cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ck44d
title: Data from: Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae)

description: Genetic diversity is essential for species to sustain their populations
 and evolutionary potential. In order to develop effective conservation
 strategies for rare species, it is necessary to understand differences in
 patterns of genetic diversity between common and rare species. Data about
 population genetic structure is important to design effective conservation
 strategies for rare species. In this study, we compared the genetic
 diversity and population genetic structure of a common species,
 Rhododendron weyrichii, to those of two rare species, Rhododendron sanctum
 and Rhododendron amagianum, with different geographic distributions. We
 analyzed five microsatellite loci in 16 populations of R. weyrichii, 9
 populations of R. sanctum, and 6 populations of R. amagianum. As expected,
 the level of genetic diversity indicated by allelic richness and gene
 diversity was lower for the rare species R. sanctum than for the common
 species R. weyrichii. However, there was no statistically significant
 difference in genetic diversity between R. weyrichii and the other rare
 species, R. amagianum. Analyses of the isolation-by-distance pattern,
 neighbor-joining trees, and Bayesian clustering indicated that R. sanctum
 had a strong population genetic structure whereas R. amagianum exhibited
 very weak genetic structure among populations and that there was moderate
 population genetic structure for R. weyrichii. Therefore, the degree and
 pattern of population genetic structure in each species was unrelated to
 its rarity and instead merely reflected its geographic distribution.
description: genotype data, three
 species of Rhododendron"genotype_data" contains genotypes of three species of Rhododendrons. This data was used in the paper entitled "Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae)" which is published from Tree Genetics and Genomes. Population number is corresponding to Figure 1 and Table 1 in the article.genotype_data.xls
DOI: 10.5061/dryad.p508s296
title: Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association

description: In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia
 facilitates its spread through vertical transmission via the eggs by
 inducing feminization of genetic males. The spread of feminizing Wolbachia
 within and across populations is therefore expected to influence mtDNA
 genetic structure by hitchhiking. To test this hypothesis, we analysed
 nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13
 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to
 100% of sampled females) was highly variable among populations. All three
 Wolbachia strains previously observed in A. vulgare were present (wVulC,
 wVulM and wVulP) with wVulC being the most prevalent (9 out of 13
 populations). The host showed a genetic structure on five microsatellite
 loci that is compatible with isolation by distance. The strong genetic
 structure observed on host mtDNA was correlated to Wolbachia prevalence:
 three mitotypes were in strong linkage disequilibrium with the three
 strains of Wolbachia. Neutrality tests showed that the mtDNA polymorphism
 is not neutral and we thus suggest that this unusual pattern of mtDNA
 polymorphism found in A. vulgare was due to Wolbachia.
description: mtDNAmtDNA sequences in
 Arlequin filetransect
 mitosequencecorrigé.arpMicrosatellitesGenetix file of microsatellite genotypes.transect fini1.gtxwolbachiaArlequin file of Wolbachia infection status
DOI: 10.5061/dryad.mr909
title: Data from: Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species

description: Landscape genetics is a powerful tool for conservation because it
 identifies landscape features that are important for maintaining genetic
 connectivity between populations within heterogeneous landscapes. However,
 using landscape genetics in poorly understood species presents a number of
 challenges, namely, limited life history information for the focal
 population and spatially biased sampling. Both obstacles can reduce power
 in statistics, particularly in individual-based studies. In this study, we
 genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to
 identify alternative statistical approaches that can be applied to poorly
 understood species in an individual-based framework. Badgers are protected
 in Wisconsin owing to an overall lack in life history information, so our
 study utilized partial redundancy analysis (RDA) and spatially lagged
 regressions to quantify how three landscape factors (Wisconsin River,
 Ecoregions and land cover) impacted gene flow. We also performed
 simulations to quantify errors created by spatially biased sampling.
 Statistical analyses first found that geographic distance was an important
 influence on gene flow, mainly driven by fine-scale positive spatial
 autocorrelations. After controlling for geographic distance, both RDA and
 regressions found that Wisconsin River and Agriculture were correlated
 with genetic differentiation. However, only Agriculture had an acceptable
 type I error rate (3–5%) to be considered biologically relevant.
 Collectively, this study highlights the benefits of combining robust
 statistics and error assessment via simulations and provides a method for
 hypothesis testing in individual-based landscape genetics.
description: WisconsinVariablesExplanatory and response variables for the regression and RDA analyses. Excel file includes geographic coordinates, first two sPCA axes scores, landscape variables, Wisconsin River, and level 3 Ecoregion categories for each individual.WIGenotypesGenotypes of all Wisconsin badgers in Genepop file format. All simulated populations had the same file format. For adegent to run correctly, this file must have a .gen extension, but diveRsity uses .txt.WI_DryadCodeAll R code for analyses including spatial autocorrelation, sPCA calculations, genetic diversity metrics, redundancy analysis, and spatial regressions.
DOI: 10.5061/dryad.52dk8
title: Data from: Heterozygosity-fitness correlations in a migratory bird: an analysis of inbreeding and single-locus effects

description: Studies in a multitude of taxa have described a correlation between
 heterozygosity and fitness, and usually conclude that this is evidence for
 inbreeding depression. Here we have used multi-locus heterozygosity
 estimates from 15 microsatellite markers to show evidence of
 heterozygosity-fitness correlations (HFCs) in a long-distance migratory
 bird, the light-bellied Brent goose. We found significant, positive
 heterozygosity-heterozygosity correlations between random subsets of the
 markers we employ, and no evidence that a model containing all loci as
 individual predictors in a multiple regression explained significantly
 more variation than a model with multi-locus heterozygosity as a single
 predictor. Collectively these results lend support to the hypothesis that
 the HFCs we have observed are a function of inbreeding depression.
 However, we do find that fitness correlations are only detectable in years
 where population-level productivity is high enough for the reproductive
 asymmetry between high and low heterozygosity individuals to become
 apparent. We suggest that lack of evidence of heterozygosity-fitness
 correlations in animal systems may be because heterozygosity is a poor
 proxy measure of inbreeding, especially when employing low numbers of
 markers, but alternatively because the asymmetries between individuals of
 different heterozygosities may only be apparent when environmental effects
 on fitness are less pronounced.
description: Individual
 GenotypesDryad Data for
 MEC110746.xlsx
DOI: 10.5061/dryad.2k376
title: Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia

description: We used a comparative approach to assess congruence of phylogeographic and
 genetic structure and diversity, demographic signals, and ratios of pollen
 to seed dispersal, in the context of species-specific life-history traits,
 for two widespread sympatric perennial plant species. We sampled Grevillea
 paradoxa and Melaleuca nematophylla across the species’ ranges throughout
 the Transitional Rainfall Zone and extending slightly into the Arid Zone
 of south-west Western Australia. Both species exhibited range-wide
 phylogeographic and contemporary genetic structure. Moderate haplotype
 diversity centred in populations on Banded Ironstone Formation (BIF)
 outcrops and within the Murchison River gorge supports a hypothesis of
 historical persistence and evolution in these mesic refugia. These
 features are likely to play important roles in evolutionary persistence
 with ongoing climate change. There was little evidence of particularly
 complex demographic histories for the region. More limited haplotype
 diversity, as well as more limited nuclear genetic diversity and
 connectivity, in G. paradoxa was consistent with predictions from
 life-history traits of shorter lifespan, lower fecundity, more limited
 seed dispersal, and shorter plants, but inconsistent with a prediction of
 greater pollen dispersal by bird pollinators. Low pollen to seed dispersal
 ratios suggest seed dispersal plays a greater than expected role in
 maintaining connectivity in this semi-arid landscape. The study highlights
 a need for research that integrates aspects of seed ecology and seed and
 pollen dispersal as well as phylogeographic and genetic patterns in
 Gondwanan shrublands and other semi-arid landscapes globally.
description: Genotype data for 12
 nuclear microsatellite loci for Grevillea paradoxa in GenAlEx
 format.Genotype data for 12
 nuclear microsatellite loci for Grevillea paradoxa in GenAlEx
 format.Gp
 ms data for dryad.xlsxGenotype data for 12
 nuclear microsatellite loci for Melaleuca nematophylla in GenAlEx
 format.Genotype data for 12
 nuclear microsatellite loci for Melaleuca nematophylla in GenAlEx
 format.Mn
 ms data for dryad.xlsxHaplotype data for
 Grevillea paradoxa in nexus format.Haplotype data for
 Grevillea paradoxa in nexus format.Gp haps data for
 dryad.nexHaplotype data for
 Melaleuca nematophylla in nexus format.Haplotype data for
 Melaleuca nematophylla in nexus format.Mn haps data for
 dryad.nex
DOI: 10.5061/dryad.p9b84
title: Data from: DNA barcoding reveals a largely unknown fauna of Gracillariidae leaf-mining moths in the Neotropics

description: Higher taxa often show increasing species richness towards tropical low
 latitudes, a pattern known as the latitudinal biodiversity gradient (LBG).
 A rare reverse LBG (with greater richness towards temperate high
 latitudes) is exhibited by Gracillariidae leaf-mining moths, in which most
 described species occur in northern temperate areas. We carried out the
 first assessment of gracillariid species diversity in two Neotropical
 regions to test whether the relatively low tropical species diversity of
 this family is genuine or caused by insufficient sampling and a strong
 taxonomic impediment. Field surveys in six French Guianan and one
 Ecuadorian site produced 516 gracillariid specimens that were DNA barcoded
 to facilitate identification and to match larvae inside leaf mines with
 adults. Species delineation from sequence data was approximated using
 Automatic Barcode Gap Discovery and Refined Single Linkage Analysis
 through the Barcode Index Number system, and the proportion of
 described/undescribed species was estimated after comparison with types of
 83% of described species. Locally, alpha-diversity far exceeds that of any
 known temperate fauna, with as many as 108 candidate species (59.3% as
 singletons) collected at one site, and with an estimated species richness
 lower bound of 240 species. Strikingly, at least 85% of the species
 collected as adults were found to be undescribed. Our sampling represents
 the most thorough survey of gracillariid species diversity in the
 Neotropics to date and the results from both our molecular and
 morphological analyses indicate that the current reverse LBG seen in this
 group is an artefact of insufficient sampling and a strong description
 deficit in the Neotropics.
description: 182_660-final1Barcode data used to generate Fig. S2
DOI: 10.5061/dryad.cb5f3
title: Data from: Evolution of alternative male morphotypes in oxyurid nematodes: a case of convergence?

description: Male dimorphism has been reported across different taxa, and is usually
 expressed as the coexistence of a larger morph with exaggerated male
 traits and a smaller one with reduced traits. The evolution and
 maintenance of male dimorphism are still poorly understood for several of
 the species in which it has been observed. Here, we analyse male
 dimorphism in several species of reptile parasitic nematodes of the genus
 Spauligodon, in which a major male morph (exaggerated morph), which
 presents the traditional male morphological traits reported for this
 taxon, coexists with a minor morph with reduced morphological traits (i.e.
 reduced genital papillae) resembling more closely the males of the sister
 genus Skrjabinodon than Spauligodon major males. Because of the level of
 uncertainty in the results of ancestral state reconstruction, it is
 unclear if the existence of male dimorphism in this group represents
 independent instances of convergent evolution or an ancestral trait lost
 multiple times. Also, although the number of major males per host was
 positively correlated with the number of females, the same did not hold
 true for minor males, whose presence was not associated with any other
 ecological factor. Nevertheless, the existence of male dimorphism in
 Spauligodon nematodes is tentatively interpreted as resulting from
 alternative reproductive tactics, with differences in presence and number
 of individuals as indicators of differences in fitness, with the lower
 numbers of minor males per host likely maintained by negative
 frequency-dependent selection.
description: Dataset
 MorphsDataset morphs: data
 used in the analyses of the factors related to MI and MA presence and
 abundance.Dataset_Morphs.csvSequence alignment of 18S ribosomal RNA (18S)Sequence alignment of 18S ribosomal RNA (18S) used for the phylogenetic analyses performed in MrBayes and PhyML (fasta format)Morphs18S.fastaSequence alignment of 28S ribosomal RNA (28S)Sequence alignment of 28S ribosomal RNA (28S) used for the phylogenetic analyses performed in MrBayes and PhyML (fasta format).Morphs28S.fastaSequence alignment of cytochrome oxidase subunit I (COI)Sequence alignment of cytochrome oxidase subunit I (COI) used for the phylogenetic analyses performed in MrBayes and PhyML (fasta format).MorphsCOI.fastaSequence alignment for the combined data-set of 28S and COISequence alignment for the combined data-set of 28S and COI used for the phylogenetic analyses performed in MrBayes used in ancestral state reconstruction (ASR).MorphsCOI_28S.fasta50% majority-rule consensus 28S and COI50% majority-rule consensus 28S and COI BI tree used in the ancestral state reconstruction (ASR) performed in MESQUITE.MorphsCOI_28S.nex.con.tre
DOI: 10.15468/dl.vf35ak
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Lampropeltis splendida",
 "Year 1960-2026"
 ]
}

 The dataset includes 79 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000807-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6121hj7
title: Data from: Prolonged fasting-induced metabolic signatures in human skeletal muscle of lean and obese men

description: Insulin resistance is a well-known physiological adaptation to prolonged
 fasting in healthy skeletal muscle. Obesity is associated with insulin
 resistance and metabolic inflexibility in skeletal muscle, and a
 pronounced increase in the risk of metabolic complications. Under the
 hypothesis that the metabolic traits of insulin resistance associated with
 prolonged fasting are different from insulin resistance associated with
 obesity, we examined nine obese and nine lean participants during 12 and
 72h of fasting, respectively. Insulin resistance in obese participants was
 associated with impaired insulin signaling, and reduced levels of
 glucose-6-phosphate and TCA-cycle intermediates. 72h of fasting in lean
 participants reduced insulin-stimulated glucose uptake to levels similar
 to obese participants fasted for 12h. This was associated with increased
 lipid oxidation, but not accumulation of diacylglycerol or acylcarnitines
 and impairment of insulin signaling. Prolonged fasting was associated with
 pronounced increases in β-hydroxybutyrate and β- hydroxybutyrylcarnitine
 levels in skeletal muscle suggesting augmented ketone body metabolism.
 Fasting induced insulin resistance may be a consequence of substrate
 competition. The underlying mechanism behind insulin resistance in obesity
 is thus not comparable to the physiological adaptations in skeletal muscle
 induced by prolonged fasting in lean participants.
description: datafiles
DOI: 10.7910/dvn/clujaw
title: Replication Data for: Fiscal Equalization in Nordic Municipalities: Institutions and Inequalities

description: Attach is the replication package for the paper.
DOI: 10.15468/dl.tjp6ch
title: Occurrence Download

description: A dataset containing 2642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alkekengi officinarum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2642 records from 187 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000808-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8dh7r
title: Data from: Age estimates for an adaptive lake fish radiation, its mitochondrial introgression, and an unexpected sister group: Sailfin silversides of the Malili Lakes system in Sulawesi

description: Background: The Malili Lakes system in central Sulawesi (Indonesia) is a
 hotspot of freshwater biodiversity in the Wallacea, characterized by
 endemic species flocks like the sailfin silversides (Teleostei:
 Atherinomorpha: Telmatherinidae) radiation. Phylogenetic reconstructions
 of these freshwater fishes have previously revealed two Lake Matano
 Telmatherina lineages (sharpfins and roundfins) forming an ancient
 monophyletic group, which is however masked by introgressive hybridization
 of sharpfins with riverine populations. The present study uses
 mitochondrial data, newly included taxa, and different external
 calibration points, to estimate the age of speciation and hybridization
 processes, and to test for phylogeographic relationships between
 Kalyptatherina from ancient islands off New Guinea, Marosatherina from SW
 Sulawesi, and the Malili Lakes flock. Results: Contrary to previous
 expectations, Kalyptatherina is the closest relative to the Malili Lakes
 Telmatherinidae, and Marosatherina is the sister to this clade.
 Palaeogeographic reconstructions of Sulawesi suggest that the closer
 relationship of the Malili Lakes radiation to Kalypatherina might be
 explained by a 'terrane-rafting' scenario, while
 proto-Marosatherina might have colonized Sulawesi by marine dispersal. The
 most plausible analysis conducted here implies an age of c. 1.9 My for the
 onset of divergence between the two major clades endemic to Lake Matano.
 Diversification within both lineages is apparently considerably more
 recent (c. 1.0 My); stream haplotypes present in the sharpfins are of even
 more recent origin (c. 0.4 My). Conclusions: Sulawesi's
 Telmatherinidae have most likely originated in the Sahul Shelf area, have
 possibly reached the island by both, marine dispersal and
 island/terrane-rafting, and have colonized the Malili Lakes system from
 rivers. Estimates for the split between the epibenthic sharpfins and the
 predominantly pelagic to benthopelagic roundfins in Lake Matano widely
 coincide with geological age estimates of this rift lake. Diversification
 within both clades clearly predates hybridization events with stream
 populations. For Lake Matano, these results support a scenario of initial
 benthic-pelagic divergence after colonization of the lake by riverine
 populations, followed by rapid radiation within both clades within the
 last 1 My. Secondary hybridization of stream populations with the
 sharpfins occurred more recently, and has thus most likely not contributed
 to the initial divergence of this benthic species flock.
description: BEAST tree
 filesBEAST MCC tree files of
 analyses [A]-[D].BEAST_tree_files.zip
DOI: 10.5061/dryad.708bb5kr
title: Data from: Prezygotic isolation between Saccharomyces cerevisiae and Saccharomyces paradoxus through differences in mating speed and germination timing

description: While prezygotic isolation between sympatric populations of closely
 related animal and plant species is well documented, far less is known
 about such evolutionary phenomena in sexual microbial species, as most are
 difficult to culture and manipulate. Using the molecular and genetic tools
 available for the unicellular fungus Saccharomyces cerevisiae, and
 applying them to S. paradoxus, we tested the behavior of individual cells
 from sympatric woodland populations of both species for evidence of
 prezygotic isolation. First, we confirmed previous observations that
 vegetative cells of both species mate preferentially with S. cerevisiae.
 Next, we found evidence for mate discrimination in spores, the stage in
 which outcrossing opportunities are most likely to occur. There were
 significant differences in germination timing between the species: under
 the same conditions, S. paradoxus spores do not begin germinating until
 almost all S. cerevisiae spores have finished. When germination time was
 staggered, neither species discriminated against the other, suggesting
 that germination timing is responsible for the observed mate
 discrimination. Our results indicate that the mechanisms of allochronic
 isolation that are well known in plants and animals can also operate in
 sexual microbes.
description: Data for Evolution
 Paper