cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hg785
title: Data from: Evolution of sociality in spiders leads to depleted genomic diversity at both population and species level

description: Across several animal taxa, the evolution of sociality involves a suite of
 characteristics, a ‘social syndrome’, that includes cooperative breeding,
 reproductive skew, primary female biased sex-ratio, and the transition
 from outcrossing to inbreeding mating system, factors that are expected to
 reduce effective population size (Ne). This social syndrome may be
 favoured by short-term benefits but come with long-term costs, because the
 reduction in Ne amplifies loss of genetic diversity by genetic drift,
 ultimately restricting the potential of populations to respond to
 environmental change. To investigate the consequences of this social life
 form on genetic diversity, we used a comparative RAD-sequencing approach
 to estimate genome-wide diversity in spider species that differ in level
 of sociality, reproductive skew, and mating system. We analysed multiple
 populations of three independent sister-species pairs of social inbreeding
 and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup.
 Heterozygosity and within population diversity were 6-10 fold lower in
 social compared to subsocial species, and demographic modelling revealed a
 tenfold reduction in Ne of social populations. Species-wide genetic
 diversity depends on population divergence and the viability of genetic
 lineages. Population genomic patterns were consistent with high lineage
 turnover, which homogenizes the genetic structure that builds up between
 inbreeding populations, ultimately depleting genetic diversity at the
 species level. Indeed, species-wide genetic diversity of social species
 was 5-8 times lower than that of subsocial species. The repeated evolution
 of species with this social syndrome is associated with severe loss of
 genome-wide diversity, likely to limit their evolutionary potential.
description: Stegodyphus africanus
 .alleles fileStegodyphus_africanus.alleles.gzStegodyphus dumicola .alleles fileStegodyphus_dumicola.alleles.gzStegodyphus lineatus .alleles fileStegodyphus_lineatus.alleles.gzStegodyphus mimosarum .alleles fileStegodyphus_mimosarum.alleles.gzStegodyphus pacificus .alleles fileStegodyphus_pacificus.alleles.gzStegodyphus sarasinorum .alleles fileStegodyphus_sarasinorum.alleles.gzStegodyphus tentoriicola .alleles fileStegodyphus_tentoriicola.alleles.gz
DOI: 10.5061/dryad.c8t69
title: Data from: Rapid categorization of natural face images in the infant right hemisphere

description: Human performance at categorizing natural visual images surpasses
 automatic algorithms, but how and when this function arises and develops
 remain unanswered. We recorded scalp electrical brain activity in 4–6
 months infants viewing images of objects in their natural background at a
 rapid rate of 6 images/second (6 Hz). Widely variable face images
 appearing every 5 stimuli generate an electrophysiological response over
 the right hemisphere exactly at 1.2 Hz (6 Hz/5). This face-selective
 response is absent for phase-scrambled images and therefore not due to
 low-level information. These findings indicate that right lateralized
 face-selective processes emerge well before reading acquisition in the
 infant brain, which can perform figure-ground segregation and generalize
 face-selective responses across changes in size, viewpoint, illumination
 as well as expression, age and gender. These observations made with a
 highly sensitive and objective approach open an avenue for clarifying the
 developmental course of natural image categorization in the human brain.
description: deHeering_Rossion_EEGDataA compressed (zipped) folder containing 2 folders, one for each experiment described in the paper. In each experiment folder, there are individual folders for each infant tested, with 2 files in each, as described in the readMe.text file
DOI: 10.15468/dl.9xarf7
title: Occurrence Download

description: A dataset containing 601 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bursera linanoe"
 ]
}

 The dataset includes 601 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000482-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hu4gju
title: Occurrence Download

description: A dataset containing 3539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Geophis"
 ]
}

 The dataset includes 3539 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000481-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.55137
title: Data from: Historical species distribution models predict species limits in western Plethodon salamanders

description: Allopatry is commonly used to predict boundaries in species delimitation
 investigations under the assumption that currently allopatric
 distributions are indicative of reproductive isolation; however, species
 ranges are known to change over time. Incorporating a temporal perspective
 of geographic distributions should improve species delimitation; to
 explore this, we investigate three species of western Plethodon
 salamanders that have shifted their ranges since the end of the
 Pleistocene. We generate species distribution models (SDM) of the current
 range, hindcast these models onto a climatic model 21 Ka, and use three
 molecular approaches to delimit species in an integrated fashion. In
 contrast to expectations based on the current distribution, we detect no
 independent lineages in species with allopatric and patchy distributions
 (Plethodon vandykei and Plethodon larselli). The SDMs indicate that
 probable habitat is more expansive than their current range, especially
 during the last glacial maximum (LGM) (21 Ka). However, with a contiguous
 distribution, two independent lineages were detected in Plethodon
 idahoensis, possibly due to isolation in multiple glacial refugia. Results
 indicate that historical SDMs are a better predictor of species boundaries
 than current distributions, and strongly imply that researchers should
 incorporate SDM and hindcasting into their investigations and the
 development of species hypotheses.
description: S1Primer and PCR
 information.SuppInfo1.pdfS2GPS points and environmental variables used for SDMs.SuppInfo2.pdfS3SuppInfo3.pdfS4SuppInfo4.pdfS5Additional SDM figures and results.SuppInfo5.pdfcytb.Pidcytb.Placytb.Pvagapd.Pidgapd.Plagapd.Pvahspa8.Pidhspa8.Plahspa8.Pvaits.PidPl1.PidM1.Pid.nexPl14.PidM14.Pid.nexPl14.PlaM14.Pla.nexPl96.PidM96.Pid.nexPl96.PlaM96.Pla.nexrag1.Pidrag1.Plarag1.Pvarpl12.Pidrpl12.Plarpl12.Pva
DOI: 10.5061/dryad.68k7g
title: Data from: Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.)

description: The soil microbial community acts as a reservoir of microbes that directly
 influences the structure and composition of the aboveground plant
 community, promotes plant growth, increases stress tolerance and mediates
 local patterns of nutrient cycling. Direct interactions between plants and
 rhizosphere-dwelling microorganisms occur at, or near, the surface of the
 root. Upon introduction and establishment, invasive plants modify the soil
 microbial communities and soil biochemistry affecting bioremediation
 efforts and future plant communities. Here, we used tag-encoded FLX
 amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and
 fungal community diversity in the rhizosphere of Berberis thunbergii DC.
 (Japanese barberry) from invasive stands in coastal Maine to investigate
 effects of soil type, soil chemistry and surrounding plant cover on the
 soil microbial community structure. Acidobacteria, Actinobacteria,
 Proteobacteria and Verrucomicrobia were the dominant bacterial phyla,
 whereas fungal communities were comprised mostly of Ascomycota and
 Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes.
 Bulk soil chemistry had more effect on the bacterial community structure
 than the fungal community. An effect of geographic location was apparent
 in the rhizosphere microbial communities, yet it was less significant than
 the effect of surrounding plant cover. These data demonstrate a high
 degree of spatial variation in the rhizosphere microbial communities of
 Japanese barberry with apparent effects of soil chemistry, location and
 canopy cover on the microbial community structure.
description: All_JB_soil_dataBacterial 16S rRNA and fungal ITS amplicon pyrosequencing data of rhizosphere and bulk soil microbial communities beneath Japanese barberry plants in Maine.
DOI: 10.5061/dryad.2pn02
title: Data from: Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna

description: Areas of suitable habitat for species and communities have arisen,
 shifted, and disappeared with Pleistocene climate cycles, and through this
 shifting landscape, current biodiversity has found paths to the present.
 Evolutionary refugia, areas of relative habitat stability in this shifting
 landscape, support persistence of lineages through time, and are thus
 crucial to the accumulation and maintenance of biodiversity. Areas of
 endemism are indicative of refugial areas where diversity has persisted,
 and endemism of intraspecific lineages in particular is strongly
 associated with late-Pleistocene habitat stability. However, it remains a
 challenge to consistently estimate the geographic ranges of intraspecific
 lineages and thus infer phylogeographic endemism, because spatial sampling
 for genetic analyses is typically sparse relative to species records. We
 present a novel technique to model the geographic distribution of
 intraspecific lineages, which is informed by the ecological niche of a
 species and known locations of its constituent lineages. Our approach
 allows for the effects of isolation by unsuitable habitat, and captures
 uncertainty in the extent of lineage ranges. Applying this method to the
 arc of rainforest areas spanning 3500 km in eastern Australia, we
 estimated lineage endemism for 53 species of rainforest dependent
 herpetofauna with available phylogeographic data. We related endemism to
 the stability of rainforest habitat over the past 120,000 years and
 identified distinct concentrations of lineage endemism that can be
 considered putative refugia. These areas of lineage endemism are strongly
 related to historical stability of rainforest habitat, after controlling
 for the effects of current environment. In fact, a dynamic stability model
 that allows movement to track suitable habitat over time was the most
 important factor in explaining current patterns of endemism. The
 techniques presented here provide an objective, practical method for
 estimating geographic ranges below the species level, and including them
 in spatial analyses of biodiversity.
description: Lineage distribution
 models for Rosauer et al 2015The zip file contains
 102 aligned raster files, comprising all of the lineage distribution
 models used in this study.lineage models for Rosauer et
 al 2015.zipStability models for
 Rosauer et al 2015Two raster layers giving
 the results of the paleo-stability analyses for rainforest. Resolution:
 2.5 minutes (0.041666 degrees)Stability.zipEndemism and richness results for Rosauer et al 20154 raster layers giving the full endemism and richness results presented in figures 4 and 5. Resolution: 0.01 degreeEndemism and Richness.zip
DOI: 10.5061/dryad.f8j71
title: Data from: Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example

description: High-density linkage maps are important tools for genome biology and
 evolutionary genetics by quantifying the extent of recombination, linkage
 disequilibrium and chromosomal rearrangements across chromosomes, sexes
 and populations. They provide one of the best ways to validate and refine
 de novo genome assemblies, with the power to identify errors in assemblies
 increasing with marker density. However, assembly of high-density linkage
 maps is still challenging due to software limitations. We describe
 Lep-MAP2, a software for ultra-dense genome-wide linkage map construction.
 Lep-MAP2 can handle various family structures and can account for
 achiasmatic meiosis to gain linkage map accuracy. Simulations show that
 Lep-MAP2 outperforms other available mapping software both in
 computational efficiency and accuracy. When applied to two large
 F2-generation recombinant crosses between two nine-spined stickleback
 (Pungitius pungitius) populations, it produced two high-density (~6
 markers/cM) linkage maps containing 18 691 and 20 054 SNPs. The two maps
 showed a high degree of synteny, but female maps were 1.5 to 2 times
 longer than male maps in all linkage groups, suggesting genome-wide
 recombination suppression in males. Comparison with the genome sequence of
 the three-spined stickleback (Gasterosteus aculeatus) revealed a high
 degree of interspecific synteny with a low frequency (&lt;5%) of
 interchromosomal re-arrangements. However, a fairly large (ca. 10Mb)
 translocation from autosome to sex chromosome was detected in both maps.
 These results illustrate the utility and novel features of Lep-MAP2 in
 assembling high-density linkage maps, and their usefulness in revealing
 evolutionarily interesting properties of genomes, such as strong
 genome-wide sex-bias in recombination rates.
description: RAD fragments and
 SNPsA
 list of 41 bp fragments names and in which base of the fragment we
 genotyped the SNPsnps-contigs.txtHP genotypeThe genotype of the first cross (HP) in LINKAGE data formatHP-snps.linkageHP SNPs IDsThe P. pungitius SNP IDs for the first cross (HP) corresponding, and in the exact same order, as the HP genotype data file.HP.snps.IDSHR-snpsThe genotype of the second cross (HR) in Linkage format.HR SNP IDsSNP IDS corresponding to the first cross (HR) genotype file. The IDs are in the exact same order as in the genotype file.HR.snps.IDS
DOI: 10.15468/dl.fveu34
title: Occurrence Download

description: A dataset containing 8936 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothrops asper"
 ]
}

 The dataset includes 8936 records from 274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000480-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7j4jz
title: Occurrence Download

description: A dataset containing 2484 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((39.87706 -3.502576, 39.89796 -3.448494, 39.91916 -3.397955, 39.94534 -3.346249, 39.97001 -3.328264, 40.00309 -3.313409, 40.01176 -3.276402, 39.98886 -3.248544, 39.99477 -3.205642, 39.94052 -3.193605, 39.88453 -3.197919, 39.84031 -3.226474, 39.81784 -3.257355, 39.80452 -3.308462, 39.79613 -3.344978, 39.80148 -3.388872, 39.80075 -3.502242, 39.87706 -3.502576))",
 "ClassKey is Mammalia"
 ]
}

 The dataset includes 2484 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000478-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b3d03
title: Data from: Resolving Cypriniformes relationships using an anchored enrichment approach

description: Background: Cypriniformes (minnows, carps, loaches, and suckers) is the
 largest group of freshwater fishes in the world (~4300 described species).
 Despite much attention, previous attempts to elucidate relationships using
 molecular and morphological characters have been incongruent. In this
 study we present the first phylogenomic analysis using anchored hybrid
 enrichment for 172 taxa to represent the order (plus three out-group
 taxa), which is the largest dataset for the order to date (219 loci,
 315,288 bp, average locus length of 1011 bp). Results: Concatenation
 analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap
 support. Species tree analysis was highly congruent with the concatenation
 analysis with only two major differences: monophyly of Cobitoidei and
 placement of Danionidae. Conclusions: Most major clades obtained in prior
 molecular studies were validated as monophyletic, and we provide robust
 resolution for the relationships among these clades for the first time.
 These relationships can be used as a framework for addressing a variety of
 evolutionary questions (e.g. phylogeography, polyploidization,
 diversification, trait evolution, comparative genomics) for which
 Cypriniformes is ideally suited.
description: CypriniformesFullTreeLociPartitionsPartition identifiers for all lociProbeDesignFilesAlignment
DOI: 10.5061/dryad.7h54h66
title: Data from: Long-term experimental hybridisation results in a heterologous transition and the evolution of a new sex chromosome in swordtail fish

description: The remarkable diversity of sex determination mechanisms known in fish may
 be fuelled by exceptionally high rates of sex chromosome turnovers or
 transitions. However, the evolutionary causes and genomic mechanisms
 underlying this variation and instability are yet to be understood. Here
 we report on an over 30-year evolutionary experiment in which we tested
 the genomic consequences of hybridisation and selection between two
 Xiphophorus fish species with different sex chromosome systems. We find
 that introgression and imposing selection for pigmentation phenotypes
 results in the retention of an unexpectedly large maternally derived
 genomic region. During the hybridisation process, the sex-determining
 region of the X chromosome from one parental species was translocated to
 an autosome in the hybrids leading to the evolution of a new sex
 chromosome. Our results highlight the complexity of factors contributing
 to patterns observed in hybrid genomes, and we experimentally demonstrate
 that hybridisation can catalyze rapid evolution of a new sex chromosome.
description: helerii_filtered_SNPsXiphophorus hellerii sex determination analysis: the vcf file contains the information of the 65,417 SNPs that passed the quality control applied and were used for the GWAS and the FST analyses.hellerii_loci_coverage_analysisXiphophorus hellerii sex determination analysis: the fasta file includes the 70,763 loci that were used in the coverage analysis.laboratory_cross_filtered_SNPsLaboratory cross hybridization analysis: the vcf file contains the information of the 34,632 SNPs that passed the quality control applied and were used to screen the segregation patterns of the parental alleles in the hybrid individuals.
DOI: 10.15468/dl.79fac4
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hemitheconyx caudicinctus"
 ]
}

 The dataset includes 299 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000479-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.266g4
title: Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment

description: Synonymous genetic differences vary by more than 20-fold among genes in
 natural isolates of Escherichia coli. One hypothesis to explain this
 heterogeneity is that genes with high levels of synonymous variation
 mutate at higher rates than genes with low synonymous variation. If so,
 then one would expect to observe similar mutational patterns in evolution
 experiments. In fact, however, the pattern of synonymous substitutions in
 a long-term evolution experiment with E. coli does not support this
 hypothesis. In particular, the extent of synonymous variation across genes
 in that experiment does not reflect the variation observed in natural
 isolates of E. coli. Instead, gene length alone predicts with high
 accuracy the prevalence of synonymous changes in the experimental
 populations. We hypothesize that patterns of synonymous variation in
 natural E. coli populations are instead caused by differences across
 genomic regions in their effective population size that, in turn, reflect
 different histories of recombination, horizontal gene transfer, selection,
 and population structure.
description: DRYAD-luscombe-reanalysisThis file contains all data, python, and R scripts needed to replicate our analysis of synonymous substitutions in a long-term evolution experiment at 40,000 generations.
DOI: 10.5061/dryad.5cr07
title: Data from: Multimodal MRI suggests that male homosexuality may be linked to cerebral midline structures

description: The neurobiology of sexual preference is often discussed in terms of
 cerebral sex dimorphism. Yet, our knowledge about possible cerebral
 differences between homosexual men (HoM), heterosexual men (HeM) and
 heterosexual women (HeW) are extremely limited. In the present MRI study
 we addressed this issue investigating measures of cerebral anatomy and
 function, which were previously reported to show sex difference.
 Specifically, we asked whether there were any signs of sex atypical
 cerebral dimorphism among HoM, if these were widely distributed (providing
 substrate for more general 'female' behavioral characteristics
 among HoM), or restricted to networks involved in self-referential sexual
 arousal. Cortical thickness (Cth), surface area (SA), subcortical
 structural volumes, and resting state functional connectivity were
 compared between 30 (HoM), 35 (HeM) and 38 (HeW). HoM displayed a
 significantly thicker anterior cingulate cortex (ACC), precuneus, and the
 left occipito-temporal cortex compared to both control groups. These
 differences seemed coordinated, since HoM also displayed stronger
 cortico-cortical covariations between these regions. Furthermore,
 functional connections within the default mode network, which mediates
 self- referential processing, and includes the ACC and precuneus were
 significantly weaker in HoM than HeM and HeW, whereas their functional
 connectivity between the thalamus and hypothalamus (important nodes for
 sexual behavior) was stronger. In addition to these singular features, HoM
 displayed 'female' characteristics, with a similar Cth in the
 left superior parietal and cuneus cortices as HeW, but different from
 HeM.\r\nThese data suggest both singular and sex atypical features and
 motivate further investigations of cerebral midline structures in relation
 to male homosexuality.
description: T1_brain_PLOS1