cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7r0d5
title: Data from: Molecular divergence in tropical tree populations occupying environmental mosaics

description: Unveiling the genetic basis of local adaptation to environmental variation
 is a major goal in molecular ecology. In rugged landscapes characterised
 by environmental mosaics, living populations and communities can
 experience steep ecological gradients over very short geographical
 distances. In lowland tropical forests, interspecific divergence in
 edaphic specialization (for seasonally flooded bottomlands and seasonally
 dry terra firme soils) has been proven by ecological studies on adaptive
 traits. Some species are nevertheless capable of covering the entire span
 of the gradient; intraspecific variation for adaptation to contrasting
 conditions may explain the distribution of such ecological generalists. We
 investigated whether local divergence happens at small spatial scales in
 two stands of Eperua falcata (Fabaceae), a widespread tree species of the
 Guiana Shield. We investigated SNP and sequence divergence as well as
 spatial genetic structure (SGS) at four genes putatively involved in
 stress response and three genes with unknown function. Significant genetic
 differentiation was observed among sub-populations within stands, and
 eight SNP loci showed patterns compatible with disruptive selection. SGS
 analysis showed genetic turnover along the gradients at three loci, and at
 least one haplotype was found to be in repulsion with one habitat. Taken
 together, these results suggest genetic differentiation at small spatial
 scale in spite of gene flow. We hypothesize that heterogeneous
 environments may cause molecular divergence, possibly associated to local
 adaptation in E. falcata.
description: SNP-bis
DOI: 10.5061/dryad.0hd1s
title: Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.

description: Determining the relationships among the major groups of cellular life is
 important for understanding the evolution of biological diversity, but is
 difficult given the enormous time spans involved. In the textbook
 'three domains' tree based on informational genes, eukaryotes
 and Archaea share a common ancestor to the exclusion of Bacteria. However,
 some phylogenetic analyses of the same data have placed eukaryotes within
 the Archaea, as the nearest relatives of different archaeal lineages. We
 compared the support for these competing hypotheses using sophisticated
 phylogenetic methods and an improved sampling of archaeal biodiversity. We
 also employed both new and existing tests of phylogenetic congruence to
 explore the level of uncertainty and conflict in the data. Our analyses
 suggested that much of the observed incongruence is weakly supported or
 associated with poorly fitting evolutionary models. All of our
 phylogenetic analyses, whether on small subunit and large subunit
 ribosomal RNA or concatenated protein-coding genes, recovered a
 monophyletic group containing eukaryotes and the TACK archaeal superphylum
 comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and
 Korarchaeota. Hence, while our results provide no support for the iconic
 three-domain tree of life, they are consistent with an extended eocyte
 hypothesis whereby vital components of the eukaryotic nuclear lineage
 originated from within the archaeal radiation.
description: 29_aebConcatenation of 29
 genes conserved in Bacteria, Archaea and eukaryotes.aeb_fasta_files.tarSingle genes conserved between Bacteria, Archaea and eukaryotes. These are the "raw" fasta files, before alignment editing.arch_euk_fasta.tarSingle genes conserved between Archaea and eukaryotes. These are the raw sequence files before editing.63_genes63AE dataset (described in article)64_genes64AE dataset (described in article)64_singles.tarThe genes used to make the 64AE dataset, after masking of poorly-aligning and uninformative sites.29_alns_cut.tarThe genes used to make the 29BAE dataset, after masking of poorly-aligning and uninformative sites.rrna.tarLSU and SSU rRNA sequence files (FASTA format) and alignment (PHYLIP format). Used to produce Figure 1 of the article.newick_trees.tarNewick tree files corresponding to Figures 1 and 2 of the article.
DOI: 10.5061/dryad.t1r3d
title: Data from: Porcine colonization of the Americas: a 60k SNP story

description: The pig, Sus scrofa, is a foreign species to the American continent.
 Although pigs originally introduced in the Americas should be related to
 those from the Iberian Peninsula and Canary islands, the phylogeny of
 current creole pigs that now populate the continent is likely to be very
 complex. Because of the extreme climates that America harbours, these
 populations also provide a unique example of a fast evolutionary
 phenomenon of adaptation. Here, we provide a genome wide study of these
 issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across
 14 countries and 183 pigs from outgroup breeds that are potential founders
 of the American populations, including wild boar, Iberian, international
 and Chinese breeds. Results show that American village pigs are primarily
 of European ancestry, although the observed genetic landscape is that of a
 complex conglomerate. There was no correlation between genetic and
 geographical distances, neither continent wide nor when analysing specific
 areas. Most populations showed a clear admixed structure where the Iberian
 pig was not necessarily the main component, illustrating how international
 breeds, but also Chinese pigs, have contributed to extant genetic
 composition of American village pigs. We also observe that many genes
 related to the cardiovascular system show an increased differentiation
 between altiplano and genetically related pigs living near sea level.
description: FinalData_HDY-12-OR0223Dataset corresponds to the article: "Porcine colonization of the Americas: A 60k SNP story." W. Burgos, C.A. Souza et al. For any correspondence, please address M. Perez-Enciso (miguel.perez@uab.es) Complete dataset contains 46259 SNP genotypes for 389 individuals. Info_sample.txt file contains information about location (Origin) and population (POPname) for each sample. MPE_378.* files contains genotypes for samples included for all analyses in the paper (PLINK format). MPE_389.* files also contains samples with high missing values that were used only in principal component analysis (PLINK format). The SNP_LD_pruned.dat file is a list of SNPs included after LD pruning. ADMIXTURE and PCA analyses were carried out using only those SNPs.
DOI: 10.5061/dryad.9h91m
title: Data from: Impact of climate changes from Middle Miocene onwards on evolutionary diversification in Eurasia: insights from the mesobuthid scorpions

description: The aridification from Middle Miocene onwards has transformed the Asian
 interior into an arid environment, and the Pleistocene
 glacial–interglacial oscillations exerted further ecological impact.
 Therefore, both aridification and glaciation would have considerably
 influenced the evolution of many mid-latitude species in temperate Asia.
 Here, we tested this perspective by a phylogeographic study of the
 mesobuthid scorpions across temperate Asia using one mitochondrial and
 three nuclear genes. Concordant mitochondrial and nuclear gene trees were
 obtained, which are consistent with species tree inferred using a Bayesian
 approach. The age of the most recent common ancestor (MRCA) of all the
 studied scorpions was estimated to be 12.49 Ma (late Middle Miocene);
 Mesobuthus eupeus diverged from the clade composing Mesobuthus caucasicus
 and Mesobuthus martensii in early Late Miocene (10.21 Ma); M. martensii
 diverged from M. caucasicus at 5.53 Ma in Late Miocene. The estimated MRCA
 ages of M. martensii and the Chinese lineage of M. eupeus were 2.37 and
 0.68 Ma, respectively. Central Asia was identified as the ancestral area
 for the lineage leading to M. martensii and M. caucasicus and the Chinese
 lineage of M. eupeus. The ancestral habitat of the genus Mesobuthus is
 likely to have been characterized by an arid environment; a shift towards
 more humid habitat occurred in the MRCA of M. martensii and a lineage of
 M. caucasicus, finally leading to the adaptation of M. martensii to humid
 environment. Our data strongly support the idea that the stepwise
 intensified aridifications from Mid-Miocene onwards drove the
 diversification of mesobuthid scorpions, and suggest that M. martensii and
 M. eupeus observed today in China originated from an ancestral lineage
 distributed in Central Asia. Both the colonization and the ensuing
 evolution of these species in East Asia appear to have been further
 moulded by Quaternary glaciations.
description: Table 1 Sampling
 localities and sample sizes of MSampleing location of M.
 martensii in China and M.eupeus from China, Mongolia and
 TajikistanTree data for
 reconstructing ancestral distributional areas50K BEAST post-burnin
 trees and MCC tree for reconstructing ancestral distribution
 areas.Table S1 Genbank
 accession numbersGenbank accession
 numbers of Mesobuthus scorpion and outgroup sequences
DOI: 10.5061/dryad.1pg07
title: Data from: Constant, cycling, hot and cold thermal environments: strong effects on mean viability but not on genetic estimates

description: It has frequently been suggested that trait heritabilities are
 environmentally sensitive, and there are genetic trade-offs between
 tolerating different environments such as hot and cold or constant and
 fluctuating temperatures. Future climate predictions suggest an increase
 in both temperatures and their fluctuations. How species will respond to
 these changes is uncertain, particularly as there is a lack of studies
 which compare genetic performances in constant vs. fluctuating
 environments. In this study, we used a nested full-sib/half-sib breeding
 design to examine how the genetic variances and heritabilities of
 egg-to-adult viability differ at high and low temperatures with and
 without daily fluctuations in temperatures using Drosophila melanogaster
 as a model organism. Although egg-to-adult viability was clearly sensitive
 to developmental temperatures, heritabilities were not particularly
 sensitive to developmental temperatures. Moreover, we found that
 egg-to-adult viabilities at different developmental temperatures were
 positively correlated, suggesting a common genetic background for
 egg-to-adult viability at different temperatures. Finding both a uniform
 genetic background coupled with rather low heritabilities insensitive to
 temperatures, our results suggest evolutionary responses are unlikely to
 be limited by temperature effects on genetic parameters or negative
 genetic correlations, but by the direct effects of stressful temperatures
 on egg-to-adult viability accompanied with low heritabilities.
description: egg-to-adult viability
 datadata.csv
DOI: 10.5061/dryad.hb3b5
title: Data from: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

description: Mutations are the ultimate source of heritable variation for evolution.
 Understanding how mutation rates themselves evolve is thus essential for
 quantitatively understanding many evolutionary processes. According to
 theory, mutation rates should be minimized for well-adapted populations
 living in stable environments, whereas hypermutators may evolve if
 conditions change. However, the long-term fate of hypermutators is
 unknown. Using a phylogenomic approach, we found that an adapting
 Escherichia coli population that first evolved a mutT hypermutator
 phenotype was later invaded by two independent lineages with mutY
 mutations that reduced genome-wide mutation rates. Applying neutral theory
 to synonymous substitutions, we dated the emergence of these mutations and
 inferred that the mutT mutation increased the point-mutation rate by
 ~150-fold, while the mutY mutations reduced the rate by ~40-60%, with a
 corresponding decrease in the genetic load. Thus, the long-term fate of
 the hypermutators was governed by the selective advantage arising from a
 reduced mutation rate as the potential for further adaptation declined.
description: Wielgossetal_2012_ArchiveThis zipped folder contains all of the data files and scripts necessary to run the statistical analyses of this manuscript.
DOI: 10.5517/ccdc.csd.cc2pdfl4
title: CCDC 2484606: Experimental Crystal Structure Determination

description: Related Article: R.Ya. Okmanov, A.A. Ziyaev, T.T. Toshmurodov, U.S. Makhmudov, A.G. Eshimbetov, S.A. Sasmakov, B. Tashkhodzhaev|2025|Chem. Data Collect.|60|101212|doi:10.1016/j.cdc.2025.101212
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.9c568
title: Data from: Dating phylogenies with sequentially sampled tips

description: We develop a Bayesian Markov chain Monte Carlo (MCMC) algorithm for
 estimating divergence times using sequentially sampled molecular
 sequences. This type of data is commonly collected during viral epidemics
 and is sometimes available from different species in ancient DNA studies.
 We derive the distribution of ages of nodes in the tree under a
 birth–death-sequential-sampling (BDSS) model and use it as the prior for
 divergence times in the dating analysis. We implement the prior in the
 MCMCtree program in the PAML package for divergence dating. The BDSS prior
 is very flexible and, with different parameters, can generate trees of
 very different shapes, suitable for examining the sensitivity of posterior
 time estimates. We apply the method to a data set of SIV/HIV-2 genes in
 comparison with a likelihood-based dating method, and to a data set of
 influenza H1 genes from different hosts in comparison with the Bayesian
 program BEAST. We examined the impact of tree topology on time estimates
 and suggest that multifurcating consensus trees should be avoided in
 dating analysis. We found posterior time estimates for old nodes to be
 sensitive to the priors on times and rates and suggest that previous
 Bayesian dating studies may have produced overconfident estimates.
description: StadlerYang2012BDS.TipDate.OnlineSuppMatOnline supplementary text and figures S1-S7HIV-2 alignmentHIV2ge.txtHIV2ge treeHIV2ge.treFlu H1 alignmentH1.txtflu H1 treeH1.treflu H1 Beast data fileH1.Beast.xmlflu H1 Beast Nulldata file for generating the priorH1.Beast.Nulldata.xmlflu H1 MCMCtree in.BV filein.BV.HKYG5flu H1 MCMCtree control filemcmctreeClock1.ctl
DOI: 10.15468/dl.pyjk2p
title: Occurrence Download

description: A dataset containing 8431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "Country is one of (Spain, France, Italy, Greece, Algeria, Türkiye, Tunisia, Portugal, Croatia, Slovenia, Morocco, Egypt, Syrian Arab Republic, Iraq, Iran (Islamic Republic of))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phlebotomus",
 "Year 1980-2026"
 ]
}

 The dataset includes 8431 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001590-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r8n7c
title: Data from: Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming correlated genetic admixture and specific temperature adaptations

description: Poleward range expansions are observed for an increasing number of
 species, which may be an effect of global warming during the past decades.
 However, it is still not clear in how far these expansions reflect simple
 geographical shifts of species ranges, or whether new genetic adaptations
 play a role as well. Here, we analyse the expansion of the wasp spider
 Argiope bruennichi into Northern Europe during the last century. We have
 used a range-wide sampling of contemporary populations and historical
 specimens from museums to trace the phylogeography and genetic changes
 associated with the range shift. Based on the analysis of mitochondrial,
 microsatellite and SNP markers, we observe a higher level of genetic
 diversity in the expanding populations, apparently due to admixture of
 formerly isolated lineages. Using reciprocal transplant experiments for
 testing overwintering tolerance, as well as temperature preference and
 tolerance tests in the laboratory, we find that the invading spiders have
 possibly shifted their temperature niche. This may be a key adaptation for
 survival in Northern latitudes. The museum samples allow a reconstruction
 of the invasion's genetic history. A first, small-scale range shift
 started around 1930, in parallel with the onset of global warming. A more
 massive invasion of Northern Europe associated with genetic admixture and
 morphological changes occurred in later decades. We suggest that the
 latter range expansion into far Northern latitudes may be a consequence of
 the admixture that provided the genetic material for adaptations to new
 environmental regimes. Hence, global warming could have facilitated the
 initial admixture of populations and this resulted in genetic lineages
 with new habitat preferences.
description: Sampling
 localitiesSampling localities of
 contemporary and historical specimens, including museum
 identifiers.Sample
 list.xlsPrimer
 sequencesPrimers, which were used
 in the studyMicrosatellite
 datanuclear SNP
 dataSNP data
 & STRUCTURE output.xlsMitochondrial
 diversityProsoma
 widthProsoma width of
 contemporary and historical specimensMorphological data
 .xlsReciprocal
 transplantReciprocal transplant
 dataTemperature preference
 & toleranceData from temperature
 preference and heat tolerance experimentsAlignment of complete
 historical COI sequencesAlignment of short
 historical COI sequencesContemporary COI
 alignment
DOI: 10.5061/dryad.k8n14
title: Data from: The estimation of tree posterior probabilities using conditional clade probability distributions

description: In this paper I introduce the idea of conditional independence of
 separated subtrees as a principle by which to estimate the posterior
 probability of trees using conditional clade probability distributions
 rather than simple sample relative frequencies. I describe an algorithm
 for these calculations and software which implements these ideas. I show
 that these alternative calculations are very similar to simple sample
 relative frequencies for high probability trees, but are substantially
 more accurate for relatively low probability trees. The method allows the
 posterior probability of unsampled trees to be calculated when these trees
 contain only clades that are in other sampled trees. Furthermore, the
 method can be used to estimate the total probability of the set of sampled
 trees which provides a measure of the thoroughness of a posterior sample.
description: cats-dogsAlignment of 1545 bp COX 1 mitochondrial gene for 6 feliforms and 6 caniforms. Original data from NCBI.rodents62 rodents and mammals, 3768 bp. TREEBASE M2481.M336TREE BASE file M336M501TREE BASE file M501M520TREE BASE file M520M755TREE BASE file M755.M767TREE BASE file M767.M1044TREE BASE file M1044.M1366TREE BASE file M1366.M1510TREE BASE file M1510.M1748TREE BASE file M1748.M1809TREE BASE file M1809.M3475TREE BASE file M3475.appendixAppendices 1-4.
DOI: 10.5061/dryad.dh53m
title: Data from: Inferring the demographic history of European Ficedula flycatcher populations

description: Background: Inference of population and species histories and population
 stratification using genetic data is important for discriminating between
 different speciation scenarios and for correct interpretation of genome
 scans for signs of adaptive evolution and trait association. Here we use
 data from 24 intronic loci re-sequenced in population samples of two
 closely related species, the pied flycatcher and the collared flycatcher.
 Results: We applied Isolation-Migration models, assignment analyses and
 estimated the genetic differentiation and diversity between species and
 between populations within species. The data indicate a divergence time
 between the species of &lt; 1 million years, significantly shorter
 than previous estimates using mtDNA, point to a scenario with
 unidirectional gene-flow from the pied flycatcher into the collared
 flycatcher and imply that barriers to hybridisation are still permeable in
 a recently established hybrid zone. Furthermore, we detect significant
 population stratification, predominantly between the Spanish population
 and other pied flycatcher populations. Conclusions: Our results provide
 further evidence for a divergence process where different genomic regions
 may be at different stages of speciation. We also conclude that
 forthcoming analyses of genotype-phenotype relations in these ecological
 model species should be designed to take population stratification into
 account.
description: dataSequence data for all
 genes and all individuals in the study
DOI: 10.5061/dryad.k1t5r
title: Data from: A multilocus perspective on phylogenetic relationships in the Namib darkling beetle genus Onymacris (Tenebrionidae)

description: Tenebrionid beetles, common constituent faunae of arid ecosystems
 worldwide, are particularly abundant in Africa’s Namib and Kalahari
 deserts. Within this region, flightless, diurnal members of the tribe
 Adesmiini are among the more intensively studied of all desert beetles,
 especially with regard to ecology. Much of this research centers on
 Onymacris, a psammophilous genus largely endemic to the Namib. Here we
 present the first molecular phylogenetic analysis conducted for Onymacris,
 emphasizing relationships among other adesmiines. Our multilocus phylogeny
 identifies a strongly supported clade containing Onymacris and two other
 genera, Eustolopus and Physadesmia—an assemblage recovered in earlier
 morphological analyses. However, Onymacris is not monophyletic; rather, we
 demonstrate its paraphyly with respect to the genus Physadesmia,
 identified as the sister taxon to the white-bodied species of Onymacris.
 In turn, the Physadesmia-‘white’ Onymacris clade is the sister group to
 the remaining (black-bodied) Onymacris. Non-monophyly of ‘black’ versus
 ‘white’ Onymacris is corroborated by distribution patterns and nodal age
 estimates, which suggest separate origins in different dune systems.
description: Onymacris phylogenetic
 dataZip file containing
 Nexus formatted data and results from Bayesian analysis of all genes.
 Includes output (results.txt), tree and parameter
 files.onymacrisPhylogeneticData.zip