cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b9p8v
title: Data from: Genomic divergence between the migratory and stationary ecotypes of Atlantic cod

description: Atlantic cod displays a range of phenotypic and genotypic variations,
 which includes the differentiation into coastal stationary and offshore
 migratory types of cod that co-occur in several parts of its distribution
 range and are often sympatric on the spawning grounds. Differentiation of
 these ecotypes may involve both historical separation and adaptation to
 ecologically distinct environments, the genetic basis of which is now
 beginning to be unravelled. Genomic analyses based on recent sequencing
 advances are able to document genomic divergence in more detail and may
 facilitate the exploration of causes and consequences of genome-wide
 patterns. We examined genomic divergence between the stationary and
 migratory types of cod in the Northeast Atlantic, using next-generation
 sequencing of pooled DNA from each of two population samples. Sequence
 data was mapped to the published cod genome sequence, arranged in more
 than 6000 scaffolds (611 Mb). We identified 25 divergent scaffolds (26 Mb)
 with a higher than average gene density, against a backdrop of overall
 moderate genomic differentiation. Previous findings of localized genomic
 divergence in three linkage groups were confirmed, including a large (15
 Mb) genomic region, which seems to be uniquely involved in the divergence
 of migratory and stationary cod. The results of the pooled sequencing
 approach support and extend recent findings based on single-nucleotide
 polymorphism markers and suggest a high degree of reproductive isolation
 between stationary and migratory cod in the North-east Atlantic.
description: GMAP of mRNA to cod
 reference genomeEnsemble mRNA is mapped
 to cod reference with GMAPcod_wg_mapping_mrna.gff3R script calculates Fst from SNP dataThis script calculates Fst from CLC genomics parsed SNP's2011-09-17-Fst.from.SNP.RDatagmgH_onstallo_barents SNP Detection_TablegmgH_onstallo_holand_SNP Detection_Table
DOI: 10.5061/dryad.np0s26r
title: Data from: Paleozoic diversification of terrestrial chitin-degrading bacterial lineages

description: Background: Establishing the divergence times of groups of organisms is a
 major goal of evolutionary biology. This is especially challenging for
 microbial lineages, due to the near-absence of preserved physical evidence
 (diagnostic body fossils or geochemical biomarkers). Horizontal gene
 transfer (HGT), can serve as a temporal scaffold between microbial groups
 and other fossil-calibrated clades, potentially improving these estimates.
 Specifically, HGT to or from organisms with fossil-calibrated age
 estimates can propagate these constraints to additional groups that lack
 fossils. While HGT is common between lineages, only a small subset of HGT
 events are potentially informative for dating microbial groups. Results:
 Constrained by published fossil-calibrated studies of fungal evolution,
 molecular clock analyses show that multiple clades of Bacteria likely
 acquired chitinase homologs via HGT during the very late Neoproterozoic
 into the early Paleozoic. These results also show that, following these
 HGT events, recipient terrestrial bacterial clades likely diversified
 ~300–500 million years ago, consistent with established timescales of
 arthropod and plant terrestrialization. Conclusions: We conclude that
 these age estimates are broadly consistent with the dispersal of chitinase
 genes throughout the microbial world in direct response to the evolution
 and ecological expansion of detrital-chitin producing groups. The
 convergence of multiple lines of evidence demonstrates the utility of
 HGT-based dating methods in microbial evolution. The pattern of
 inheritance of chitinase genes in multiple terrestrial bacterial lineages
 via HGT processes suggests that these genes, and possibly other genes
 encoding substrate-specific enzymes can serve as a "standard
 candle" for dating microbial lineages across the Tree of Life.
description: chronogramsSet of output chronogram files for each set of model parameters.datedistsSet of date dist files for each set of model parameters.Chitinase AlignmentFASTAchitinase_2018_05_09.fastaChitinase Alignment TenCharFasta file with 10 character nameschitinase_2018_05_09_TenChar.fastaChitinase Alignment TenCharPhylip filechitinase_2018_05_09_TenChar.phylipChitinase N-Terminal Region BacteriaN-terminal region aligned just for bacterian_terminus_chitinase_2018_04_17_Muscle.fastaChitinase Conserved Domainfungi-bacteria conserved regionSh_1pS_conserved_domain_chitinase_2018_04_17_Muscle_edit.fastaChitinase Gene Tree (RAxML)Maximum likelihood gene tree.RAxML_bipartitions.Sh_chitinase_2018_05_09_TenChar_Muscle_color_newick.treeChitinase gene tree (Phylobayes)Bayesian gene tree.out_chitinase_2018_05_10_PB_TREE.con.tre
DOI: 10.5061/dryad.41793
title: Data from: Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing

description: Recent genomic studies show that introgression can occur at a genome-wide
 scale among recently diverged lineages. However, introgression is
 difficult to distinguish from incomplete lineage sorting (ILS), and these
 processes are expected to occur together. Moreover, ncDNA introgression is
 less easily detected than mtDNA introgression, and as such its prevalence
 is less well understood. The Chinese horseshoe bat (Rhinolophus sinicus)
 occurs as three distinct forms on mainland China: the subspecies R. s.
 septentrionalis and two parapatric clades of R. s. sinicus (Central and
 East R. s. sinicus). Previous work suggested widespread mtDNA
 introgression between these subspecies; however, no ncDNA introgression
 was detected. In this study we sampled the coding genomes of all three
 forms of R. sinicus in order to perform a more sensitive test for ncDNA
 introgression against an expected background of ILS. We assembled 3548
 nuclear protein-coding genes from these and three congeneric species, and
 built a high-confidence species tree using maximum likelihood and Bayesian
 concordance methods. Phylogenetic analysis suggested a mosaic genome for
 Central R. s. sinicus derived from R. s. septentrionalis and East R. s.
 sinicus. Nuclear DNA introgression between Central R. s. sinicus and R. s.
 septentrionalis was supported by three different tests, whereas ILS could
 not be ruled out completely. Our findings, in line with other recent
 results, indicate that recently diverged taxa undergo large-scale
 secondary introgression, and that this process likely operates alongside
 ILS to give rise to phylogenomic discordances or even mosaic genomes.
description: data and
 scripts1)
 R_ferrumequinum_Trinity_assemblies.fas is assemblies of RNAseq using
 Trinity; 2) Homo_cds_11158ortho_vs_RFE_Trinity.tblastx is the results from
 tblastx. 3) parse_results_from_tblastx.pl,
 extract_sequences_from_tblastx_results.pl, are scripts used to extract
 sequences from tblastx results
DOI: 10.5061/dryad.7sb0f
title: Data from: Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

description: Extant variation in temperate and boreal plant species has been influenced
 by both demographic histories associated with Pleistocene glacial cycles
 and adaptation to local climate. We used sequence capture to investigate
 the role of these neutral and adaptive processes in shaping diversity in
 black cottonwood (Populus trichocarpa). Nucleotide diversity and
 Tajima's D were lowest at replacement sites and highest at intergenic
 sites, while LD showed the opposite pattern. With samples grouped into
 three populations arrayed latitudinally, effective population size was
 highest in the north, followed by south and centre, and LD was highest in
 the south followed by the north and centre, suggesting a possible northern
 glacial refuge. FST outlier analysis revealed that promoter, 5′-UTR and
 intronic sites were enriched for outliers compared with coding regions,
 while no outliers were found among intergenic sites. Codon usage bias was
 evident, and genes with synonymous outliers had 30% higher average
 expression compared with genes containing replacement outliers. These
 results suggest divergent selection related to regulation of gene
 expression is important to local adaptation in P. trichocarpa. Finally,
 within-population selective sweeps were much more pronounced in the
 central population than in putative northern and southern refugia, which
 may reflect the different demographic histories of the populations and
 concomitant effects on signatures of genetic hitchhiking from standing
 variation.
description: migrate_input_fileInput file for intergenic regions Migrate analysis described in the paper.SRA058855Raw Illumina HiSeq data used for all empirical analyses described in the paper.FASTA_alignmentsComplete FASTA alignments, one file per genomic regions, for all captured sequences described in the paper. Data are phased using Fastphase as described and provided as two haplotypes per sample (A and B)fasta_files_Ptv2_fasta.tar.gzbayescan_out_with_annotationsOutput of BayeScan analyses described in the paper. One tab for each site type. Poplar gene model and best Arabidopsis hit are given for each site. In the case of promoter regions, these annotations refer to the nearest gene downstream of the site.
DOI: 10.5061/dryad.925mv
title: Data from: On the use of climate covariates in aquatic species distribution models: are we at risk of throwing the baby out?

description: Species distribution models (SDMs) in river ecosystems can incorporate
 climate information by using air temperature and precipitation as
 surrogate measures of instream conditions or by using independent models
 of water temperature and hydrology to link climate to instream habitat.
 The latter approach is preferable but constrained by the logistical burden
 of developing water temperature and hydrology models. We therefore
 assessed whether regional scale, freshwater SDM predictions are
 fundamentally different when climate data versus instream temperature and
 hydrology are used as covariates. Maximum Entropy (MaxEnt) SDMs were built
 for 15 freshwater fishes using one of two covariate sets: (1) air
 temperature and precipitation (climate variables) in combination with
 physical habitat variables; or (2) water temperature, hydrology (instream
 variables) and physical habitat. Three procedures were then used to
 compare results from climate vs. instream models. First, equivalence tests
 assessed average pairwise differences (site-specific comparisons
 throughout each species’ range) among climate and instream models. Second,
 ‘congruence’ tests determined how often the same stream segments were
 assigned high habitat suitability by climate and instream models. Third,
 Schoener’s D and Warren’s I niche overlap statistics quantified range-wide
 similarity in predicted habitat suitability values from climate vs.
 instream models. Equivalence tests revealed small, pairwise differences in
 habitat suitability between climate and instream models (mean pairwise
 differences in MaxEnt raw scores for all species &lt; 3×10-4).
 Congruence tests showed a strong tendency for climate and instream models
 to predict high habitat suitability at the same stream segments (median
 congruence = 68%). D and I statistics reflected a high margin of overlap
 among climate and instream models (median D = 0.78, median I = 0.96).
 Overall, we found little support for the hypothesis that SDM predictions
 are fundamentally different when climate versus instream covariates are
 used to model fish species’ distributions at the scale of the Columbia
 Basin.
description: McGarvey_EtAl_RawDataThese are raw data files (.csv) for the 15 freshwater fishes modeled in "On the use of climate covariates in aquatic species distribution models: are we at risk of throwing the baby out?" (McGarvey et al.). The files are formatted for MaxEnt ('species with data' format) and include MaxEnt batch files that can be used to re-run the models.
DOI: 10.5061/dryad.53hm6
title: Data from: Geographic patterns of song variation reveal timing of song acquisition in a wild avian population

description: Geographic patterns of song variation are common in passerines and can
 develop as a consequence of the mechanisms of song acquisition and
 dispersal. In particular, the timing of dispersal relative to the sensory
 learning phase and the time of song crystallization is important. For
 example, when the sensory phase continues after dispersal or when males
 learn new songs every breeding season, i.e. open-ended learner,
 neighborhoods can develop where males share their songs. In this study, we
 utilize a unique, comprehensive dispersal and song recording dataset to
 investigate the existence and development of micro-geographic song
 variation in a wild passerine population. Machine learning song analysis
 methods allow us to overcome perceptual bias in the classification of the
 songs of New Zealand hihi (Notiomystis cincta). We show that males share
 more song elements of their repertoire with their neighbors than with more
 distant males or with males from the same natal area, implying that
 repertoire is acquired post-dispersal. Finally, we suggest that high
 levels of male competition have driven the development of post-dispersal
 vocal learning behavior in this species.
description: dispersalDispersal data of males, i.e. nest box where born and nest box of territory during time of study (2005)nestbox_distancePairwise distance matrix, in meters, for nest boxes on Tiritiri Matangi Island.Song recordingsMales song recording (1879 songs), file name format is [male id]_[song id].wavdata_recordings.tar.bz2
DOI: 10.7910/dvn/frltib
title: Daily and Annual NO2 Concentrations for the Contiguous United States, 1-km Grids, Version 1.10 (2000-2016)

description: The Daily and Annual NO2 Concentrations for the Contiguous United States, 1-km Grids, Version 1.10 (2000-2016) data set contains daily predictions of Nitrogen Dioxide (NO2) concentrations at a high resolution (1-km grid cells) for the years 2000 to 2016. An ensemble modeling framework was used to assess NO2 levels with high accuracy, which combined estimates from three machine learning models (neural network, random forest, and gradient boosting), with a generalized additive model. Predictor variables included NO2 column concentrations from satellites, land-use variables, meteorological variables, predictions from two chemical transport models, GEOS-Chem and the U.S. Environmental Protection Agency (EPA) Community Multiscale Air Quality Modeling System (CMAQ), along with other ancillary variables. The annual predictions were calculated by averaging the daily predictions for each year in each grid cell. The ensemble produced a cross-validated R-squared value of 0.79 overall, a spatial R-squared value of 0.84, and a temporal R-squared value of 0.73. In version 1.10, the completeness of daily NO2 predictions have been enhanced by employing linear interpolation to impute missing values. Specifically, for days with small spatial patches of missing data with less than 100 grid cells, inverse distance weighting interpolation was used to fill the missing grid cells. Other missing daily NO2 predictions were interpolated from the nearest days with available data. Annual predictions were updated by averaging the imputed daily predictions for each year in each grid cell. These daily and annual NO2 predictions allow public health researchers to respectively estimate the short- and long-term effects of NO2 exposures on human health, supporting the U.S. EPA for the revision of the National Ambient Air Quality Standards for daily average and annual average concentrations of NO2. The data are available in RDS and GeoTIFF formats for statistical research and geospatial analysis.
description: To provide daily and annual Nitrogen Dioxide (NO2) concentration data in the U.S. at a resolution of 1-km (about 30 arc-seconds) for public health research to respectively estimate short- and long-term effects on human health, and for other related research.
DOI: 10.5061/dryad.40s3g
title: Data from: Dramatic niche shifts and morphological change in two insular bird species

description: Colonizations of islands are often associated with rapid morphological
 divergence. We present two previously unrecognized cases of dramatic
 morphological change and niche shifts in connection with colonization of
 tropical forest-covered islands. These evolutionary changes have concealed
 the fact that the passerine birds madanga, Madanga ruficollis, from Buru,
 Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé,
 Gulf of Guinea, are forest-adapted members of the family Motacillidae
 (pipits and wagtails). We show that Madanga has diverged mainly in
 plumage, which may be the result of selection for improved camouflage in
 its new arboreal niche, while selection pressures for other morphological
 changes have probably been weak owing to preadaptations for the novel
 niche. By contrast, we suggest that Amaurocichla's niche change has
 led to divergence in both structure and plumage.
description: Supplementary Table
 S1List of samples, with
 GenBank accession numbersTable S1 Madanga
 Samples.xlsRSOS-140364 contents and
 captions ESMsContents and captions to
 data files.Supplementary Table
 S2Measurements of Madanga
 ruficollis and the other species in clade A in Fig. 1.Table
 S2.pdfTable S3 PCA
 MadangaOutput from PCA of
 morphological characters.Fig. S1. MB Madanga
 Passeriformes AllLoci 4partsRelationships of broad
 selection of Passeriformes, including Madanga ruficollis and Amaurocichla
 bocagii, based on concatenated ND2, ODC, myo and CHD1Z, analysed by
 Bayesian inferenece, partitioned by locus.PassMadangaAllLociAlignment and settings for analysis shown in Fig. S1.Fig. S2. MB Madanga All Loci 7partsBayesian inference tree of Madanga ruficollis, Amaurocichla bocagii and representatives of all clades of Anthus and Motacilla found in previous studies, including all “small pipits” (except A. petrosus, which was previously considered conspecific with A. spinoletta). Based on mitochondrial cytb and ND2, and nuclear ODC, myo and CHD1Z sequence data analysed in seven partitions (by locus and codon; see MadangaAllLoci.nxs).MadangaAllLociAlignment and settings for analysis shown in Fig. S2.Fig. S3. MB single-locus analysesSingle-locus analyses of the same taxa as in Supplementary Figure S2.Fig. S4. BEAST Madanga CytbChronogram for the same taxa as in Supplementary Figures 2 and 3, based on cytb sequences and a relaxed molecular clock (2.1% / million years), inferred by Bayesian inference, with 95% highest posterior density intervals for the node ages.MadaCytbShortXml file for analysis in Fig. S4.Photos AMNHPhotos of Madanga ruficollis and Amaurocichla bocagii from the American Museum of Natural History, including x-rays of Madanga ruficollis.
DOI: 10.5061/dryad.8g5g6j4
title: Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

description: Genetic predictions of height differ among human populations and these
 differences have been interpreted as evidence of polygenic adaptation.
 These differences were first detected using SNPs genome-wide significantly
 associated with height, and shown to grow stronger when large numbers of
 sub-significant SNPs were included, leading to excitement about the
 prospect of analyzing large fractions of the genome to detect polygenic
 adaptation for multiple traits. Previous studies of height have been based
 on SNP effect size measurements in the GIANT Consortium meta-analysis.
 Here we repeat the analyses in the UK Biobank, a much more homogeneously
 designed study. We show that polygenic adaptation signals based on large
 numbers of SNPs below genome-wide significance are extremely sensitive to
 biases due to uncorrected population structure. More generally, our
 results imply that typical constructions of polygenic scores are sensitive
 to population structure and that population-level differences should be
 interpreted with caution.
description: UK Biobank custom height
 association statistics on ~700k genotyped SNPsThe zip file contains
 six files: (1) ukb_cal_v2_height_allancestry_10pcs_assoc_linear.tsv (2)
 ukb_cal_v2_height_allancestry_nopcs_assoc_linear.tsv (3)
 ukb_cal_v2_height_britishancestry_10pcs_assoc_linear.tsv (4)
 ukb_cal_v2_height_britishancestry_nopcs_assoc_linear.tsv (5)
 ukb_cal_v2_height_sibs_perm_qfam.tsv (6)
 ukb_cal_v2_height_wbsibs_perm_qfam.tsv (1) - (4) are height GWAS estimates
 on all samples / white British samples using 10 PCs as covariates or no
 PCs as covariates. Sex was included as covariate in all analyses. (3) is
 equivalent to the UK Biobank height GWAS from the Neale lab. The remaining
 small differences can be explained by genotype differences in the UK
 Biobank imputed data and genotyped data. (5) and (6) are family based
 estimates from 20166 sibling pairs of any ancestry (5) and 17358 sibling
 pairs where both siblings are of white British ancestry (6) in the UK
 Biobank. Pairs of samples with IBS0 &gt; 0.0018 and Kinship coefficient
 &gt; 0.185 were identified as sibling pairs. For the analyses in Sohail,
 Maier et al., only the subset of ~300,000 SNPs with SDS scores was used.
 For a description of the columns in files (1)-(4) please see the PLINK
 documentation for the ‘--linear’ command. Column “A2” has been added and
 denotes the non-effect allele. For a description of the columns in files
 (5) and (6) please see the PLINK documentation for the ‘--qfam’ command.
 Column “A2” has been added and denotes the non-effect allele. “EMP1” and
 “NP” refer to permutation p-value and number of permutations,
 respectively. Please note: These data are derived from the UK Biobank
 Resource under Application Number 18597.sohail_maier_2018.zip
DOI: 10.5061/dryad.t50j5
title: Data from: Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species

description: Polyploidization events are frequent among flowering plants, and the
 duplicate genes produced via such events contribute significantly to plant
 evolution. We sequenced the genome of wild radish (Raphanus raphanistrum),
 a Brassicaceae species that experienced a whole-genome triplication event
 prior to diverging from Brassica rapa. Despite substantial gene gains in
 these two species compared with Arabidopsis thaliana and Arabidopsis
 lyrata, ∼70% of the orthologous groups experienced gene losses in R.
 raphanistrum and B. rapa, with most of the losses occurring prior to their
 divergence. The retained duplicates show substantial divergence in
 sequence and expression. Based on comparison of A. thaliana and R.
 raphanistrum ortholog floral expression levels, retained radish duplicates
 diverged primarily via maintenance of ancestral expression level in one
 copy and reduction of expression level in others. In addition, retained
 duplicates differed significantly from genes that reverted to singleton
 state in function, sequence composition, expression patterns, network
 connectivity, and rates of evolution. Using these properties, we
 established a statistical learning model for predicting whether a
 duplicate would be retained postpolyploidization. Overall, our study
 provides new insights into the processes of plant duplicate loss,
 retention, and functional divergence and highlights the need for further
 understanding factors controlling duplicate gene fate.
description: RrContigs.fa.fasta.tar.gzSequence of Raphanus raphanistrum genomic contigsRrCDS.fa.tar.gzRaphanus raphanistrum coding sequencesRrPep.fa.tar.gzRaphanus raphanistrum peptide sequencesRr_gene_pseu.gff.mod.tar.gzRaphanus raphanistrum gene and pseudogene GFF file