cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8346r
title: Data from: Bayesian analysis of biogeography when the number of areas is large

description: Historical biogeography is increasingly studied from an explicitly
 statistical perspective, using stochastic models to describe the evolution
 of species range as a continuous-time Markov process of dispersal between
 and extinction within a set of discrete geographic areas. The main
 constraint of these methods is the computational limit on the number of
 areas that can be specified. We propose a Bayesian approach for inferring
 biogeographic history that extends the application of biogeographic models
 to the analysis of more realistic problems that involve a large number of
 areas. Our solution is based on a ‘data-augmentation’ approach, in which
 we first populate the tree with a history of biogeographic events that is
 consistent with the observed species ranges at the tips of the tree. We
 then calculate the likelihood of a given history by adopting a mechanis-
 tic interpretation of the instantaneous-rate matrix, which specifies both
 the exponential waiting times between biogeographic events and the
 relative probabilities of each biogeographic change. We develop this
 approach in a Bayesian framework, marginalizing over all possible
 biogeographic histories using Markov chain Monte Carlo (MCMC). Besides
 dramatically increasing the number of areas that can be accommodated in a
 biogeographic analysis, our method allows the parameters of a given
 biogeographic model to be estimated and different biogeographic models to
 be objectively compared. Our approach is implemented in the program,
 BayArea.
description: Biogeographic history of
 Malesian RhododendronBiogeographic history of
 Malesian Rhododendron. The region was parsed into 20 discrete geographic
 areas following Brown et al. (2006). Each circle corresponds to a discrete
 area whose geographic coordinates is summarized by its location on the
 map. Posterior probability of being present in an area is proportional to
 the opacity of the circle, with the data at the tips being observed with
 probability one. Circles are colored according to their position relative
 to Wallace’s Line. We infer a continental Asian origin for Malesian
 rhododendrons. This figure complements the summarized results presented in
 FIgure 7 in the manuscript and is best explored using
 zoom.supp_vireya_map.pdfVireya phylogenyTime-calibrated phylogeny of Rhododendron section Vireya from Webb & Ree (2012).malaysia.55.treeVireya biogeographical coordinatesGeographical coordinates used to represent biogeographical areas of Rhododendron section Vireya as defined by Brown et al. (2006b).malaysia.geoVireya species occurrence dataPresence-absence species occurrence data for Rhododendron section Vireya as reported by Brown et al. (2006b).malaysia.brown2006b.bgd
DOI: 10.5061/dryad.kh7f2
title: Data from: Thermal adaptation and acclimation of ectotherms from differing aquatic climates

description: To elucidate the mechanisms of thermal adaptation and acclimation in
 ectothermic aquatic organisms from differing climates, we used a
 common-garden experiment for thermal stress to investigate the heat shock
 response of redband trout (Oncorhynchus mykiss gairdneri) from desert and
 montane populations. Evidence for adaptation was observed as expression of
 heat shock genes in fish from the desert population was more similar to
 control (unstressed) fish and significantly different (P ≤ 0.05) from
 those from the montane population, while F1 crosses were intermediate.
 High induction of heat shock proteins (Hsps) in the montane strain
 appeared to improve short-term survival during first exposure to high
 water temperatures, but high physiological costs of Hsp production may
 have led to lower long-term survival. In contrast, the desert strain had
 significantly lower heat shock response than the montane fish and F1
 crosses, suggesting that these desert fish have evolved alternative
 mechanisms to deal with thermal stress that provide better balance of
 physiological costs. Genomewide tests of greater than 10 000 SNPs found
 multiple SNPs that were significantly associated with survival under
 thermal stress, including Hsp47 which consistently appeared as a strong
 candidate gene for adaption to desert climates. Candidate SNPs identified
 in this study are prime targets to screen more broadly across this
 species' range to predict the potential for adaptation under
 scenarios of climate change. These results demonstrate that aquatic
 species can evolve adaptive responses to thermal stress and provide
 insight for understanding how climate change may impact ectotherms.
description: Heat_Shock_Gene_ExpressionNormalized gene expression values for six heat shock genes for liver tissues from heat stressed strains of O. mykiss gairderniSNP_Genotypes_PLINKinput.pedSNP genotypes from survivors and mortalities of O. mykiss gairdneri under thermal stress.List of SNPsThis file includes a list of all 10,497 SNPs along with their RAD tag IDs, allele sequences, and SNP position. See ReadMe tab for further details.Narum et al. SNP list.xlsx
DOI: 10.5061/dryad.1mt1h
title: Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia

description: Tropical rainforests in Southeast Asia have been affected by climatic
 fluctuations during past glacial eras. To examine how the accompanying
 changes in land areas and temperature have affected the genetic properties
 of rainforest trees in the region, we investigated the phylogeographic
 patterns of a widespread dipterocarp species, Shorea leprosula. Two types
 of DNA markers were used: expressed sequence tag-based simple sequence
 repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both
 sets of markers revealed clear genetic differentiation between populations
 in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra).
 However, in the southwestern part of Borneo genetic admixture of the
 lineages was observed in the two marker types. Coalescent simulation based
 on cpDNA sequence variation suggested that the two lineages arose 0.28 to
 0.09 million years before present, and that following their divergence
 migration from Malay/Sumatra to Borneo strongly exceeded migration in the
 opposite direction. We conclude that the genetic structure of S. leprosula
 was largely formed during the middle Pleistocene and was subsequently
 modified by eastward migration across the subaerially exposed Sunda Shelf.
description: EST-SSR
 genotypesEST-SSR genotypes of 724
 individuals of Shorea leprosula used in the publication. Samples were
 collected in the natural populations of Malay Peninsula, Sumatra and
 Borneo and a plantation forest in Java. The data are in a format suitable
 for the program GenAlEx (Peakall and Smouse 2006)..genotypes.csvchloroplast DNA sequencesFinal DNA sequence assembly for the four noncoding chloroplast DNA regions of 177 individuals of Shorea leprosula used in the publication. Samples were collected in the natural populations of Malay Peninsula, Sumatra and Borneo and a plantation forest in Java..DRYADseqfin.nexSample locationsLocations of the 27 populations of Shorea leprosula and numbers of samples analyzed in the publication. The three populations in Sarawak has been excluded from our EST-SSR analysis due to their small sample sizes..poploc.fin.csvIM input fileAn input file for the analysis of an Isolation-with-migration model between the Malay/Sumatra and the Borneo population groups of Shorea leprosula, based on the polymorphisms in the four noncoding chloroplast DNA regions..inputfile.txtIM setting fileParameter setting for the analysis of an Isolation-with-migration model between the Malay/Sumatra and the Borneo population groups of Shorea leprosula, based on the polymorphisms in the four noncoding chloroplast DNA regions..settings.txt
DOI: 10.7927/jrdr-r298
title: IPCC AR6 Synthesis Report LR Figure 3.3 (e): Examples of regional key risks in different regions

description: Risks identified, due to global warming, are of at least medium confidence level. Key risks are identified based on the magnitude of adverse consequences (pervasiveness of the consequences, degree of change, irreversibility of consequences, potential for impact thresholds or tipping points, potential for cascading effects beyond system boundaries); likelihood of adverse consequences; temporal characteristics of the risk; and ability to respond to the risk, e.g., by adaptation.
DOI: 10.5061/dryad.q50qs
title: Data from: Contrasting historical and recent gene flow among African buffalo herds in the Caprivi Strip of Namibia

description: Population genetic structure is often used to infer population
 connectivity, but genetic structure may largely reflect historical rather
 than recent processes. We contrasted genetic structure with recent
 gene-flow estimates among 6 herds of African buffalo (Syncerus caffer) in
 the Caprivi Strip, Namibia, using 134 individuals genotyped at 10
 microsatellite loci. We tested whether historical and recent gene flows
 were influenced by distance, potential barriers (rivers), or landscape
 resistance (distance from water). We also tested at what scales
 individuals were more related than expected by chance. Genetic structure
 across the Caprivi Strip was weak, indicating that historically, gene flow
 was strong and was not affected by distance, barriers, or landscape
 resistance. Our analysis of simulated data suggested that genetic
 structure would be unlikely to reflect human disturbances in the last
 10–20 generations (75–150 years) because of slow predicted rates of
 genetic drift, but recent gene-flow estimates would be affected. Recent
 gene-flow estimates were not consistently affected by rivers or distance
 to water but showed that isolation by distance appears to be developing.
 Average relatedness estimates among individuals exceeded random
 expectations only within herds. We conclude that historically, African
 buffalo moved freely throughout the Caprivi Strip, whereas recent gene
 flow has been more restricted. Our findings support efforts to maintain
 the connectivity of buffalo herds across this region and demonstrate the
 utility of contrasting genetic inferences from different time scales.
description: Microsatellite data for
 134 African buffalo, Genepop Format134 African buffalo
 genetic samples collected 2006-2009 in the Caprivi Strip, Namibia,
 genotyped at 10 microsatellite loci, presented in Genepop format for the 6
 herds (populations) in the studyBuff134_10loc6popUnityResistanceSamplingPolygonsThese are circuitscape cumulative resistance estimates using the sampling polygons for the 5 native populations (excluding Mudumu, the translocated population)UnityResistanceHomeRangePolygonsThese are circuitscape cumulative resistance estimates for 5 buffalo populations (excluding Mudumu, the translocated population) but using home range rather than sampling polygonsBuff118_10classes_SPAGEDISpaGeDi file, 10 microsatellite loci, all buffalo except for those in the translocated population of Mudumu, set for 10 distance classes. To change number of distance classes, change "-10" in row two to another value (e.g., "-20" for 20 distance classes)BuffaloSampleLocationsGIS data: Point locations for genetic samplesAnalysisClipGIS layer: polygon to clip analyses to extent used in paperAllMainRiversGIS data: all large rivers in and around Caprivi Strip; these data were used when generating resistance layers describing distance from riversVetFenceLocation of the veterinary fence on the southern edge of the Caprivi Strip that limits buffalo movements.
DOI: 10.5061/dryad.8674d
title: Data from: Transposon variants and their effects on gene expression in Arabidopsis

description: Transposable elements (TEs) make up the majority of many plant genomes.
 Their transcription and transposition is controlled through siRNAs and
 epigenetic marks including DNA methylation. To dissect the interplay of
 siRNA-mediated regulation and TE evolution, and to examine how TE
 differences affect nearby gene expression, we investigated genome-wide
 differences in TEs, siRNAs and gene expression among three Arabidopsis
 thaliana accessions. Both TE sequence polymorphisms and presence of linked
 TEs are positively correlated with intraspecific variation in gene
 expression. The expression of genes within 2 kb of conserved TEs is more
 stable than that of genes next to variant TEs harboring sequence
 polymorphisms. Polymorphism levels of TEs and closely linked adjacent
 genes are positively correlated as well. We also investigated the
 distribution of 24 nt long siRNAs, which mediate TE repression. TEs
 targeted by uniquely mapping siRNAs are on average farther from coding
 genes, apparently because they more strongly suppress expression of
 adjacent genes. Furthermore, siRNAs, and especially uniquely mapping
 siRNAs, are enriched in TE regions missing in other accessions. Thus,
 targeting by uniquely mapping siRNAs appears to promote sequence deletions
 in TEs. Overall, our work indicates that siRNA-targeting of TEs may
 influence removal of sequences from the genome and hence evolution of gene
 expression in plants.
description: TE annotation of
 Arabidopsis thaliana accession Bur-0TE annotation for
 Arabidopsis thaliana accession Bur-0. Coordinates are extracted from Bur-0
 genome assembly (http://1001genomes.org/projects/MPIWang2012/). File
 format: TE id | Chromosome | start position | stop
 position.Bur-0.TE.txtTE annotation of Arabidopsis thaliana accession C24TE annotation for Arabidopsis thaliana accession C24. Coordinates are extracted from C24 genome assembly (http://1001genomes.org/projects/MPIWang2012/). File format: TE id | Chromosome | start position | stop position.C24.TE.txt
DOI: 10.5061/dryad.vq587
title: Data from: Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment

description: Matching is an important step for increasing interoperability between
 heterogeneous ontologies. Here, we present alignments we produced as
 domain experts, using a manual mapping process, between the Hymenoptera
 Anatomy Ontology and other existing arthropod anatomy ontologies
 (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The
 resulting alignments contain from 43 to 368 mappings (correspondences),
 all derived from domain-expert input. Despite the many pairwise
 correspondences, only 11 correspondences were found in common between all
 ontologies, suggesting either major intrinsic differences between each
 ontology or gaps in representing each group’s anatomy. Furthermore, we
 compare our findings with putative correspondences from Bioportal (derived
 from LOOM software) and summarize the results in a total evidence
 alignment. We briefly discuss characteristics of the ontologies and issues
 with the matching process.
description: TGMA_obo_fileOntology OBO file version for mosquitoes (Culicidae) used during the matching process.TGMA.oboTADS_obo_fileOntology OBO file version for ticks (Ixodidae) used during the matching process.TADS.oboSPD_obo_fileOntology OBO file version for spiders (Araneae) used during the matching process.SPD.oboHAO_obo_fileOntology OBO file version for wasps, bees and ants (Hymenoptera) used during the matching process.HAO.oboFBbt_obo_fileOntology OBO file version for the fruit fly (Drosophila melanogaster) used during the matching process.FBbt.oboArthropod_Alignment_obo_xrefsThe final alignment in an OBO format Xref document.Arthropod_Alignment.oboHAO vs TGMA (mosquito)Excel aligment between Hymenoptera (HAO) and Culicidae (TGMA).HAO vs TADS (tick)Excel aligment between Hymenoptera (HAO) and Ixodidae(TADS).HAO vs SPD (spider)Excel aligment between Hymenoptera (HAO) and Araneae (SPD).HAO vs FBbt (Drosophila)Excel aligment between Hymenoptera (HAO) and Drosophila melanogaster (FBbt).Arthropod_Alignment_Cytoscape_NetworkArthropod alignment Cytoscape network file.Appendix_A_Intersection_HAO_SPD_TADSList of correspondences found in common between HAO, SPD & TADS.Appendix_B_Intersection_HAO_TGMA_FBbtList of correspondences found in common between HAO, TGMA & FBbt.Appendix_C_Intersection_AllList of correspondences found in common between all included ontologies.Appendix_D_SPD_HAO_Manual_vs_LOOMComparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & SPD.Appendix_E_TGMA_HAO_Manual_vs_LOOMComparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & TGMA.Appendix_F_FBbt_HAO_Manual_vs_LOOMComparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & FBbt.
DOI: 10.5061/dryad.rh0mv
title: Data from: Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta

description: Ecological factors may contribute to reproductive isolation if
 differential local adaptation causes immigrant or hybrid fitness
 reduction. Because local adaptation results from the interaction between
 natural selection and adaptive traits, it is crucial to investigate both
 to understand ecological speciation. Previously, we used niche modelling
 to identify local water availability as an environmental correlate of
 incipient ecological speciation between two subspecies in Boechera
 stricta, a close relative of Arabidopsis. Here, we performed several
 large-scale glasshouse experiments to investigate the divergence of
 various physiological, phenological and morphological traits. Although we
 found no significant difference in physiological traits, the Western
 subspecies has significantly faster growth rate, larger leaf area, less
 succulent leaves, delayed reproductive time and longer flowering duration.
 These trait differences are concordant with previous results that habitats
 of the Western genotypes have more consistent water availability, while
 Eastern genotypes inhabit locations with more ephemeral water supplies. In
 addition, by comparing univariate and multivariate divergence of complex
 traits (QST) to the genomewide distribution of SNP FST, we conclude that
 the aspects of phenology and morphology (but not physiology) are under
 divergent selection. In addition, we also identified several highly
 diverged traits without obvious water-related functions.
description: SNP_genotypeGenotype calls from 23379 SNPsExperiment1Phenotypic values measured in experiment 1Experiment2Phenotypic values measured in experiment 2Experiment3Phenotypic values measured in experiment 3
DOI: 10.5061/dryad.cm1qb
title: Data from: A comparative analysis of the mechanisms underlying speciation on Lord Howe Island

description: On Lord Howe Island, speciation is thought to have taken place in situ in
 a diverse array of distantly related plant taxa (Metrosideros, Howea and
 Coprosma; Proc. Natl Acad. Sci. USA 108, 2011, 13188). We now investigate
 whether the speciation processes were driven by divergent natural
 selection in each genus by examining the extent of ecological and genetic
 divergence. We present new and extensive, ecological and genetic data for
 all three genera. Consistent with ecologically driven speciation, outlier
 loci were detected using genome scan methods. This mechanism is supported
 by individual-based analyses of genotype–environment correlations within
 species, demonstrating that local adaptation is currently widespread on
 the island. Genetic analyses show that prezygotic isolating barriers
 within species are currently insufficiently strong to allow further
 population differentiation. Interspecific hybridization was found in both
 Howea and Coprosma, and species distribution modelling indicates that
 competitive exclusion may result in selection against admixed individuals.
 Colonization of new niches, partly fuelled by the rapid generation of new
 adaptive genotypes via hybridization, appears to have resulted in the
 adaptive radiation in Coprosma – supporting the ‘Syngameon hypothesis’.
description: Genetic_datasetGenetic data for individuals included in this studyEcological_datasetEcological data collected for individuals included in this study
DOI: 10.5061/dryad.qp367
title: Data from: Resolving ambiguity of concatenation in multi-locus sequence data for the construction of phylogenetic supermatrices

description: The construction of supermatrices from mining of DNA metadata is
 problematic due to incomplete species identification and incongruence of
 gene trees that hamper sequence concatenation based on Linnaean binomials.
 We applied methods from graph theory to minimize ambiguity of
 concatenation globally over a large data set. An initial step establishes
 sequence clusters for each locus that broadly correspond to Linnaean
 species. These clusters frequently are not consistent with binomials and
 specimen identifiers, which greatly complicates the concatenation of
 clusters across multiple loci. A multipartite heuristic algorithm is used
 to match clusters across loci and to generate a global set of concatenates
 that minimizes conflict of taxonomic names. The procedure was applied to
 all available data on GenBank for the Coleoptera (beetles) including
 &gt;10500 taxon labels for &gt;23500 sequences of four loci. The
 BlastClust algorithm was used in the initial clustering step, resulting in
 11241 clusters or divergent singletons. Clusters were first used for name
 assignment of unidentified sequences resulting in 510 new identifications
 (13.9% of total unidentified sequences) of which nearly half were by
 clustering of a specimen at a secondary locus. Concatenation was
 straightforward only for 12.8% of all binomials represented by a singleton
 sequence at each locus with an available entry, while the majority of
 binomials were associated to multi-sequence clusters in at least one
 locus. Concatenation of clusters is particularly problematic where limits
 of DNA-based clusters are inconsistent with the Linnaean binomials, either
 containing more than one binomial or splitting a binomial among multiple
 clusters. The current data set contained 1518 such clusters (13.5% of
 total). By applying a scoring scheme for full and partial name matches in
 pairs of clusters, the maximum weight set of concatenates produced a
 matrix of minimally 7366 terminals. Varying the match weights for partial
 matches had little effect on the number of terminals, although if partial
 matches were disallowed, the number of terminals increased greatly. Trees
 from the resulting supermatrices generally produced tree topologies in
 good agreement with the Linnaean taxonomy, with fewer terminals compared
 to trees generated according to standard species labels. The study
 illustrates a strategy for assembling the Tree-of-Life from an ever more
 complex primary database.
description: Matched sequence
 clusters across 4 lociMatchedMOTU.xlsKey for taxon identifiers used in concatenationTaxonStringKey.xls
DOI: 10.17909/cxk9-jt29
title: BZ Cam GALEX images