adds to a small, but growing, number
 of studies that estimate key evolutionary parameters in wild salmonid
 populations. Such information is vital in modelling the impacts of
 introgression by escaped farm salmon.
description: Representation
 dataRepresentation data for
 all cohorts and sampling occasions/life stagesSize at age
 dataSize at age data for all
 cohorts and sampling occasions/life stages.
DOI: 10.5061/dryad.k04q2kd
title: Data from: Food-web structure varies along environmental gradients in a high-latitude marine ecosystem

description: Large-scale patterns in species diversity and community composition are
 associated with environmental gradients, but the implications of these
 patterns for food-web structure are still unclear. Here, we investigated
 how spatial patterns in food-web structure are associated with
 environmental gradients in the Barents Sea, a highly productive shelf sea
 of the Arctic Ocean. We compared food webs from 25 subregions in the
 Barents Sea and examined spatial correlations among food-web metrics, and
 between metrics and spatial variability in seawater temperature, bottom
 depth and number of days with ice cover. Several food-web metrics were
 positively associated with seawater temperature: connectance, level of
 omnivory, clustering, cannibalism, and high variability in generalism,
 while other food-web metrics such as modularity and vulnerability were
 positively associated with sea ice and negatively with temperature.
 Food-web metrics positively associated with habitat heterogeneity were:
 number of species, link density, omnivory, path length, and trophic level.
 This finding suggest that habitat heterogeneity promotes food-web
 complexity in terms of number of species and link density. Our analyses
 reveal that part of the variation in food-web structure along the
 environmental gradients is related to species turnover, however the higher
 interaction turnover compared to species turnover along these gradients
 indicates a consistent modification of the food-web structure along
 environmental gradients. This could indicate that interacting species
 co-vary in space. In conclusion, our study shows how environmental
 heterogeneity via environmental filtering, not only drives turnover in
 species composition, but also how it influences the structure of food webs
 over large spatial scales.
description: Barents Sea food
 websThe excel file contains
 25 food webs of the Barents Sea. Sheet 1: Species names; Sheet 2.
 Subregion-by-species matrix; Sheet 3: Pairwise list of trophospecies
 interactions; Sheet 4: The Barents Sea metaweb.
DOI: 10.5281/zenodo.18298140
title: Supplementary-Unraveling sediment organic carbon sources in coastal wetlands:Insights from fraction-specific signatures
DOI: 10.15468/dl.38nryn
title: Occurrence Download

description: A dataset containing 613 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Historical biogeographic assessment of intertidal cirriped species along the Iberian coast and north of Morocco by Fischer-Piette"
 ]
}

 The dataset includes 613 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000674-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m58q16m
title: Data from: Dynamic colonization history in a rediscovered Isle Royale carnivore

description: Island ecosystems are globally threatened, and efforts to restore
 historical communities are widespread. Such conservation efforts should be
 informed by accurate assessments of historical community composition to
 establish appropriate restoration targets. Isle Royale National Park is
 one of the most researched island ecosystems in the world, yet little is
 actually known about the biogeographic history of most Isle Royale taxa.
 To address this uncertainty and inform restoration targets, we determined
 the phylogeographic history of American martens (Martes americana), a
 species rediscovered on Isle Royale 76 years after presumed extirpation.
 We characterized the genetic composition of martens throughout the Great
 Lakes region using nuclear and mitochondrial markers, identified the
 source of Isle Royale martens using genetic structure analyses, and used
 demographic bottleneck tests to evaluate (eliminate redundancy of test). 3
 competing colonization scenarios. Martens exhibited significant structure
 regionally, including a distinct Isle Royale cluster, but mitochondrial
 sequences revealed no monophyletic clades or evolutionarily significant
 units. Rather, martens were historically extirpated and recolonized Isle
 Royale from neighbouring Ontario, Canada in the late 20th century. These
 findings illustrate the underappreciated dynamics of island communities,
 underscore the importance of historical biogeography for establishing
 restoration baselines, and provide optimism for extirpated and declining
 Isle Royale vertebrates whose reintroductions have been widely debated.
description: Microsatellite Genotype
 Data - STRUCTURAMA inputSTRUCTURAMA file
 containing genotypic microsatellite data.SupportingData1_genotypes.inSupporting Data 2_SequencesCytB and CO1 sequences with associated GenBank accession numbers.
DOI: 10.5061/dryad.8p800
title: Data from: Phylogenetic relationships in Calyptranthes (Myrtaceae) with particular emphasis on its monophyly relative to Myrcia s. l.

description: Calyptranthes is the largest clade of Myrcia s. l., and is a group of
 considerable diversity in the threatened Atlantic forest biome of Brazil,
 as well as in the Amazon, Caribbean, and Cerrado. Here an expanded,
 geographically and morphologically representative sample of Calyptranthes
 is tested for monophyly; the majority of species are shown to emerge as a
 monophyletic clade embedded within Myrcia s. l. A single species,
 Calyptranthes multiflora, emerges in an independent clade, suggesting
 wider non-monophyly. Patterns of relationships within the group are
 detected, and these correlate more closely with geography than with
 morphology, and suggest that the oldest lineages of Calyptranthes are from
 what is now the Amazon forest, with later radiations to the Caribbean,
 Atlantic forest, and Cerrado biomes.
description: Matrix in plain
 textMatrix in plain text
 corresponding to publication named in submission. Please contact the
 corresponding author for taxonomic and nomenclatural details of
 accessions.Calyptranthes_dryad.txt
DOI: 10.15468/dl.dckvsh
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of northeastern Portugal"
 ]
}

 The dataset includes 659 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000675-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.17sr0
title: Data from: Reproductive character displacement of epicuticular compounds and their contribution to mate choice in Drosophila subqinaria and D. recens

description: Interactions between species can alter selection on sexual displays used
 in mate choice within species. Here we study the epicuticular pheromones
 of two Drosophila species that overlap partially in geographic range and
 are incompletely reproductively isolated. D. subquinaria shows a pattern
 of reproductive character displacement against D. recens, and partial
 behavioral isolation between conspecific sympatric vs. allopatric
 populations, whereas D. recens shows no such variation in mate choice.
 First, using manipulative perfuming experiments, we show that females use
 pheromones as signals for mate discrimination both between species and
 among populations of D. subquinaria. Second, we show that patterns of
 variation in epicuticular compounds, both across populations and between
 species, are consistent with those previously shown for mating
 probabilities: pheromone compositions differ between populations of D.
 subquinaria that are allopatric vs. sympatric with D. recens, but are
 similar across populations of D. recens regardless of overlap with D.
 subquinaria. We also identify differences in pheromone composition among
 allopatric regions of D. subquinaria. In sum, our results suggest that
 epicuticular compounds are key signals used by females during mate
 recognition, and that these traits have diverged among D. subquinaria
 populations in response to reinforcing selection generated by the presence
 of D. recens.
description: Epicuticular compounds
 after perfumingThis file contains the
 raw GC data from perfuming experiments. The 'target male' is the
 type of male that was extracted, and 'males perfumed with' shows
 the type of males that the target male was housed with for 7 days before
 extraction. Also included are control non-perfumed males. GC data is raw
 and peaks are labeled 1 through 23. Each line in the file has the data for
 one male.perfuming_CHC_dryad.txtCHC character displacement data - femalesThis file contains the raw GC data for females included in the assay for reproductive character displacement. Each line has the data for one female included in the study. For each female, the species, population, and whether the population is from the region of sympatry or allopatry is indicated. See Table 1 of the paper for a description of the population abbreviations. GC data is raw and peaks are labeled 1 through 21.RCD_CHC_data_females_dryad.txtCHC character displacement data - malesThis file contains the raw GC data for males included in the assay for reproductive character displacement. Each line has the data for one male included in the study. For each male, the species, population, and whether the population is from the region of sympatry or allopatry is indicated. See Table 1 of the paper for a description of the population abbreviations. GC data is raw and peaks are labeled 1 through 24.RCD_CHC_data_males_dryad.txt
DOI: 10.5061/dryad.6jp04633
title: Data from: Costs and benefits of polyandry in a placental poeciliid fish Heterandria formosa are in accordance with the parent-offspring conflict theory of placentation

description: In viviparous species, a conflict over maternal resource allocation may
 arise between mothers and embryos, between siblings, and between maternal
 and paternal genes within an embryo due to relatedness asymmetries. We
 performed two experiments to study the effects of polyandry and brood
 relatedness on offspring growth in a placental fish (Heterandria formosa).
 Polyandry was beneficial as it increased the probability of pregnancy,
 possibly to avoid genetic incompatibility. However, females mated to four
 males produced offspring that had a longer maturation time than those of
 monandrous females. When within-brood relatedness was manipulated, the
 size of the newborn offspring decreased with time in low relatedness
 treatment, while in highly related broods offspring size was constant. Low
 within-brood relatedness may lead to less cooperative offspring in terms
 of resource extraction from the mother, which may lead to impaired
 development during gestation. Offspring conflict may thus reduce the
 benefits of polyandry in viviparous species.
description: male_behaviour_polyandryThis data file contains data about male behaviour during the polyandry experimentpolyandry_sl_at_birthThis data file contains data on offspring sizes (standard length) at birth in the polyandry experimentpolyandry_male_offspringThis data file contains male offspring sizes and ages at maturity in the polyandry experimentpolyandry_female_offspringThis data file contains female offspring sizes and ages at maturity in the polyandry experimentpolyandry_number_of_offspring_producedThis data file contains numbers of offspring produced, proportion of dead-borne offspring and time until first birth in the polyandry experimentBrood_relatedness_offspring_sizesThis file contains offspring sizes at birth in the brood relatedness experiment.Brood_relatedness_survival_analysisThis file contains data used in survival analysis as well as offspring production data from the brood relatedness experiment.