cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.arqptr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cabdio morar",
 "HasCoordinate is true",
 "Geometry POLYGON((-78 12, -73 12, -73 0, -78 0, -78 12))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032517-251025141854904/datasets/export for details.
DOI: 10.15468/dl.kh2dvd
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-106.3188 21.89913, -106.1688 21.89913, -106.1688 22.04913, -106.3188 22.04913, -106.3188 21.89913))"
 ]
}

 The dataset includes 149 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032518-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ps75fu
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Callichthys callichthys",
 "HasCoordinate is true",
 "Geometry POLYGON((-78 12, -73 12, -73 0, -78 0, -78 12))"
 ]
}

 The dataset includes 23 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032519-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.afmqz7
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-106.1688 21.89913, -106.0188 21.89913, -106.0188 22.04913, -106.1688 22.04913, -106.1688 21.89913))"
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032520-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fw5uvb
title: Occurrence Download

description: A dataset containing 410660 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Sus scrofa",
 "Year 1960-2024"
 ]
}

 The dataset includes 410660 records from 2672 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032490-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d4vr0
title: Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

description: Recent studies have shown that one of the parental subgenomes in ancient
 polyploids is generally more dominant - having both retained more genes
 and being more highly expressed - a phenomenon termed subgenome dominance.
 The genomic features that determine how quickly and which subgenome
 dominates within a newly formed polyploid remain poorly understood. To
 investigate the rate of subgenome dominance emergence, we examined gene
 expression, gene methylation, and transposable element (TE) methylation in
 a natural, less than 140 year old allopolyploid (Mimulus peregrinus), a
 resynthesized inter-species triploid hybrid (M. robertsii), a
 resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M.
 guttatus and M. luteus). We show that subgenome expression dominance
 occurs instantly following the hybridization of two divergent genomes and
 significantly increases over generations. Additionally, CHH methylation
 levels are significantly reduced in regions near genes and within TEs in
 the first generation hybrid, intermediate in the resynthesized
 allopolyploid, and are repatterned differently between the dominant and
 recessive subgenomes in the natural allopolyploid. In addition, subgenome
 differences in levels of TE methylation mirror the increase in expression
 bias observed over the generations following hybridization. These findings
 provide important insights into genomic and epigenomic shock that occurs
 following hybridization and polyploid events.
description: Mimulus Annotation and
 Expression AnalysesGene expression data
 (raw counts and RPKM) for all transcriptome libraries analyzed in the
 manuscript. In addition, genome annotation and orthogroups for syntenic
 orthologs that were further analyzed, with full descriptions, are in the
 zipped file.Mimulus_TPC_Dryad.zipMimulus_luteus.faaFasta file of M. luteus genome assemblyMimulus_luteus_complete_w_single_exons_standard_renamed_genes.gffGFF genome annotation file of Mimulus luteus. This GFF file provides gene annotation for the M. luteus genome assembly published in this paper.Mimulus_guttatus_complete_w_single_exons_standard_renamed_genes.gffGFF genome annotation file of Mimulus guttatus. This GFF file provides gene annotation for the M. guttatus genome v2.0 on available on Phytzome.AlignmentsThis folder contains coding sequence alignments and single copy ortholog alignments used to conduct phylogenetic analyses in this paper.alignments.tar
DOI: 10.5061/dryad.12ck0
title: Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)

description: The capacity of an individual to battle infection is an important fitness
 determinant in wild vertebrate populations. The major histocompatibility
 complex (MHC) genes are crucial for a host’s adaptive immune system to
 detect pathogens. However, anthropogenic activities may disrupt natural
 cycles of co-evolution between hosts and pathogens. In this study we
 investigated the dynamic sequence and expression variation of host
 parasite interactions in brook charr (Salvelinus fontinalis) in a context
 of past human disturbance via population supplementation from domestic
 individuals. To do so, we developed a new method to examine selection
 shaping MHC diversity within and between populations and found a complex
 interplay between neutral and selective processes that varied among lakes
 that were investigated. We provided evidence for a lower introgression
 rate of domestic alleles and found that parasite infection increased with
 domestic genomic background of individuals. We also documented an
 association between individual MHC alleles and parasite taxa. Finally,
 longer cis regulatory minisatellites were positively correlated with MHC
 II down-regulation and domestic admixture, suggesting that inadvertent
 selection during domestication resulted in a lower immune response
 capacity, through a trade-off between growth and immunity, which explained
 the negative selection of domestic alleles at least under certain
 circumstances.
description: 2009
 dataThis dataset contains:
 gene expression values, physiological parameters, Q_values, Minisatellites
 length, MHCIIb alleles, parasitological parameters.data_2009_MEC-13-1125.xlsx2008-2009_parasites_dataThis dataset contains parasitological informations for the individuals sampled in 2008 and 2009. The lakes, refere to Amanites (AMA), Belles de jour (BEL), Caribou (Car), Méthot (MET), Main de fer (MAI) and Petit Saint-Bernard (BER).data_2008-2009_parasites_MEC-13-1125.xlsxMHCIIb_genotypes_dataThis dataset was generated with the genotyping pipeline described in the manuscript. It contains MHCIIb genotypes for all populations. Lakes refere to : Amanites (AMA), Belles-de-Jour (BEL), Methot (MET), Arcand (ARC), Rivard (RIV), Veillette (VEI), Caribou (CAR), Main de fer (MAI), Sorbier (SOR) and Petit saint Bernard (BER).data_genotype_2008_MHCII.xlsxData of the laboratory experimentThis dataset contains the following variables: MHCIIb gene expression values, physiological parameters (weight, length and Fulton condition index), Minisatellites groups (either long or short based on the number of repeat), family and temperature.data_laboratory-experiment.xlsx454 raw MHC2b sequencesThis file contains raw 454 sequences of the MHC2b gene.454_seq_2011090210000039.zipMHC_alleles_sequencesSequences of the 29 MHC2b alleles described in the study. These sequences were aligned with muscle, using MEGAv5 and are in the fasta format.MHC_alleles_aligned_10-04-2012.fasta
DOI: 10.5061/dryad.31v06
title: Data from: Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior

description: Gene-environment interactions impact the development of neuropsychiatric
 disorders, but the relative contributions are unclear. Here, we identify
 gut microbiota as sufficient to induce depressive-like behaviors in
 genetically distinct mouse strains. Daily gavage of saline in non-obese
 diabetic (NOD) mice induced a social avoidance behavior that was not
 observed in C57BL/6 mice. This was not observed in NOD animals with
 depleted microbiota via oral administration of antibiotics. Transfer of
 intestinal microbiota, including members of the Clostridiales,
 Lachnospiraceae and Ruminococcaceae, from vehicle-gavaged NOD donors to
 microbiota-depleted C57BL/6 recipients was sufficient to induce social
 avoidance and change gene expression and myelination in the prefrontal
 cortex. Metabolomic analysis identified increased cresol levels in these
 mice, and exposure of cultured oligodendrocytes to this metabolite
 prevented myelin gene expression and differentiation. Our results thus
 demonstrate that the gut microbiota modifies the synthesis of key
 metabolites affecting gene expression in the prefrontal cortex, thereby
 modulating social behavior.
description: Supplemental Table 1 -
 supplement of Figure 3Unique OTUs in
 NOD_vehicle compared to NOD_baseline-2Supplemental Table 2 -
 supplement of Figure 4S2mPFC_RNASeqSupplemental Table 3 - supplement of figure 6S1Unique OTUs in C57BL6 transplanted with NODvehicle cecal contendSupplemental Table 3 - supplement of figure 6s1.Unique OTUs in C57BL6 transplanted with NODvehicle cecal contend.xlsxSupplemental Table 4 - supplement of Figure 6S2Shared Operational Taxonomic Units (OTUs) in mice displaying a decreased social behavior (NOD_vehicle and C57BL_6 transplanted with NOD microbiota)Supplemental Table 5 - supplement of Figure 7List of metabolites detected in the cecumSupplemental Table 6 – supplement of Figure 7Pathway analysis results (metabolomics)Supplemental Table 7IlluminaMiSeq_16S data_run1_seqsSupplemental Table 8IlluminaMiSeq_16S data_run2_seqs.run2Supplemental Table 9 - supplement of Figure 4qRT_PCR primer listSupplemental Table 10 - supplement of Figure 6S2bacterial qPCR primersSupplemental Table 10- supplement of Figure 6S2. bacterial qPCR primers.xlsx
DOI: 10.5061/dryad.nh8ph
title: Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

description: Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species
 that is native to North America, and is being developed as a future
 biofuels feedstock crop. Switchgrass is present primarily in two ecotypes:
 a northern upland ecotype composed of tetraploid and octoploid accessions,
 and a southern lowland ecotype composed of primarily tetraploid
 accessions. We employed high-coverage exome capture sequencing (~2.4 Tb)
 to genotype 537 individuals from 45 upland and 21 lowland populations.
 From these data, we identified ~27 million single nucleotide polymorphisms
 (SNPs), of which 1,590,653 high confidence SNPs were used in downstream
 analyses of diversity within and between the populations. From the 66
 populations, we identified five primary population groups within the
 upland and lowland ecotypes, a result that was further supported through
 genetic distance analysis. We identified conserved, ecotype restricted
 non-synonymous SNPs that are predicted to impact protein function in genes
 that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes
 involved in flowering which may contribute to the phenotypic differences
 between the two ecotypes. We also identified, relative to the
 near-reference Kanlow population, 17,228 up-copy number variants (CNVs),
 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a
 total of 9,979 genes, including two upland-specific CNV-clusters. In
 total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel
 providing a firm foundation to identify functional variation associated
 with phenotypic traits of interest for biofuel feedstock production.
description: dendogram.treePvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff3Pvirgatum_v1.1_273_hardmasked_ChrUn.coordPvirgatum_v1.1_273_hardmasked_ChrUn.fastaSNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_functionSNIPE_all_plates_matrix_biallelic_only_nomissing.variant_functionswitchgrass_upland_panel_down_cnv_list.txtswitchgrass_upland_panel_up_cnv_list.txtSNIPE_all_plates_matrix_biallelic_only_nomissing.txtSNIPE_all_plates_matrix_unfiltered.txt
DOI: 10.5061/dryad.gv536
title: Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

description: Imprinted gene expression occurs during seed development in plants and is
 associated with differential DNA methylation of parental alleles,
 particularly at proximal transposable elements (TEs). Imprinting
 variability could contribute to observed parent-of-origin effects on seed
 development. We investigated intraspecific variation in imprinting,
 coupled with analysis of DNA methylation and small RNAs, among three
 Arabidopsis strains with diverse seed phenotypes. The majority of
 imprinted genes were parentally biased in the same manner among all
 strains. However, we identified several examples of allele-specific
 imprinting correlated with intraspecific epigenetic variation at a TE. We
 successfully predicted imprinting in additional strains based on
 methylation variability. We conclude that there is standing variation in
 imprinting even in recently diverged genotypes due to intraspecific
 epiallelic variation. Our data demonstrate that epiallelic variation and
 genomic imprinting intersect to produce novel gene expression patterns in
 seeds.
description: Normalized small RNA
 read counts from whole seedsNormalized reads per
 million (RPM) values in 300 bp windows across the entire A. thaliana
 genome for 21-24 nucleotide small RNAs from ColxCol, LerxLer, CvixCvi,
 ColxLer, LerxCol, CvixCol and ColxCvi whole seeds 6 days after
 pollination.norm.s.txt.sRNAfiles.tar.gzAllele-specific classification of small RNAs from whole seedsSmall RNAs overlapping Col-Cvi or Col-Ler SNPs were classified according to strain origin from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi and CvixCol whole seeds 6 days after pollination.SNP_counts.txt.sRNAfiles.tar.gzMean methylation in Arabidopsis embryo and endospermMean methylation in overlapping 300 bp windows for embryo and endosperm from ColxCol, LerxLer, CvixCvi, CvixCol, ColxCvi, LerxCvi, and CvixLer seeds dissected 6 days after pollination. CG, CHG, and CHH methylation are quantified in separate files.window.mean.tar.gzWeighted methylation in Arabidopsis embryo and endospermWeighted methylation values in 300 nt windows for Arabidopsis embryo and endosperm from ColxCol, LerxLer, CvixCvi, ColxCvi, CvixCol, LerxCvi, and CvixLer seeds dissected 6 days after pollination.weighted_summary.tar.gzmRNA-seq read counts for Arabidopsis embryo and endospermTotal and allele-specific mRNA-seq read counts, along with FPKM values, are quantified for genes and TEs from embryo and endosperm tissue from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi and CvixLer seeds dissected 6 days after pollination, along with whole seeds from ColxCvi and CvixCol.stats_per_locus.tar.gzAllele-specific mRNA SNP counts for Arabidopsis embryo and endospermThe number of mRNA-seq reads matching each Col-Ler, Col-Cvi, or Ler-Cvi SNP is reported for data from ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi, and CvixLer embryo and endosperm dissected 6 days after pollination, along with ColxCvi and CvixCol whole seeds.snp_counts.tar.gz
DOI: 10.5061/dryad.m99v4
title: Data from: Next generation lineage discovery: a case study of tuberous Claytonia L.

description: PREMISE OF THE STUDY: Species formation is an intuitive endpoint of
 reproductive isolation, but circumscribing taxa that arise during
 speciation can be difficult because of gene flow, morphological
 continuity, hybridization or polyploidization, and low sequence variation
 among newly diverged lineages. Nonetheless, species complexes are
 ubiquitous and their classification is essential for understanding how
 diversity influences ecosystem function. METHODS: We used modern
 sequencing technology to identify lineages of perennial Claytonia L., and
 assessed correspondence between genetic lineages and
 morphological/ecological variation. Subsets of 18 taxa from 63 populations
 were used for (a) lineage discovery using network and coalescent analyses,
 (b) leaf shape analyses using elliptical Fourier analysis and ordination,
 and (c) ecological analyses (soil chemistry, climate) using ANOVA and
 ordination. KEY RESULTS: Samples mainly aggregated into groups
 representing each of the previously recognized species in each of the
 genetic data sets. Compared to the double digest RADseq dataset, genome
 skimming data provided more resolution and further opportunity to probe
 into patterns of nuclear and chloroplast genome diversity. Morphological
 and ecological associations are significantly different (albeit
 intergrading) among the taxa investigated. A new species, Claytonia
 crawfordii, is described based on morphological data presented here.
 CONCLUSIONS: Genetic data presented in this study provide some of the
 first insights into phylogenetic relationships among recently diverged
 perennial Claytonia, and are suggestive of past hybridization among
 caudicose and tuberous species. Given prior difficulties in understanding
 species boundaries among newly diverged plant lineages, this case study
 demonstrates the revolutionary breakthrough for systematics research that
 high throughput sequencing represents.
description: Data from: Next
 Generation Lineage Discovery: a Case Study of Tuberous Claytonia
 L.Compressed zip file
 including Data, Scripts, Figures, Tables, and Supplemental
 AppendicesDRYAD.zip
DOI: 10.5061/dryad.mj43d20
title: Data from: Turning one into five: integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor "structor"

description: Seed harvesting ants are ecosystem engineers that shape vegetation,
 nutrient cycles, and microclimate. Progress in ecological research is,
 however, slowed down by poor species delimitation. For example, it has not
 been resolved to date, how many species the European harvester ant Messor
 "structor" (Latreille, 1798) represents. Since its first
 description, splitting into additional taxa was often proposed but not
 accepted later on due to inconsistent support from morphology and ecology.
 Here, we took an iterative integrative-taxonomy approach – comparing
 multiple, independent data sets on the same sample – and used traditional
 morphometrics, Wolbachia symbionts, mitochondrial DNA, amplified fragment
 length polymorphism, and ecological niche modelling. Using the
 complementarity of the data sets applied, we resolved multiple, strong
 disagreements over the number of species, ranging from four to ten, and
 the allocation of individuals to species. We consider most plausible a
 five-species hypothesis and conclude the taxonomic odyssey by redescribing
 Messor structor, M. ibericus Santschi, 1925, and M. muticus (Nylander,
 1849) stat.rev., and by describing two new species, M. ponticus sp.n. and
 M. mcarthuri sp.n. The evolutionary explanations invoked in resolving the
 various data conflicts include pronounced morphological crypsis,
 incomplete lineage-sorting or ongoing cospeciation of endosymbionts, and
 peripatric speciation – these ants’ significance to evolutionary biology
 parallels that to ecology. The successful solution of this particular
 problem illustrates the usefulness of the integrative approach to other
 systematic problems of comparable complexity and the importance of
 understanding evolution to drawing correct conclusions on species’
 attributes, including their ecology and biogeography.
description: All repository data of
 Steiner et al.Contains the data files
 in one zip ArchiveSteiner_et_al_Turning_one_into_five.zipGenbank associations of five MLST genes and wsp gene for wMes strainswMes_GenBank.txt
DOI: 10.5061/dryad.ng95t
title: Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar

description: Drosophila simulans is a closely relative of the genetic model D.
 melanogaster. In an effort to improve the genomic resources for D.
 simulans, we assembled and annotated the genome of a strain originating
 from Madagascar (M252), the ancestral range of D. simulans. The comparison
 of the M252 genome to other available D. simulans assemblies confirmed its
 high quality, but also highlighted genomic regions that are difficult to
 assemble with NGS data. The annotation of M252 provides a clear
 improvement with alternative splicing for 52% of the multiple-exon genes,
 UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being
 reported. We anticipate that the M252 genome will be a valuable resource
 for many research questions.
description: dsim-all-chromosome-M252_draft_4-chrnamesokGenome assembly of the Drosophila simulans M252 straindsim-M252-popgen-ann-r1.1Annotation of the Drosophila simulans M252 assembly for protein-coding genes and pseudogenes. Features reported in the GTF file are exon, intron, CDS and UTR.SimulansM252Annotation-r1.1Detailed protocol for annotation of the Drosophila simulans M252 assembly including scripts and URLs to access external programs.
DOI: 10.26023/4p71-1z0z-e505
title: MITTEN-CI: University of Illinois Flux Tower Data. Version 1.0

description: Flux tower observations from the University of Illinois flux towers that were deployed 0, 9, 20, 30, 60, and 120km from the shore of Lake Michigan during the Maritime to Inland Transitions Towards ENvironments for Convection Initiation (MITTEN-CI) campaign. They were deployed in and west-east line from the west side of Holland, Michigan to south of Mulliken, Michigan.
DOI: 10.5061/dryad.2875k
title: Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

description: Bacteria can evolve rapidly under positive selection owing to their vast
 numbers, allowing their genes to diversify by adapting to different
 environments. We asked whether the same genes that evolve rapidly in the
 long-term evolution experiment with Escherichia coli (LTEE) have also
 diversified extensively in nature. To make this comparison, we identified
 ~2000 core genes shared among 60 E. coli strains. During the LTEE, core
 genes accumulated significantly more nonsynonymous mutations than flexible
 (i.e., noncore) genes. Furthermore, core genes under positive selection in
 the LTEE are more conserved in nature than the average core gene. In some
 cases, adaptive mutations appear to modify protein functions, rather than
 merely knocking them out. The LTEE conditions are novel for E. coli, at
 least in relation to its evolutionary history in nature. The constancy and
 simplicity of the environment likely favor the complete loss of some
 unused functions and the fine-tuning of others.
description: LTEE-core-genes-projectData, Analysis Scripts, and Results for LTEE-core-genome manuscriptDRYAD-LTEE-core-genome.zip