cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6j205
title: Data from: Inconsistent reproductive isolation revealed by interactions between Catostomus fish species

description: Interactions between species are central to evolution and ecology, but we
 do not know enough about how outcomes of interactions between species vary
 across geographic locations, in heterogeneous environments, or over time.
 Ecological interactions between species are known to vary, but
 evolutionary interactions such as reproductive isolation are often assumed
 to be consistent. Hybridization among Catostomus fish species occurs over
 a large and heterogeneous geographic area and across taxa with distinct
 evolutionary histories, and allows us to assess consistency in species
 interactions. We analyzed hybridization among six Catostomus species and
 found extreme variation in hybridization across locations. Variation in
 hybridization outcomes might result from uneven fitness of hybrids across
 locations, polymorphism in genetic incompatibilities, chance, unidentified
 historical contingencies, or some combination thereof. Our results suggest
 caution in assuming that one or a few instances of hybridization represent
 all interactions between the focal species, as species interactions vary
 substantially across locations.
description: Input file for entropy
 analysisGenotype likelihoods
 (simplified from VCF) at 11,221 SNPs for 2785 individual Catostomus fish.
 This file was used for analyses of hybridization.entropy_common0.7.mpglartificial reference genomeThis reference was made by completing a denovo assembly of a subset of the data using smng (see manuscript text) and all reads were assembled to this reference for variant calling.split_sucker_ref_mm90.fastaFull VCF fileAll variant sites initially identified for analysis of hybridization. This VCF was produced using samtools and bcftools, and contains information for 2785 Catostomus individuals.variants_0.7.vcf
DOI: 10.15468/dl.c94tb7
title: Occurrence Download

description: A dataset containing 21615 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sightings Map of Invasive Plants in Portugal"
 ]
}

 The dataset includes 21615 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000439-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mp040
title: Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

description: Massively parallel sequencing is rapidly emerging as an efficient way to
 quantify biodiversity at all levels, from genetic variation and expression
 to ecological community assemblage. However, the number of reads produced
 per sequencing run far exceeds the number required per sample for many
 applications, compelling researchers to sequence multiple samples per run
 in order to maximize efficiency. For studies that include a PCR step, this
 can be accomplished using primers that include an index sequence allowing
 sample origin to be determined after sequencing. The use of indexed
 primers assumes they behave no differently than standard primers; however,
 we found that indexed primers cause substantial template sequence-specific
 bias, resulting in radically different profiles of the same environmental
 sample. Likely the outcome of differential amplification efficiency due to
 primer-template mismatch, two indexed primer sets spuriously change the
 inferred sequence abundance from the same DNA extraction by up to 77.1%.
 We demonstrate that a double PCR approach alleviates these effects in
 applications where indexed primers are necessary.
description: library1_S1_L001_R1_001.fastqlibrary1_S1_L001_R2_001.fastqlibrary2_S2_L001_R1_001.fastqlibrary2_S2_L001_R2_001.fastqRK16sTS1_S1_L001_R1_001.fastqRK16sTS1_S1_L001_R2_001.fastqRK16sTS2_S2_L001_R1_001.fastqRK16sTS2_S2_L001_R2_001.fastqRK16sTS3_S3_L001_R1_001.fastqRK16sTS3_S3_L001_R2_001.fastqSequencing MetadataFile contains names of environmental samples, primer and index sequences, and library information corresponding to sequenced libraries.sequencing-metadata.csv
DOI: 10.5061/dryad.gt12rn3
title: Data from: Bidirectional adaptive introgression between two ecologically divergent sparrow species

description: Natural hybrid zones can be used to dissect the mechanisms driving key
 evolutionary processes by allowing us to identify genomic regions
 important for establishing reproductive isolation and that allow for
 transfer of adaptive variation. We leverage whole-genome data in a system
 where two bird species, the saltmarsh (Ammospiza caudacutus) and Nelson’s
 (A. nelsoni) sparrow, hybridize despite their relatively high background
 genetic differentiation and past ecological divergence. Adaptive
 introgression is plausible in this system because Nelson’s sparrows are
 recent colonists of saltwater marshes, compared to the specialized
 saltmarsh sparrow that has a longer history of salt-marsh adaptation.
 Comparisons among whole-genome sequences of 34 individuals from allopatric
 and sympatric populations show that ongoing gene flow is shaping the
 genomic landscape, with allopatric populations exhibiting genome-wide FST
 estimates close to double of that observed in sympatry. We characterized
 patterns of introgression across the genome and identify regions that
 exhibit biased introgression into hybrids from only one parental species.
 These regions offer compelling candidates for genes related to tidal marsh
 adaptations suggesting that adaptive introgression is an important
 consequence of hybridization. These findings highlight the value of
 considering the landscapes of both genome-wide introgression and
 divergence when characterizing the evolutionary forces that drive
 speciation.
description: Walsh et al.
 2018_Evolution.RawSNPDataVCF containing variant
 data for 34 whole genomes analyzed in this study. These include allopatric
 Nelson's sparrows (AlloNESP), allopatric saltmarsh sparrows
 (AlloSALS), sympatric Nelson's sparrows (SymNESP), sympatric
 saltmarsh sparrows (SymSALS), and one seaside sparrow used as an outgroup
 (SESP). See methods for variant calling/filtering
 parameters.Walsh et al.
 2018_Evolution_RawSNPData.vcf
DOI: 10.5061/dryad.g0f4hv0
title: Data from: Clitellate worms (Annelida) in lateglacial and Holocene sedimentary DNA records from the Polar Urals and northern Norway

description: While there are extensive macro- and microfossil records of a range of
 plants and animals from Quaternary records, earthworms and their close
 relatives among annelids are not preserved as fossils, and therefore we
 have limited knowledge of their Quaternary distributions. This lack of
 fossils means that clitellate worms (Annelida) are currently underused in
 palaeoecological research, even though they can provide valuable
 information about terrestrial and aquatic environmental conditions. Their
 DNA might be preserved in sediments, which offers an alternative method
 for detection. Here we analyse lacustrine sediments from lakes in the
 Polar Urals, Arctic Russia, covering the period 24,000-1,300 cal. years
 BP, and NE Norway (10,700-3,300 cal. years BP) using a universal mammal
 16S rDNA marker. While mammals were recorded using the marker (reindeer
 was detected twice in the Polar Urals core at 23,000 and 14,000 cal. years
 BP, and four times in the Norwegian core at 11,000 cal. years BP and
 between 3,600-3,300 cal. years BP), worm extracellular DNA “bycatch” was
 rather high. In this paper we present the first reported worm detection
 from ancient DNA. Our results demonstrate that both aquatic and
 terrestrial clitellates can be identified in late-Quaternary lacustrine
 sediments, and the ecological information retrievable from this group
 warrants further research with a more targeted approach.
description: FilterBarcodingR script used for the Filtering of the OBITOOLS output.Sample_tag_primer_URAL-MamExcel file containing the primer tags and sample names for the Polar Urals run. The primer information was used by OBITOOLS to demultiplex the data.Sample_tag_primer_Varanger-MamP007Excel file containing the primer tags and sample names for the Varanger run. The primer information was used by OBITOOLS to demultiplex the data.URAL-Mam.un.an.C1.L13.obiclean.r5.HpS.M-iden.ann.sort_10_23_1_2_1The filtered OBITOOLS output for the Polar Urals run.Hubia2-Mammal.ali.uniq.c2.cl.M-iden.ann.sort_10_23_1_2_1The filtered Varanger OBITOOLS outputGZO-35_merged.fastqFirst part of the merged forward and reverse reads for the Varanger core.GZO-36_merged.fastqSecond part of the merged forward and reverse reads for the Varanger core.GZO-37_merged.fastqFirst part of the merged forward and reverse reads for the Polar Urals core.GZO-38_merged.fastqSecond part of the merged forward and reverse reads for the Polar Urals core.GZO-39_merged.fastqThird part of the merged forward and reverse reads for the Polar Urals core.GZO-40_merged.fastqFourth part of the merged forward and reverse reads for the Polar Urals core.
DOI: 10.15468/dl.vq8td4
title: Occurrence Download

description: A dataset containing 595 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bees from Sistema Central Western Montains 1987"
 ]
}

 The dataset includes 595 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000437-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.436h0
title: Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.

description: Discrepancies between morphology-based taxonomy and phylogenetic
 systematics are common in Scleractinian corals. In Pocillopora corals,
 nine recently identified genetic lineages disagree fundamentally with the
 17 recognized Pocillopora species, including 5 major Indo-Pacific
 reef-builders. Pocillopora corals hybridize in the Tropical Eastern
 Pacific, so it is possible that some of the disagreement between the
 genetics and taxonomy may be due to introgressive hybridization. Here we
 used 6769 genome-wide SNPs from Restriction-site Associated DNA sequencing
 (RAD-Seq) to conduct phylogenomic comparisons among three common,
 Indo-Pacific Pocillopora species - P.'damicornis, P. eydouxi and P.
 elegans - within and between populations in the Tropical Eastern Pacific
 (TEP) and the Central Pacific. Genome-wide RAD-Seq comparisons of Central
 and TEP Pocillopora confirm that the morphospecies P.'damicornis, P.
 eydouxi and P. elegans are not monophyletic, but instead fall into three
 distinct genetic groups. However, hybrid samples shared fixed alleles with
 their respective parental species and, even without strict monophyly, P.
 damicornis share a common set of 33 species- specific alleles across the
 Pacific. RAD-Seq data confirm the pattern of one-way introgressive
 hybridization among TEP Pocillopora, suggesting that introgression may
 play a role in generating shared, polyphyletic lineages among currently
 recognized Pocillopora species. Levels of population differentiation
 within genetic lineages indicate significantly higher levels of population
 differentiation in the Tropical Eastern Pacific than in the Central West
 Pacific.
description: P8-loci
 alignmentLoci that were found in
 all 8 samples were assembled in the more conservative ‘P8’ dataset, which
 was used to calculate pairwise population genetic metrics (e.g.
 heterozygosity, private alleles, pairwise distances) and to verify and
 support P2 results.P8-loci.phyP2-loci alignmentAll loci that were recovered from at least two samples were compiled in the extensive ‘P2’ dataset, which was used for all analyses, unless stated otherwise.P2-loci.phyPdamT1P_Pst1Pocillopora damicornis - Type 1 - Panama - Digested with Pst1, single-end RADSeq.PdamT3P1GC_Pst1Pocillopora damicornis - Type 3 - Panama, Gulf of Chiriquí - Digested with Pst1, single-end RADSeqPdamT3P2GP_Pst1.fqPocillopora damicornis - Type 3 - Panama, Gulf of Panama - Digested with Pst1, single-end RADSeqPdamT5JA_Pst1.fqPocillopora damicornis - Type 5 - Japan - Digested with Pst1, single-end RADSeqPdamT13P_Pst1.fqPocillopora damicornis - Type 1/3 Het - Panama - Digested with Pst1, single-end RADSeqPdamT5TU_Pst1.fqPocillopora damicornis - Type 5 - French Polynesia, Tuamotus - Digested with Pst1, single-end RADSeqPeleT1P_Pst1.fqPocillopora elegans - Type 1 - Panama - Digested with Pst1, single-end RADSeqPeydT1P_Pst1.fqPocillopora eydouxi - Type 1 - Panama - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.42m1p
title: Data from: Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics

description: Malaria vectors are exposed to intense selective pressures due to
 large-scale intervention programs that are underway in most African
 countries. One of the current priorities is therefore to clearly assess
 the adaptive potential of Anopheline populations, which is critical to
 understand and anticipate the response mosquitoes can elicit against such
 adaptive challenges. The development of genomic resources that will
 empower robust examinations of evolutionary changes in all vectors
 including currently understudied species is an inevitable step toward this
 goal. Here we constructed double-digest Restriction Associated DNA (ddRAD)
 libraries and generated 6461 Single Nucleotide Polymorphisms (SNPs) that
 we used to explore the population structure and demographic history of
 wild-caught Anopheles moucheti from Cameroon. The genome-wide distribution
 of allelic frequencies among samples best fitted that of an old population
 at equilibrium, characterized by a weak genetic structure and extensive
 genetic diversity, presumably due to a large long term effective
 population size. Estimates of FST and Linkage Disequilibrium (LD) across
 SNPs reveal a very low genetic differentiation throughout the genome and
 the absence of segregating LD blocks among populations, suggesting an
 overall lack of local adaptation. Our study provides the first
 investigation of the genetic structure and diversity in An. moucheti at
 the genomic scale. We conclude that, despite a weak genetic structure,
 this species has the potential to challenge current vector control
 measures and other rapid anthropogenic and environmental changes thanks to
 its great genetic diversity.
description: Anopheles
 moucheti_part1Fastq files for
 Anopheles moucheti individuals from Cameroon - part 1moucheti_part1.tar.gzAnopheles moucheti_part2Fastq files for Anopheles moucheti individuals from Cameroon - part 2moucheti_part2.tar.gzAnopheles moucheti_part3Fastq files for Anopheles moucheti individuals from Cameroon - part 3moucheti_part3.tar.gzAnopheles moucheti_part4Fastq files for Anopheles moucheti individuals from Cameroon - part 4moucheti_part4.tar.gzAnopheles moucheti_part5Fastq files for Anopheles moucheti individuals from Cameroon - part 5moucheti_part5.tar.gzAnopheles moucheti data fileInformation on Anopheles moucheti samples sequenced from CameroonAn.moucheti_datafile.xlsx
DOI: 10.5061/dryad.gp23s
title: Data from: RAD-mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

description: How loss of genetic exchanges (recombination) evolves between sex
 chromosomes is a long-standing question. Suppressed recombination may
 evolve when a sexually antagonistic (SA) polymorphism occurs in a
 partially sex-linked, “pseudo-autosomal’ region (or “PAR”), maintaining
 allele frequency differences between the two sexes, and creating selection
 for closer linkage with the fully sex-linked region of the Y chromosome in
 XY systems, or the W in ZW sex chromosome systems. Most evidence
 consistent with the SA polymorphism hypothesis is currently indirect, and
 more studies of the genetics and population genetics of PAR genes are
 clearly needed. The sex chromosomes of the plant Silene latifolia are
 suitable for such studies, as they evolved recently and the loss of
 recombination could still be ongoing. Here, we used RAD sequencing to
 genetically map sequences in this plant, which has a large genome (~ 3
 gigabases) and no available whole genome sequence. We mapped 83 genes on
 the sex chromosomes, and comparative mapping in the related species S.
 vulgaris supports previous evidence for additions to an ancestral PAR, and
 identified at least 12 PAR genes. We describe evidence that recombination
 rates have been reduced in meiosis of both sexes, and differences in
 recombination between S. latifolia families suggest ongoing recombination
 suppression. Large allele frequency differences between the sexes were
 found at several loci closely linked to the PAR boundary, and genes in
 different regions of the PAR showed striking sequence diversity patterns
 that help illuminate the evolution of the PAR.
description: SNP file from
 SamtoolsSNPs called from each
 RAD-tag and the paired read2 sequence(s)all_snps_samtools_filter_d200-2000q60.vcfJoinmap input filesMarkers generated by RAD-Sequencing and validated by genotyping in this studyJoinMap.xlsxContig coverage info for all contigs and candidate hemizygous genesCoverage information from the parents and all the progeny and normalized by the total number of reads in each individuals. And the coverage information for the 22 candidate hemizygous genesCoverage.xlsxPrimers for genotyping and population studyPrimers.docxStatistics for Figure2&3Read_mapping_results.zipReads mapped to the assembled RAD contigsRead_Mapping_results.zipall_contigs_first_and_second_readsAssembled RAD contigs including read1 and read2Sequence alignmentsAligned Sanger sequences for all individuals and lociSequence_alignments.zip
DOI: 10.5061/dryad.g0n2d
title: Data from: Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins

description: Protein folding occurs as a set of transitions between structural states
 within an energy landscape. An oversimplified view of the folding process
 emerges when transiently populated states are undetected because of
 limited instrumental resolution. Using force spectroscopy optimized for
 1-microsecond resolution, we reexamined the unfolding of individual
 bacteriorhodopsin molecules in native lipid bilayers. The experimental
 data reveal the unfolding pathway in unprecedented detail. Numerous newly
 detected intermediates—many separated by as few as two or three amino
 acids—exhibited complex dynamics, including frequent refolding and state
 occupancies of &lt;10 μs. Equilibrium measurements between such states
 enabled the folding free-energy landscape to be deduced. These results
 sharpen the picture of the mechanical unfolding of membrane proteins and,
 more broadly, enable experimental access to previously obscured protein
 dynamics.
description: Fig 1CFig1C_figS6A.csvFig 1DFig1D.csvFig 1EFig1E.csvFig 1FFig1F.csvFig 2Fig 3Figure 3 and Fig S8A.csvFig 4ABFig4AB.csvFig 4CFig4C.csvFig S1AFigS1A.csvFig S1BFigS1B.csvFig S2AFig S2BFig S2CFig S2DFig S2EFig S2FFig S2GFig S2HFig S2IFig S2JFig S2KFig S2LFig S2MFig S2NFig S3AFigS3A.csvFig S3BFigS3B.csvFig S3CFigureS3C.csvFig S4AFig S4BFig S5FigS5.csvFig S6AFig1C_figS6A.csvFig S6BFigS6B.csvFig S6CFigS6C.csvFig S6DFigS6D.csvFig S6EFigS6E.csvFig S7Fig S8AFigure 3 and Fig S8A.csvFig S8BCFig S7 and S8BC.xlsxFig S9AFigS9A.csvFig S9BFigS9B.csvFig S9CFigS9C.csvFig S9DFigS9D.csvFig S10AFigS10A.csvFig S10BFigS10B.csvFig S10CFigS10C.csvFig S11AFigS11A.csvFig S11BFigS11B.csvFig S13AFigS13A.csvFig S13BFigS13B.csvFig S13CFigS13C.csv
DOI: 10.5061/dryad.d331n
title: Data from: Human blood and mucosal regulatory T cells express activation markers and inhibitory receptors in inflammatory bowel disease

description: Background: FOXP3+ regulatory T cells (Tregs) are critical for preventing
 intestinal inflammation. However, FOXP3+ T cells are paradoxically
 increased in the intestines of patients with the inflammatory bowel
 disease (IBD) ulcerative colitis (UC) or Crohn's disease (CD). We
 determined whether these FOXP3+ cells in IBD patients share or lack the
 phenotype of such cells from patients without IBD. Methods: We quantified
 and characterized FOXP3+ Treg populations, as well as FOXP3- CD4+ T cells,
 in the lamina propria lymphocytes (LPL) of intestine surgically resected
 from patients with and without IBD, and in the blood of controls or
 Crohn's patients with or without disease activity. Results: In all
 samples, a similar fraction of FOXP3+ cells expressed the
 "natural" Treg (nTreg) marker Helios, suggesting that, in IBD,
 these cells are not entirely "induced" Tregs (iTregs) derived
 from activated effector T cells. Helios+ and Helios- FOXP3+ T cells
 demonstrated similar expression of maturation markers, activation markers,
 and inhibitory molecules between IBD patients and controls, while FOXP3-
 cells paradoxically expressed more of the inhibitory receptors CD39,
 CTLA4, and PD-1 in inflamed mucosa. Greater expression of activation
 markers was also seen in both Helios+ and Helios- Tregs, relative to
 FOXP3- cells, in both IBD patients and controls, indicating that Tregs are
 effectively activated by antigen in IBD. Conclusions: Extensive
 immunophenotyping revealed that Helios+ and Helios- mucosal Tregs exist at
 a similar frequency, and have a similar expression of inhibitory molecules
 and activation markers in patients with IBD as in healthy controls.
description: Lord1: Supplementary
 DataRaw data used to draw
 conclusions in paper and figures. Concat Lord[1-5].bin together into
 Lord.zipLord1.binLord2: Supplementary DataConcat Lord[1-5].bin together into Lord.zipLord2.binLord3: Supplementary DataConcat Lord[1-5].bin together into Lord.zipLord3.binLord4: Supplementary DataConcat Lord[1-5].bin together into Lord.zipLord4.binLord5: Supplementary DataConcat Lord[1-5].bin together into Lord.zipLord5.bin