cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9fr76
title: Data from: Near-stasis in the long-term diversification of Mesozoic tetrapods

description: How did evolution generate the extraordinary diversity of vertebrates on
 land? Zero species are known prior to ~380 million years ago, and more
 than 30,000 are present today. An expansionist model suggests this was
 achieved by large and unbounded increases, leading to substantially
 greater diversity in the present than at any time in the geological past.
 This model contrasts starkly with empirical support for constrained
 diversification in marine animals, suggesting different macroevolutionary
 processes on land and in the sea. We quantify patterns of vertebrate
 standing diversity on land during the Mesozoic–early Paleogene interval,
 applying sample-standardization to a global fossil dataset containing
 27,260 occurrences of 4,898 non-marine tetrapod species. Our results show
 a highly stable pattern of Mesozoic tetrapod diversity at regional and
 local levels, underpinned by a weakly positive, but near-zero, long-term
 net diversification rate over 190 million years. Species diversity of
 non-flying terrestrial tetrapods less than doubled over this interval,
 despite the origins of exceptionally diverse extant groups within mammals,
 squamates, amphibians, and dinosaurs. Therefore, although speciose groups
 of modern tetrapods have Mesozoic origins, rates of Mesozoic
 diversification inferred from the fossil record are slow compared to those
 inferred from molecular phylogenies. If high speciation rates did occur in
 the Mesozoic, then they seem to have been balanced by extinctions among
 older clades. An apparent 4-fold expansion of species richness after the
 Cretaceous/Paleogene (K/Pg) boundary deserves further examination in light
 of potential taxonomic biases, but is consistent with the hypothesis that
 global environmental disturbances such as mass extinction events can
 rapidly adjust limits to diversity by restructuring ecosystems, and
 suggests that the gradualistic evolutionary diversification of tetrapods
 was punctuated by brief but dramatic episodes of radiation.
description: Data and scripts from
 Mesozoic tetrapod diversificationData and scripts from:
 Near-stasis in the long-term diversification of Mesozoic tetrapods Roger
 B. J. Benson, Richard J. Butler, John Alroy, Philip D. Mannion, Matthew T.
 Carrano, Graeme T. Lloyd PLOS Biology, 2016DRYAD
 upload.zip
DOI: 10.5061/dryad.gr2c7
title: Data from: Marine biodiversity in Juan Fernández and Desventuradas Islands, Chile: global endemism hotspots

description: The Juan Fernández and Desventuradas islands are among the few oceanic
 islands belonging to Chile. They possess a unique mix of tropical,
 subtropical, and temperate marine species, and although close to
 continental South America, elements of the biota have greater affinities
 with the central and south Pacific owing to the Humboldt Current, which
 creates a strong biogeographic barrier between these islands and the
 continent. The Juan Fernández Archipelago has ~ 700 people, with the major
 industry being the fishery for the endemic lobster, Jasus frontalis. The
 Desventuradas Islands are uninhabited except for a small Chilean military
 garrison on San Félix Island. We compared the marine biodiversity of these
 islands across multiple taxonomic groups. At San Ambrosio Island (SA), in
 Desventuradas, the laminarian kelp (Eisenia cokeri), which is limited to
 Desventuradas in Chile, accounted for &gt;50% of the benthic cover at
 wave exposed areas, while more sheltered sites were dominated by sea
 urchin barrens. The benthos at Robinson Crusoe Island (RC), in the Juan
 Fernández Archipelago, comprised a diverse mix of macroalgae and
 invertebrates, a number of which are endemic to the region. The biomass of
 commercially targeted fishes was &gt; 2 times higher in remote sites
 around RC compared to sheltered locations closest to port, and overall
 biomass was 35% higher around SA compared to RC, likely reflecting fishing
 effects around RC. The number of endemic fish species was extremely high
 at both islands, with 87.5% of the species surveyed at RC and 72% at SA
 consisting of regional endemics. Remarkably, endemics accounted for 99% of
 the numerical abundance of fishes surveyed at RC and 96% at SA, which is
 the highest assemblage-level endemism known for any individual marine
 ecosystem on earth. Our results highlight the uniqueness and global
 significance of these biodiversity hotspots exposed to very different
 fishing pressures.
description: Desventuradas_Juan_Fernandes_FishUnderwater counts of fishes on transectsDesventuradas_Juan_Fernandes_mobile_invertsUnderwater counts of mobile invertebratesDesventuradas_Juan_Fernandes_Sessile_BenthosUnderwater counts of sessile benthos
DOI: 10.5061/dryad.t3j7m
title: Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

description: Next-generation sequencing techniques, such as RNA sequencing, have
 provided a wealth of genomic information for nonmodel species.
 Transcriptomic information can be used to quantify the patterns of gene
 expression, which can identify how environmental differences invoke
 organismal stress responses and provide a gauge in predicting species
 adaptability. In our study, we used RNA sequencing to characterize the
 first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to
 identify the genes expressed during the early life history stages and
 which could be important for future genomic studies. RNA was extracted
 from naupliar T. newberryi that were reared in a laboratory-controlled
 setting and in two different water types, a native and a non-native
 condition. A total of six replicates, three per condition, were sequenced
 with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality
 reads were produced and de novo assembly was used to construct a T.
 newberryi transcriptome that was approximately 24.8 M base pairs. More
 than 10 000 peptides were predicted from the assembly, and genes were
 sorted into gene ontology categories. The use of different water
 conditions allowed for a preliminary differential gene expression analysis
 in order to compare the changes in gene expression between conditions.
 There were 299 differentially expressed genes between water conditions
 that might serve as a focal point for future genomic studies of Triops
 acclimation to different environments. The Triops transcriptome could
 serve as vital genomic information for additional studies on Branchiopod
 crustaceans.
description: Triops newberryi
 transcriptome annotationsAn excel file containing
 all of the functional characterizations from the different annotation
 databases including, Swiss-Prot, Pfam-A, TIGRFAM,
 SUPERFAMILY.Horn_etal_Tnewberryi
 Transcriptome Annotations.xlsxedgeR
 R-scriptAn R file including the
 code used to run the differential expression analysis in the package
 edgeR.edgR_RScript.RTriops newberry transcriptome read countsAn excel file containing the raw read counts for the contigs identified by the annotations as coding sequences. These read counts are the input for the edgeR package to perform differential gene expression analysis.Tnewberry Transcriptome Cds Read Counts.xlsxTriops newberryi CateGOrizer resultsAn excel file containing the results from the program CateGOrizer. The file indicates the GO class id, term and how many contigs were classified under a specific GO term. This raw data was used to make Figure 1 in the Horn et al. manuscript.Triops newberryi CateGOrizer Results.xlsx
DOI: 10.5061/dryad.1pq21
title: Data from: Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays

description: Single nucleotide polymorphism (SNP) markers were identified and validated
 for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri,
 using double digest restriction-site associated DNA (ddRAD) reads using
 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained
 (mean read length 289 ± 183 bp) detecting a total of 5399 contigs (mean
 contig length: 396 ± 91 bp). Mining this data set, a panel of 143 in
 silico SNPs was selected. Eighty-two of these SNPs were successfully
 validated and 61 were polymorphic: 14 in P. falkneri, 21 in P. motoro, 3
 in both species and 26 fixed for alternative variants in both species,
 thus being useful for population analyses and hybrid detection.
description: Contigs sequences
 analyzed in this study.This file with txt
 extension, contains the analyzed all contigs in this
 study.454_contigs.txtGenotypes, variants and other information from 143 SNPs analyzed143 SNP name, variants, dataset of the contig (source), annotation, GenBank accession number, external PCR primer sequences (Forward and Reverse), tailed extension primer (showing tails in lower case), extension primer direction and multiplexs are shown. Unfeasible SNPs are indicated in red colour.Genotypes_variants.xlsxInformation from samples 89 genotype ddRad loci identified.This file contains information from samples 89 genotyped .Information_samples.xlsxThis file contains the access information in NCBI of 39 samples used of to develop the SNPs.This file contains the access information in NCBI of 39 samples used to develop the SNPs.Table_ information_NCBI(SRA).docx
DOI: 10.5061/dryad.9m6n2
title: Data from: Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams

description: Introgressive hybridization between native and introduced species is a
 growing conservation concern. For native cutthroat trout and introduced
 rainbow trout in western North America, this process is thought to lead to
 the formation of hybrid swarms and the loss of monophyletic evolutionary
 lineages. Previous studies of this phenomenon, however, indicated that
 hybrid swarms were rare except when native and introduced forms of
 cutthroat trout co-occurred. We used a panel of 86 diagnostic, single
 nucleotide polymorphisms to evaluate the genetic composition of 3865 fish
 captured in 188 locations on 129 streams distributed across western
 Montana and northern Idaho. Although introgression was common and only 37%
 of the sites were occupied solely by parental westslope cutthroat trout,
 levels of hybridization were generally low. Of the 188 sites sampled, 73%
 contained ≤5% rainbow trout alleles and 58% had ≤1% rainbow trout alleles.
 Overall, 72% of specimens were nonadmixed westslope cutthroat trout, and
 an additional 3.5% were nonadmixed rainbow trout. Samples from seven sites
 met our criteria for hybrid swarms, that is, an absence of nonadmixed
 individuals and a random distribution of alleles within the sample; most
 (6/7) were associated with introgression by Yellowstone cutthroat trout.
 In streams with multiple sites, upstream locations exhibited less
 introgression than downstream locations. We conclude that although the
 widespread introduction of nonnative trout within the historical range of
 westslope cutthroat trout has increased the incidence of introgression,
 sites containing nonadmixed populations of this taxon are common and
 broadly distributed.
description: WCT_introgression_dataFile contains SNP data for all field samples included in the paper. Additionally, information in table S1 has been included allowing SNPs to be identified by both sequence and source.
DOI: 10.5061/dryad.4gn47
title: Data from: Evolution of haploid selection in predominantly diploid organisms

description: Diploid organisms manipulate the extent to which their haploid gametes
 experience selection. Animals typically produce sperm with a diploid
 complement of most proteins and RNA, limiting selection on the haploid
 genotype. Plants, however, exhibit extensive expression in pollen, with
 actively transcribed haploid genomes. Here we analyze models that track
 the evolution of genes that modify the strength of haploid selection to
 predict when evolution intensifies and when it dampens the “selective
 arena” within which male gametes compete for fertilization. Considering
 deleterious mutations, evolution leads diploid mothers to strengthen
 selection among haploid sperm/pollen, because this reduces the mutation
 load inherited by their diploid offspring. If, however, selection acts in
 opposite directions in haploids and diploids (“ploidally antagonistic
 selection”), mothers evolve to reduce haploid selection to avoid
 selectively amplifying alleles harmful to their offspring. Consequently,
 with maternal control, selection in the haploid phase either is maximized
 or reaches an intermediate state, depending on the deleterious mutation
 rate relative to the extent of ploidally antagonistic selection. By
 contrast, evolution generally leads diploid fathers to mask mutations in
 their gametes to the maximum extent possible, whenever masking (e.g.,
 through transcript sharing) increases the average fitness of a father’s
 gametes. We discuss the implications of this maternal–paternal conflict
 over the extent of haploid selection and describe empirical studies needed
 to refine our understanding of haploid selection among seemingly diploid
 organisms.
description: Model
 analysesMathematica 8.0 file in
 which we derive and analyze the model equations in the
 paper.MaintenanceOfGametophyticSelection2015.nbModel Analyses (PDF format)A PDF print-out of the Mathematica 8.0 file.MaintenanceOfGametophyticSelection2015.pdf
DOI: 10.5061/dryad.5n0v4
title: Data from: Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map

description: Understanding the genetic architecture of phenotypic traits can provide
 important information about the mechanisms and genomic regions involved in
 local adaptation and speciation. Here, we used genotyping-by-sequencing
 and a combination of previously published and newly generated data to
 construct sex-specific linkage maps for sockeye salmon (Oncorhynchus
 nerka). We then used the denser female linkage map to conduct quantitative
 trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The
 female linkage map consisted of 6322 loci distributed across 29 linkage
 groups and was 4082 cM long, and the male map contained 2179 loci found on
 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for
 thermotolerance, 5 for length, 9 for weight, and 6 for condition factor.
 QTL were distributed nonrandomly across the genome and were often found in
 hotspots containing multiple QTL for a variety of phenotypic traits. These
 hotspots may represent adaptively important regions and are excellent
 candidates for future research. Comparing our results with studies in
 other salmonids revealed several regions with overlapping QTL for the same
 phenotypic trait, indicating these regions may be adaptively important
 across multiple species. Altogether, our study demonstrates the utility of
 genomic data for investigating the genetic basis of important phenotypic
 traits. Additionally, the linkage map created here will enable future
 research on the genetic basis of phenotypic traits in salmon.
description: lepmap input
 fileGenotypes from all five
 crosses formatted for the mapping program lepmap. The SISSAQ12X03H
 identifier corresponds to cross GH1, the SN411X10H identifier corresponds
 to cross GH2, the HX6 identifier corresponds to cross D3, the HX8
 identifier corresponds to cross D4, and the HX13 identifier corresponds to
 cross D5.lepmap_input_file.linkagerqtl input for cross HX6cross HX6 corresponds to cross D3 in the manuscriptHX6_rqtl_input.csvrqtl input for cross HX8Cross HX8 corresponds to cross D4 in the manuscriptHX8_rqtl_input.csvrqtl input for cross HX13Cross HX13 corresponds to cross D5 in the manuscriptHX13_rqtl_input.csv
DOI: 10.5061/dryad.5b5v4
title: Data from: Disruptive selection without genome-wide evolution across a migratory divide

description: Transcontinental migration is a fascinating example of how animals can
 respond to climatic oscillation. Yet, quantitative data on fitness
 components are scarce, and the resulting population genetic consequences
 are poorly understood. Migratory divides, hybrid zones with a transition
 in migratory behaviour, provide a natural setting to investigate the
 micro-evolutionary dynamics induced by migration under sympatric
 conditions. Here, we studied the effects of migratory programme on
 survival, trait evolution and genome-wide patterns of population
 differentiation in a migratory divide of European barn swallows. We
 sampled a total of 824 individuals from both allopatric European
 populations wintering in central and southern Africa, respectively, along
 with two mixed populations from within the migratory divide. While most
 morphological characters varied by latitude consistent with
 Bergmann's rule, wing length co-varied with distance to wintering
 grounds. Survival data collected during a 5-year period provided strong
 evidence that this covariance is repeatedly generated by disruptive
 selection against intermediate phenotypes. Yet, selection-induced
 divergence did not translate into genome-wide genetic differentiation as
 assessed by microsatellites, mtDNA and &gt;20 000 genome-wide SNP
 markers; nor did we find evidence of local genomic selection between
 migratory types. Among breeding populations, a single outlier locus mapped
 to the BUB1 gene with a role in mitotic and meiotic organization. Overall,
 this study provides evidence for an adaptive response to variation in
 migration behaviour continuously eroded by gene flow under current
 conditions of nonassortative mating. It supports the theoretical
 prediction that population differentiation is difficult to achieve under
 conditions of gene flow despite measurable disruptive selection.
description: von_Ronn_SWALLOW.vcfVCF file containing the filtered SNPs called from the STACKs pipeline used in the population genomic analyses.von_Ronn_SWALLOW_locBayescan files containing the unfiltered SNPs called from the STACKs pipeline used in the outlier analyses - both location and migration groupings are provided.von_Ronn_SWALLOW_migBayescan files containing the unfiltered SNPs called from the STACKs pipeline used in the outlier analyses - both location and migration groupings are provided.msats_rawmicrosatellite genotypesdirect_assort_matecarbon and nitrogen stable isotope values of breeding pairscmr_datacmr data used to measure and visualize selection on wing lengthsia_datainidvidual carbon and nitrogen stable isotope valuesmorph_datamorphological data
DOI: 10.5061/dryad.4jv4s
title: Data from: Segregated water observed in a putative fish embryo cryopreservative

description: Development of new cryopreservation strategies has major potential in
 medicine and agriculture and is critical to the conservation of endangered
 species that currently cannot be preserved. A critical property of any
 potential cryopreservative solution is its ability to prevent
 cell-damaging ice formation during cooling and subsequent heating. This
 study focuses on the freezing behaviour of promising model cryoprotective
 solutions. We perform neutron scattering analysis, combined with computer
 modelling, of the water structure after quench cooling these solutions. It
 is found that water in this solution forms nano-clusters encapsulated by
 the surrounding matrix of cryoprotectant solute molecules. We posit that
 these small volumes inhibit ice formation, because water does not have
 space for the structural relaxation required to crystallize on the
 timescale of the cooling process.
description: cryopreservation EPSR
 folderThis is the entire EPSR
 folder for the data and simulations and analysis shown in this
 paper.cryopres.zip
DOI: 10.5061/dryad.80f4f
title: Data from: Genetic stock composition of marine bycatch reveals disproportional impacts on depleted river herring genetic stocks

description: Bycatch of mid-trophic level anadromous fishes that connect marine and
 freshwater ecosystems is a growing conservation concern. Anadromous
 alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) are
 important components of coastal freshwater and marine food webs, but have
 experienced dramatic declines in the abundances of spawning adults.
 Freshwater-focused restoration efforts have yielded few consistent signs
 of recovery; raising concerns that bycatch in Northwest Atlantic
 commercial fisheries may be negating these conservation actions. Using
 data from 15 microsatellites genotyped for baseline populations and
 bycatch, we conducted genetic stock identification to understand how
 bycatch was partitioned among previously identified regional genetic
 stocks. We then combined this information with fishery observer data to
 estimate genetic stock-specific bycatch mortality for the southern New
 England Atlantic herring fishery (2012-2013). Bycatch overall, but
 especially in the Atlantic herring fishery, was disproportionately
 assigned to the most severely depleted genetic stocks (alewife Southern
 New England stock – 70% of assignments; blueback herring Mid-Atlantic
 stock – 78% of assignments). These genetic stocks overlap in the region
 surrounding Long Island Sound, suggesting that bycatch taken from this
 area in recent years may be negatively impacting recovery efforts in this
 region. Our study suggests that mitigating bycatch on the southern New
 England fishing grounds may benefit recovery efforts for alewife and
 blueback herring genetic stocks that have experienced the greatest
 declines in spawning adult abundances.
description: gpiper_0.1.targpiper is an R package that is required to run the program gsi_sim used in the study. Please see the Readme file for instructions.herring_0.0.1.tar'Herring' is an R package that contains all the data and the code required for reproduction of the results in the study.Table S2 - Individual bycatch mixturesThis is a MS Excel spreadsheet that contains posterior mean estimated mixing proportions for each individual in the mixture sample (i.e., the bycatch). These estimates were calculated using gsi_sim.