cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9k1h0
title: Data from: A signature of dynamic biogeography: enclaves indicate past species replacement

description: Understanding how species have replaced each other in the past is
 important to predicting future species turnover. While past species
 replacement is difficult to detect after the fact, the process may be
 inferred from present-day distribution patterns. Species with abutting
 ranges sometimes show a characteristic distribution pattern, where a
 section of one species range is enveloped by that of the other. Such an
 enclave could indicate past species replacement: when a species is partly
 supplanted by a competitor, but a population endures locally while the
 invading species moves around and past it, an enclave forms. If the two
 species hybridize and backcross, the receding species is predicted to
 leave genetic traces within the expanding one under a scenario of species
 replacement. By screening dozens of genes in hybridizing crested newts, we
 uncover genetic remnants of the ancestral species, now inhabiting an
 enclave, in the range of the surrounding invading species. This
 independent genetic evidence supports the past distribution dynamics we
 predicted from the enclave. We suggest that enclaves provide a valuable
 tool in understanding historical species replacement, which is important
 because a major conservation concern arising from anthropogenic climate
 change is increased species replacement in the future.
description: Files associated with
 the HZAR analysisFiles associated with
 the HZAR analysisHZAR.zipIon Torrent outputIon Torrent outputIon_Torrent_output.zipITProcessedPartAProcessed Ion Torrent data part AITProcessedPartBProcessed Ion Torrent data part BITProcessedPartCProcessed Ion Torrent data part CITProcessedPartDProcessed Ion Torrent data part DITProcessedPartEProcessed Ion Torrent data part EITProcessedPartFProcessed Ion Torrent data part FITProcessedPartGProcessed Ion Torrent data part GITProcessedPartHProcessed Ion Torrent data part HITProcessedPartIProcessed Ion Torrent data part IITProcessedPartJProcessed Ion Torrent data part JITProcessedPartKProcessed Ion Torrent data part KITProcessedPartLProcessed Ion Torrent data part LITRawPartARaw Ion Torrent data part AITRawPartBRaw Ion Torrent data part BITRawPartCRaw Ion Torrent data part CITRawPartDRaw Ion Torrent data part DITRawPartERaw Ion Torrent data part EITRawPartFRaw Ion Torrent data part FITRawPartGRaw Ion Torrent data part GMEGAFiles associated with the MEGA analysisSTRUCTURE-MainK4runFiles associated with the Structure analysis determining KSTRUCTURE-referencePartAFiles associated with the Structure analysis on the full data set part ASTRUCTURE-referencePartBFiles associated with the Structure analysis on the full dataset part BExclave_samplingSampling (kmz file for Google Earth)
DOI: 10.5061/dryad.93fv2
title: Data from: Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory

description: In yeast and humans, previous experiences can lead to epigenetic
 transcriptional memory: repressed genes that exhibit mitotically heritable
 changes in chromatin structure and promoter recruitment of poised RNA
 polymerase II preinitiation complex (RNAPII PIC), which enhances future
 reactivation. Here, we show that INO1 memory in yeast is initiated by
 binding of the Sfl1 transcription factor to the cis-acting Memory
 Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory
 requires a remodeled form of the Set1/COMPASS methyltransferase lacking
 Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits
 the SET3C complex, which plays an essential role in maintaining this mark.
 Finally, while active INO1 is associated with Cdk8- Mediator, during
 memory, Cdk8+ Mediator recruits poised RNAPII PIC lacking the Kin28 CTD
 kinase. Aspects of this mechanism are generalizable to yeast and conserved
 in human cells. Thus, COMPASS and Mediator are repurposed to promote
 epigenetic transcriptional poising by a highly conserved mechanism.
description: yohheiBrickner.fastq
DOI: 10.5061/dryad.k6636
title: Data from: The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion

description: Range expansions are complex evolutionary and ecological processes. From
 an evolutionary standpoint, a populations' adaptive capacity can
 determine the success or failure of expansion. Using individual-based
 simulations, we model range expansion over a two-dimensional,
 approximately continuous landscape. We investigate the ability of
 populations to adapt across patchy environmental gradients and examine how
 the effect sizes of mutations influence the ability to adapt to novel
 environments during range expansion. We find that genetic architecture and
 landscape patchiness both have the ability to change the outcome of
 adaptation and expansion over the landscape. Adaptation to new
 environments succeeds via many mutations of small effect or few of large
 effect, but not via the intermediate between these cases. Higher genetic
 variance contributes to increased ability to adapt, but an alternative
 route of successful adaptation can proceed from low genetic variance
 scenarios with alleles of sufficiently large effect. Steeper environmental
 gradients can prevent adaptation and range expansion on both linear and
 patchy landscapes. When the landscape is partitioned into local patches
 with sharp changes in phenotypic optimum, the local magnitude of change
 between subsequent patches in the environment determines the success of
 adaptation to new patches during expansion.
description: Zip folder of Nemo
 simulation inputs and output data.This zip folder contains
 scripts for generating input files for the modified version of Nemo
 described in text and available on Github, and requires the aNEMOne R
 package also described in text and on Github. Output stats files from Nemo
 are also included which are summary statistics over the whole landscape
 through time for each simulation. These can be used to generate all of the
 expansion rate results. Files within the "ind_seln" folders
 contain output data on individual fitness values across the landscape at a
 given point in time. These can be used to generate all of the fitness
 results and spatial-specific information. Files within the
 "Quanti" folder contain output data on genotypes across all loci
 for every individual across the landscape at a given time point. These can
 be used to generate the values of effect size differences in the two-patch
 models. There is also a folder labeled
 "Compiled_SimulationResults" which contains the relevant
 calculations from all of the above described output file
 sets.DataArchiving.zip
DOI: 10.5061/dryad.3kd7c
title: Data from: Global mammal betadiversity show parallel assemblage structure in similar but isolated environments

description: The taxonomic, phylogenetic and trait dimensions of betadiversity each
 provide unique insight into the importance of historical isolation and
 environmental conditions in shaping global diversity. These three
 dimensions should, in general, be positively correlated. However, if
 similar environmental conditions filter species with similar trait values,
 then assemblages located in similar environmental conditions, but
 separated by large dispersal barriers, may show high taxonomic, high
 phylogenetic, but low trait betadiversity. Conversely, we expect lower
 phylogenetic diversity but higher trait biodiversity among assemblages
 that are connected but are in differing environmental conditions. We
 calculated all pairwise comparisons of ~110x110 km grid-cells across the
 globe for ~5,000 mammal species (~70 million comparisons). We considered
 realms as units representing geographic distance and historical isolation
 and biomes as units with similar environmental conditions. While
 betadiversity dimensions were generally correlated, we highlight
 geographic regions of decoupling among betadiversity dimensions. Our
 analysis shows that assemblages from tropical forests in different realms
 had low trait dissimilarity while phylogenetic betadiversity was
 significantly higher than expected, suggesting potential convergent
 evolution. Low trait betadiversity was surprisingly not found between
 isolated deserts, despite harsh environmental conditions. Overall, our
 results provide evidence for parallel assemblage structure of mammal
 assemblages driven by environmental conditions at a global scale.
description: Global mammal
 betadiversity 1R file containing values
 for taxonomic, phylogenetic and trait turnover calculated for all
 terrestrial mammals at 1-degree grid-cell resolution. Environmental
 dissimilarities, geographic distances and realm / biome information is
 also provided. The files can be combined using
 HJ-Split.BetaDistEnvBIOMEturn.RData.001Global mammal betadiversity 2BetaDistEnvBIOMEturn.RData.002Global mammal betadiversity 3BetaDistEnvBIOMEturn.RData.003Global mammal betadiversity 4BetaDistEnvBIOMEturn.RData.004Global mammal betadiversity 5BetaDistEnvBIOMEturn.RData.005
DOI: 10.5061/dryad.1fj75
title: Data from: Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands

description: Genetic pollution of a native species through hybridization with an
 invasive species poses an insidious conservation threat. To expose genetic
 pollution, molecular methods employing multilocus data are required. We
 present a case study of genetic pollution via hybridization of a native
 crested newt species, Triturus cristatus, by the invasive T. carnifex on
 the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next
 generation sequencing and one mitochondrial marker by Sanger sequencing
 for four populations from the native range of both parent species and
 eleven ponds on the Veluwe. We use three population genetic approaches
 (HIest, BAPS and Structure) to determine the genetic composition of the
 Veluwe newts based on all nuclear markers, a subset of 18 diagnostic
 markers and the complementary 32 non-diagnostic markers, with and without
 parental populations. BAPS underestimates genetic pollution, whereas
 Structure is comparatively accurate compared to HIest, although
 Structure’s relative advantage decreases with the diagnosticity of the
 markers. Data simulation confirms these findings. Genetic composition of
 the Veluwe ponds ranges from completely native, via different degrees of
 genetic admixture, to completely invasive. The observed hybrid zone
 appears to be bimodal, suggesting negative selection against hybrids. A
 genetic footprint of the native species is present in invasive
 populations, evidencing that the invasive locally replaced the native
 species. Genetic pollution is currently confined to a small area, but the
 possibility of further expansion cannot be excluded. Removal of genetic
 pollution will not be easy. We emphasize the need for legal guidance to
 manage genetic pollution.
description: Triturus
 transcriptome-based gene models in FASTA formatTriturus
 transcriptome-based gene models in FASTA formatFASTA.zipRaw Ion Torrent reads in FASTQ formatRaw Ion Torrent reads in FASTQ formatFASTQ.zipBWA alignments in SAM formatBWA alignments in SAM formatSAM.zipRaw SNP reports in VCF formatRaw SNP reports in VCF formatVCF.zipScripts associated with the bioinformatics pipelineScripts associated with the bioinformatics pipelineScripts_Ion_Torrent_Triturus.zipInput files for the data simulationInput files for the data simulationData Simulation input.zipInput files for HIest, Structure and BAPSInput files for HIest, Structure and BAPSHIest, Structure and BAPS input.zipND4 SPF filesND4 SPF filesND4.SPFFiltered SNP report used to construct consensus sequencesFiltered SNP report used to construct consensus sequencesStatistics.zip
DOI: 10.5061/dryad.g5q6g80
title: Data from: Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR ‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics

description: PREMISE OF THE STUDY: Polyploidy has been long recognized as an important
 force in plant evolution. Previous studies had suggested widespread
 occurrence of polyploidy and the allopolyploid origin of several species
 in the diverse Neotropical genus Lachemilla (Rosaceae). Nonetheless, this
 evidence has relied mostly on patterns of cytonuclear discordance, and
 direct evidence from nuclear allelic markers is still needed. METHODS:
 Here we used PCR target enrichment in combination with high throughput
 sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA
 cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions
 representing 48 species of Lachemilla, and explore the allopolyploid
 origin of species in this group. KEY RESULTS: We were able to identify
 multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in
 33 species of Lachemilla, showing that this condition is common and
 widespread in the genus. Additionally, we found evidence for three
 autopolyploid species. We also established multiple, independent origins
 of several allopolyploid species. Finally, based solely on the cpDNA
 phylogeny, we identified that the monotypic genus Farinopsis Chrtek
 & Soják is the sister group of Lachemilla and allied genera within
 subtribe Fragariinae. CONCLUSIONS: Our study demonstrates the utility of
 the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted
 evolution of this region is not complete. Additionally, with a robust
 chloroplast phylogeny in place, the direction of hybridization events can
 be established, and multiple, independent origins of allopolyploid species
 can be identified.
description: Data from: Extensive
 allopolyploidy in the Neotropical genus Lachemilla (Rosaceae) revealed by
 PCR-based target enrichment of the nuclear ribosomal DNA cistron and
 plastid phylogenomics. AJBThis package contains
 the all the alignments and trees from the phylogenetic analyses from the
 paper. Also, it includes the demultiplexed reads ready to run
 Fluidimg2PURC in two separate files.Aligments_and_Results.zipDemultiplexed_reads_pt_1This file contains the first part of the microfluidic PRC reads from the Access Array SystemDemultiplexed_reads_pt_2This file contains the first part of the microfluidic PRC reads from the Juno SystemChloroplast_alignment_with_annotations_and_primersThis is a Geneious file with the chloroplast alignment used to primer design with primer and gene annotations.
DOI: 10.5061/dryad.db543
title: Data from: External mechanical work in the galloping racehorse

description: Horse locomotion is remarkably economical. Here we measure external
 mechanical work of the galloping horse and relate it to published
 measurements of metabolic cost. Seven Thoroughbred horses were galloped
 (ridden) over force plates, under a racing surface. Twenty-six full
 strides of force data were recorded and used to calculate external
 mechanical work of galloping. The mean sum of decrements of mechanical
 energy was -876J (± 280J) per stride and increments were 2163J (± 358J)
 per stride as horses were accelerating. Combination with published values
 for internal work and metabolic costs for galloping yield an apparent
 muscular efficiency of 37-46% for galloping which would be reduced by
 energy storage in leg tendons. Knowledge about external work of galloping
 provides further insight into the mechanics of galloping from both an
 evolutionary and performance standpoint.
description: Data
 SummaryTables of analysed data,
 trial information and subject information.Raw
 DataRaw data for trial shown
 in figure 1Horse2Trial4RAW.txtProcessed dataSummed force data in vertical and cranio-caudal directions for trial shown in Figure 1.Horse2Trial4Processed.csvVideo DataVideo data for trial shown in Figure 1Horse2Trial4_Camera1.aviVideo Data 2Video data for trial shown in Figure 1Horse2Trial4_Camera2.avi
DOI: 10.5061/dryad.j4j12v0
title: Data from: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

description: The columbine genus Aquilegia is a classic example of an adaptive
 radiation, involving a wide variety of pollinators and habitats. Here we
 present the genome assembly of A. coerulea 'Goldsmith',
 complemented by high-coverage sequencing data from 10 wild species
 covering the world-wide distribution. Our analyses reveal extensive allele
 sharing among species, and demonstrate that introgression and selection
 played a role in the Aquilegia radiation. We also present the remarkable
 discovery that the evolutionary history of an entire chromosome differs
 from that of the rest of the genome - a phenomenon which we do not fully
 understand, but which highlights the need to consider chromosomes in an
 evolutionary context.
description: Aquilegia kept
 positionszipped text file of all
 genomic positions kept for population genetics analysis of 10 Aquilegia
 speciesAQ.only.kept.positions.txt.gzAquilegia and Semiaquilegia kept positionszipped text file of all genomic positions kept for population genetics analysis of 10 Aquilegia species and SemiaquilegiaAQ.Semi.kept.positions.txt.gzREADME fileREADME file for data in this repositorybiallelic SNPszipped vcf of all bialleleic SNPs called in 10 Aquilegia species plus Semiaquilegia. Species are referred to by short names as follows: species name.in.vcf geography Aquilegia_aurea IIUF europe Aquilegia_barnebyi IIUC north_america Aquilegia_chrysantha IIWY north_america Aquilegia_japonica IIWU asia Aquilegia_formosa IIWT north_america Aquilegia_longissima IIWX north_america Aquilegia_oxysepala IIWW asia Aquilegia_vulgaris IIUH europe Aquilegia_pubescens D14R north_america Aquilegia_sibirica IIUI asia Semiaquilegia SRR4 asiaAQ.Semi.all.biallelic.SNPs.vcf.gz
DOI: 10.5061/dryad.t4f4g85
title: Data from: Phylogenomics and the evolution of hemipteroid insects

description: Hemipteroid insects (Paraneoptera), with over 10% of all known insect
 diversity, are a major component of terrestrial and aquatic ecosystems.
 Previous phylogenetic analyses have not consistently resolved the
 relationships among major hemipteroid lineages. We provide maximum
 likelihood-based phylogenomic analyses of a taxonomically comprehensive
 dataset comprising sequences of 2,395 single-copy, protein-coding genes
 for 193 samples of hemipteroid insects and outgroups. These analyses yield
 a well-supported phylogeny for hemipteroid insects. Monophyly of each of
 the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is
 strongly supported, as are most relationships among suborders and
 families. Thysanoptera (thrips) is strongly supported as sister to
 Hemiptera. However, as in a recent large-scale analysis sampling all
 insect orders, trees from our data matrices support Psocodea (bark lice
 and parasitic lice) as the sister group to the holometabolous insects
 (those with complete metamorphosis). In contrast, four-cluster likelihood
 mapping of these data does not support this result. A molecular dating
 analysis using 23 fossil calibration points suggests hemipteroid insects
 began diversifying before the Carboniferous, over 365 million years ago.
 We also explore implications for understanding the timing of
 diversification, the evolution of morphological traits, and the evolution
 of mitochondrial genome organization. These results provide a phylogenetic
 framework for future studies of the group.
description: README - Supplementary
 Archives 1 - 7README of all
 Supplementary Archives 1-7Johnson_et_al_2018_DRYAD_README.pdfSupplementary Archive 1Supplementary Archive 1: Ortholog SetSupplementary_Archive_1_Ortholog_Set.tar.gzSupplementary Archive 2Supplementary Archive 2: Multiple sequence alignments (MSAs) of included genes (amino-acid and nucleotide level)Supplementary_Archive_2_GeneMSAs_aa_nt.tar.gzSupplementary Archive 3Supplementary Archive 3: main data setsSupplementary_Archive_3_main_data_sets.tar.gzSupplementary Archive 4Supplementary Archive 4: Phylogenetic trees and bootstrap convergence resultsSupplementary_Archive_4_phylogenies_bootstraps.tar.gzSupplementary Archive 5 - part ISupplementary Archive 5 - part I: primary amino-acid dataset resorted ; FcLM datasets Hypothesis i-iiSupplementary_Archive_5_FCLM_and_permutations_partI.tar.gzSupplementary Archive 5 - part IISupplementary Archive 5 - part II: FcLM datasets Hypothesis iii-viSupplementary_Archive_5_FCLM_and_permutations_partII.tar.gzSupplementary Archive 5 - part IIISupplementary Archive 5 - part III: FcLM datasets Hypothesis vii-ixSupplementary_Archive_5_FCLM_and_permutations_partIII.tar.gzSupplementary Archive 6Supplementary Archive 6: morphological character description and morphological data matricesSupplementary_Archive_6_Morphology.tar.gzSupplementary Archive 7Supplementary Archive 7: dataset used for divergence date analyses and supplementary materialSupplementary_Archive_7_divgergence_date_analyses.tar.gz
DOI: 10.5061/dryad.72c2g
title: Data from: Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

description: Few clades of plants have proven as difficult to classify as cacti. One
 explanation may be an unusually high level of convergent and parallel
 evolution (homoplasy). To evaluate support for this phylogenetic
 hypothesis at the molecular level, we sequenced the genomes of four cacti
 in the especially problematic tribe Pachycereeae, which contains most of
 the large columnar cacti of Mexico and adjacent areas, including the
 iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We
 assembled a high-coverage draft genome for saguaro and lower coverage
 genomes for three other genera of tribe Pachycereeae (Pachycereus,
 Lophocereus, and Stenocereus) and a more distant outgroup cactus,
 Pereskia. We used these to construct 4,436 orthologous gene alignments.
 Species tree inference consistently returned the same phylogeny, but gene
 tree discordance was high: 37% of gene trees having at least 90% bootstrap
 support conflicted with the species tree. Evidently, discordance is a
 product of long generation times and moderately large effective population
 sizes, leading to extensive incomplete lineage sorting (ILS). In the best
 supported gene trees, 58% of apparent homoplasy at amino sites in the
 species tree is due to gene tree-species tree discordance rather than
 parallel substitutions in the gene trees themselves, a phenomenon termed
 “hemiplasy.” The high rate of genomic hemiplasy may contribute to apparent
 parallelisms in phenotypic traits, which could confound understanding of
 species relationships and character evolution in cacti.
description: Phylogenomic data for
 saguaro and PachycereeaeAssemblies, annotations,
 and phylogenomic data sets for analyses of saguaro and
 Pachycereeaesaguaro.datadryad.v3.tar.gz