cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8m648
title: Data from: Complex patterns of local adaptation in Teosinte

description: Populations of widely distributed species encounter and must adapt to
 local environmental conditions. However, comprehensive characterization of
 the genetic basis of adaptation is demanding, requiring genome wide
 genotype data, multiple sampled populations, and an understanding of
 population structure and potential selection pressures. Here, we used SNP
 genotyping and data on numerous environmental variables to describe the
 genetic basis of local adaptation in 21 populations of teosinte, the wild
 ancestor of maize. We found complex hierarchical genetic structure created
 by altitude, dispersal events and admixture among subspecies that
 complicated identification of locally beneficial alleles. Patterns of
 linkage disequilibrium revealed four large inversion polymorphisms showing
 clinal patterns of frequency. Population differentiation and environmental
 correlations suggest that both inversions and intergenic polymorphisms are
 involved in local adaptation.
description: SNP genotypes and
 related information for Zea mays ssp. parviglumis. Z. m. ssp. mexicana and
 Tripsacum dactyloidesPyhajarvi_et_al_SNPdata.zip
DOI: 10.6084/m9.figshare.31144627
title: Supplementary Material (Colombia land of mammals)

description: The supplementary material includes the complete and updated checklist of mammal species recorded in Colombia, with their taxonomic assignment and species-level natural history trait information, as well as the data used for the spatial analyses presented in the study.
DOI: 10.6084/m9.figshare.31144627.v1
title: Supplementary Material (Colombia land of mammals)

description: The supplementary material includes the complete and updated checklist of mammal species recorded in Colombia, with their taxonomic assignment and species-level natural history trait information, as well as the data used for the spatial analyses presented in the study.
DOI: 10.5061/dryad.sm41s
title: Data from: Local dynamics of a fast evolving sex-ratio system in Drosophila simulans

description: By distorting Mendelian transmission to their own advantage, X-linked
 meiotic drive elements can rapidly spread in natural populations,
 generating a sex-ratio bias. One expected consequence is the triggering of
 a coevolutionary arms race between the sex chromosome that carries the
 distorter and suppressors counteracting its effect. Such an arms race has
 been theoretically and experimentally established, and can have many
 evolutionary consequences. However, its dynamics in contemporary
 populations is still poorly documented. Here, we investigate the fate of
 the young X-linked Paris driver in Drosophila simulans from Sub-Saharan
 Africa to the Middle East. We provide the first example of the early
 dynamics of distorters and suppressors: we find consistent evidence that
 the driving chromosomes have been rising in the Middle East during the
 last decade. In addition, identical haplotypes are at high frequencies
 around the two co-evolving drive loci in remote populations, implying that
 the driving X chromosomes share a recent common ancestor, and suggesting
 that East Africa could be the cradle of the Paris driver. The segmental
 duplication associated with drive presents an unusual structure in West
 Africa, which could reflect a secondary state of the driver. Together with
 our previous demonstration of driver decline in the Indian Ocean where
 suppression is complete, these data provide a unique picture of the
 complex dynamics of a coevolutionary arms race currently taking place in
 natural populations of D. simulans.
description: Haplotype
 fileExcel file with
 haplotypes at all loci in all populations with genotypes at the markers in
 the junction region.Algt_CG12065Alignment for the CG12065 markerAlgt_CG33181Alignment for the CG33181 markerAlgt_CragAlignment for the Crag markerAlgt_JunctionAlignment for the Junction markerAlgt_NRGAlignment for the NRG markerAlgt_org1Alignment for the org-1 markerAlgt_Trf2Alignment for the Trf2 markerAlgt_Trf4-1Alignment for the Trf4-1 markerAlgt_vermilionAlignment for the vermilion markerqPCRdataRaw data (Cq) for the qPCR experimentBiogeoSRR script for data analysis and figures
DOI: 10.5061/dryad.nk151
title: Data from: Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation

description: Asexual lineages are thought to be prone to extinction because of
 deleterious mutation accumulation (Muller's ratchet). Here we analyze
 genomic effects of hybridity, polyploidy and allelic divergence in
 apomictic plants, and identify loci under divergent selection among
 sexual/apomictic lineages. RNAseq was used to sequence the flower-specific
 transcriptomes of 5 genotypes of the Ranunculus auricomus complex,
 representing 3 sexual and 2 apomictic reproductive biotypes. The 5
 sequence libraries were pooled and de novo assembly performed, and the
 resultant assembly was used as a backbone for a subsequent alignment of
 each separate library. High quality single nucleotide (SNP) and
 insertion-deletion (indel) polymorphisms were mined from each library.
 Annotated genes for which open reading frames (ORF) could be determined
 were analyzed for signatures of divergent versus stabilizing selection. A
 comparison between all genotypes supports the hypothesis of Pleistocene
 hybrid origin of both apomictic genotypes from R. carpaticola and R.
 cassubicifolius, with subsequent allelic divergence of apomictic lineages
 (Meselson effect). Pairwise comparisons of non-synonymous (dN) to
 synonymous (dS) substitution rate ratios between apomictic and sexual
 genotypes for 1231 genes demonstrated similar distributions for all
 comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS
 ratios. Gene ontology analyses of these outliers revealed significant
 enrichment of genes associated with reproduction including meiosis and
 gametogenesis, following predictions of divergent selection between sexual
 and apomictic reproduction, although no significant signal of genome-wide
 mutation accumulation could be identified. The results suggest that gene
 function should be considered in order to understand effects of mutation
 accumulation in asexual lineages.
description: Asexual genome evolution
 in the apomictic Ranunculus auricomus complex: examining the effects of
 hybridization and mutation accumulation.fFsta file Ranunculus
 sequencesRanunculusBlastxSequences.fastaPresence/absence SNPs matrixPresence absence SNPs matrix. Nexus FileSNP_data_nexus
DOI: 10.34894/frxkrt
title: Interviewproject VNO-NCW

description: Transcriptions of Interview project VNO-NCW, which can be accessed here:
https://hdl.handle.net/10622/COLL00640

Interviewproject met oud-bestuurders van VNO-NCW in opdracht van het Internationaal Instituut voor Sociale Geschiedenis (IISG). De interviews zijn afgenomen door journalist Leonard Ornstein. De opnames zijn gemaakt en gemonteerd door Cees Hartman van Hartman Videoproducties. Onderzoeker Dennie Oude Nijhuis en zijn assistent Christien van der Harst hebben voorafgaand onderzoek verricht en interviewvragen voorbereid. Projectleiding was in handen van IISG-directeur Henk Wals en vanaf april 2020 van Frank de Jong (IISG Collectievorming).
DOI: 10.5061/dryad.fb6qg
title: Data from: A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

description: In sheep, coat colour (and pattern) is one of the important traits of
 great biological, economic and social importance. However, the genetics of
 sheep coat colour has not yet been fully clarified. We conducted a
 genome-wide association study of sheep coat colours by genotyping 47 303
 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in
 Finland. We identified 35 SNPs associated with all the coat colours
 studied, which cover genomic regions encompassing three known pigmentation
 genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were
 confirmed in further tests between white versus non-white individuals, but
 none of the 35 associations were significant in the analysis of only
 non-white colours. Across the tests, the s66432.1 in ASIP showed
 significant association (P=4.2 × 10−11 for all the colours; P=2.3 × 10−11
 for white versus non-white colours) with the variation in coat colours and
 strong linkage disequilibrium with other significant variants surrounding
 the ASIP gene. The signals detected around the ASIP gene were explained by
 differences in white versus non-white alleles. Further, a genome scan for
 selection for white coat pigmentation identified a strong and striking
 selection signal spanning ASIP. Our study identified the main candidate
 gene for the coat colour variation between white and non-white as ASIP, an
 autosomal gene that has been directly implicated in the pathway regulating
 melanogenesis. Together with ASIP, the two other newly identified genes
 (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a
 new resource for enriching sheep coat-colour genetics and breeding.
description: Finnsheep coat colour
 phenotypesFinnsheep
 colours.xlsFinnsheep 50K SNP
 genotypesFinnSheep_99.txt
DOI: 10.5061/dryad.48f62
title: Data from: Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

description: Cichlid fishes are a key model system in the study of adaptive radiation,
 speciation and evolutionary developmental biology. More than 1600 cichlid
 species inhabit freshwater and marginal marine environments across several
 southern landmasses. This distributional pattern, combined with parallels
 between cichlid phylogeny and sequences of Mesozoic continental rifting,
 has led to the widely accepted hypothesis that cichlids are an ancient
 group whose major biogeographic patterns arose from Gondwanan vicariance.
 Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids
 demanded by the vicariance model now represents a key calibration for
 teleost molecular clocks, this putative split pre-dates the oldest cichlid
 fossils by nearly 90 Myr. Here, we provide independent palaeontological
 and relaxed-molecular-clock estimates for the time of cichlid origin that
 collectively reject the antiquity of the group required by the Gondwanan
 vicariance scenario. The distribution of cichlid fossil horizons, the age
 of stratigraphically consistent outgroup lineages to cichlids and
 relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear
 genes all deliver overlapping estimates for crown cichlid origin centred
 on the Palaeocene (ca 65–57 Ma), substantially post-dating the tectonic
 fragmentation of Gondwana. Our results provide a revised macroevolutionary
 time scale for cichlids, imply a role for dispersal in generating the
 observed geographical distribution of this important model clade and add
 to a growing debate that questions the dominance of the vicariance
 paradigm of historical biogeography.
description: cichlidCONCATAligned DNA sequences from 10 nuclear genes for 158 percomorph speciescichlidRAxMLTree file resulting from RAxML analysis of the 10 nuclear gene dataset.cichlidRLC_LGNaxml file used in relaxed molecular clock analyses in BEAST.cichlidRLC_SUMTime calibrated phylogenetic tree summarized from the posterior set of trees resulting from the BEAST analyses.R_scripts_dataZipped folder containing analytical scripts and data for estimating the age of cichlid fishes using paleontological data.
DOI: 10.5061/dryad.606j6
title: Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013

description: Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have
 been declining in size and body condition for decades, as climate change
 causes earlier sea ice breakup, reduced hunting time on the ice, and an
 increasingly long fasting season. As Western Hudson Bay females have
 decreased in size, rates of litter production and average litter size have
 also decreased, while cub mortality and average time to independence have
 increased. Although these changes have potential evolutionary
 consequences, little is yet known about the adaptive genetic variation in
 body size or fat accumulation that would have to underlie any such change.
 In this study, we used high-throughput Illumina sequencing to develop SNPs
 from pooled blood and fat transcriptomes, using samples from five adult
 female polar bears and five (unrelated) dependent cubs. In total, we
 generated 371,258 transcripts of which 36,755 were deemed to be “full
 length” (i.e., covered more than 90% of their best BLAST hit), and we
 identified 63,020 SNPs. Since this study was conducted, we have used a
 subset of these SNPs to develop an Illumina BeadArray for quantitative
 genetics research in Western Hudson Bay.
description: Custom Perl script for
 extracting SNPsPerl program used to
 extract SNPs. Properly accounts for REFSKIP characters (i.e.,
 "&lt;" and "&gt;") that result from spliced alignments
 and seemed to be problematic in more widely available SNP calling
 packages, such as samtools and varscan.getsnpsfrommpileup.plSNP VCF fileVCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were: coverage &gt;= 10, freq. of minor allele &gt;= 0.2, read support for minor allele &gt;= 3, number of alleles = 2. All SNPs were also verified using the program SysCall, and were retained only if the posterior probability of being a variant was &gt;= 0.95.pb_syscallsnps.vcf.txtContig annotation filePutative gene and gene ontology annotations for transcripts that were deemed to be "full length" (i.e., cover &gt;= 90% of their best blastx hit in RefSeq). These sequences are available on NCBI under the BioProject accession PRJNA193538.annotations.annot
DOI: 10.15468/dl.rkesnz
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f)",
 "TaxonKey is Cornu aspersum",
 "Year 1000-2016"
 ]
}

 The dataset includes 23 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001600-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7h65f
title: Data from: Genome-wide admixture and ecological niche modeling reveal the maintenance of species boundaries despite long history of interspecific gene flow

description: 1.The maintenance of species boundaries despite interspecific gene flow
 has been a continuous source of interest in evolutionary biology. Many
 hybridizing species have porous genomes with regions impermeable to
 introgression, conferring reproductive barriers between species. 2.We used
 ecological niche modeling to study the glacial and postglacial
 recolonization patterns between the widely hybridizing spruce species
 Picea glauca and P. engelmannii in western North America. 3.Genome-wide
 estimates of admixture based on a panel of 311 candidate gene single
 nucleotide polymorphisms (SNP) from 290 genes were used to assess levels
 of admixture and introgression, and to identify loci putatively involved
 in adaptive differences or reproductive barriers between species. 4.Our
 paleoclimatic modeling suggests these two closely related species have a
 long history of hybridization and introgression, dating to at least 21,000
 years ago, yet species integrity is maintained by a combination of strong
 environmental selection and reduced current interspecific gene flow. 5.20
 loci showed evidence of divergent selection, including six loci that were
 both Fst outliers and associated with climatic gradients, and fourteen
 loci that were either outliers or showed associations with climate. These
 included genes responsible for carbohydrate metabolism, signal
 transduction, and transcription factors.
description: Genome-wide admixture in
 the Picea glauca x P. engelmannii hybrid zone_311SNPsThis file contains
 Illumina genomic data for 311 candidate gene single nucleotide
 polymorphisms (SNPs) tested in 700 individuals of P.glauca, P.engelmannii
 and their hybrids in British Columbia (Canada). The file has a format
 similar to the "Structure" (Pritchard et al.2000) program, in
 which the first column is the genotype ID, second column is the population
 ID and all other columns are the SNP IDs. Please note that each SNP is
 described by two columns, each containing one allele. Missing values are
 denoted by "-9", according to the Structure format
 requirements.SNPs_311.txtGenome-wide admixture in the Picea glauca x P. engelmannii hybrid zone_Small data setSNPs_86.txtClimate_dataThis file contains the location (latitude, longitude and elevation) of the 771 sampled individuals (white spruce, Engelmann spruce and their hybrids). It also contains the climatic variables used in the environmental association analysis. 21 different climatic variables are included for each of the sampled individuals.
DOI: 10.5061/dryad.jt440
title: Data from: Phylogenomics resolves evolutionary relationships among ants, bees, and wasps

description: Eusocial behavior has arisen in few animal groups, most notably in the
 aculeate Hymenoptera, a clade comprising ants, bees, and stinging wasps.
 Phylogeny is crucial to understanding the evolution of the salient
 features of these insects, including eusociality. Yet the phylogenetic
 relationships among the major lineages of aculeate Hymenoptera remain
 contentious. We address this problem here by generating and analyzing
 genomic data for a representative series of taxa. We obtain a single
 well-resolved and strongly supported tree, robust to multiple methods of
 phylogenetic inference. Apoidea (spheciform wasps and bees) and ants are
 sister groups, a novel finding that contradicts earlier views that ants
 are closer to ectoparasitoid wasps. Vespid wasps (paper wasps, yellow
 jackets, and relatives) are sister to all other aculeates except
 chrysidoids. Thus, all eusocial species of Hymenoptera are contained
 within two major groups, characterized by transport of larval provisions
 and nest construction, likely prerequisites for the evolution of
 eusociality. These two lineages are interpolated among three other clades
 of wasps whose species are predominantly ectoparasitoids on concealed
 hosts, the inferred ancestral condition for aculeates. This phylogeny
 provides a new framework for exploring the evolution of nesting, feeding,
 and social behavior within the stinging Hymenoptera.
description: Archive containing data
 from aculeate phylogeny by Johnson et al.; Current
 BiologyThis zip file contains
 data associated with this publication. For detailed description of
 contents please see ReadMe file.AculeateDryadData.zip
DOI: 10.5061/dryad.1s2j3
title: Data from: Deciphering the fine-structure of tribal admixture in the Bedouin population using genomic data

description: The Bedouin Israeli population is highly inbred and structured with a very
 high prevalence of recessive diseases. Many studies in the past two
 decades focused on linkage analysis in large, multiple consanguineous
 pedigrees of this population. The advent of high-throughput technologies
 motivated researchers to search for rare variants shared between smaller
 pedigrees, integrating data from clinically similar yet seemingly
 non-related sporadic cases. However, such analyses are challenging
 because, without pedigree data, there is no prior knowledge regarding
 possible relatedness between the sporadic cases. Here, we describe models
 and techniques for the study of relationships between pedigrees and use
 them for the inference of tribal co-ancestry, delineating the complex
 social interactions between different tribes in the Negev Bedouins of
 southern Israel. Through our analysis, we differentiate between tribes
 that share many yet small genomic segments because of co-ancestry versus
 tribes that share larger segments because of recent admixture. The
 emergent pattern is well correlated with the prevalence of rare mutations
 in the different tribes. Tribes that do not intermarry, mostly because of
 social restrictions, hold private mutations, whereas tribes that do
 intermarry demonstrate a genetic flow of mutations between them. Thus,
 social structure within an inbred community can be delineated through
 genomic data, with implications to genetic counseling and genetic mapping.
description: Affymetrix SNP array for
 the LAB Bedouin sampleThe LAB dataset consists
 of 30 individuals from 16 different tribes as indicated in Supplementary
 Table S1. Genotyping was done using Affymetrix GeneChip Human Mapping 250K
 Nsp Arrays, according to the manufacturer's guidelines together with
 50 controls from the same population.data.snp.newheader.txt.gz
DOI: 10.82294/dvnavulmy
title: COPUS. Territorio: Norte Santander. Sector: Cultura. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: nformación recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Norte de Santander.
DOI: 10.5061/dryad.390ng
title: Data from: Convergence of gut microbiomes in myrmecophagous mammals

description: Mammals have diversified into many dietary niches. Specialized
 myrmecophagous (ant- and termite-eating) placental mammals represent a
 textbook example of evolutionary convergence driven by extreme diet
 specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves
 thus provide a model system for understanding the potential role of gut
 microbiota in the convergent adaptation to myrmecophagy. Here, we expand
 upon previous mammalian gut microbiome studies by using high-throughput
 barcoded Illumina sequencing of the 16S rRNA gene to characterize the
 composition of gut microbiota in 15 species representing all placental
 myrmecophagous lineages and their close relatives from zoo- and
 field-collected samples. We confirm that both diet and phylogeny drive the
 evolution of mammalian gut microbiota, with cases of convergence in global
 composition, but also examples of phylogenetic inertia. Our results reveal
 specialized placental myrmecophages as a spectacular case of large-scale
 convergence in gut microbiome composition. Indeed, neighbour-net networks
 and beta-diversity plots based on UniFrac distances show significant
 clustering of myrmecophagous species (anteaters, aardvarks and
 aardwolves), even though they belong to phylogenetically distant lineages
 representing different orders. The aardwolf, which diverged from
 carnivorous hyenas only in the last 10 million years, experienced a
 convergent shift in the composition of its gut microbiome to become more
 similar to other myrmecophages. These results confirm diet adaptation to
 be a major driving factor of convergence in gut microbiome composition
 over evolutionary timescales. This study sets the scene for future
 metagenomic studies aiming at evaluating potential convergence in
 functional gene content in the microbiomes of specialized mammalian
 myrmecophages.
description: File1_mapping_Delsuc_MueggeV2V4_Soils_n196_June17_2013Mapping file for QIIME analysesOTU_biom_filesThese otu/.biom files were used in our study.