cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dg513
title: Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone

description: Contact zones provide an excellent arena in which to address questions
 about how genomic divergence evolves during lineage divergence. They allow
 us to both infer patterns of genomic divergence in allopatric populations
 isolated from introgression and to characterize patterns of introgression
 after lineages meet. Thusly motivated, we analyze genome-wide
 introgression data from four contact zones in three genera of lizards
 endemic to the Australian Wet Tropics. These contact zones all formed
 between morphologically cryptic lineage-pairs within morphologically
 defined species, and the lineage-pairs meeting in the contact zones
 diverged anywhere from 3.1 to 5.8 million years ago. By characterizing
 patterns of molecular divergence across an average of 11K genes and
 fitting geographic clines to an average of 7.5K variants, we characterize
 how patterns of genomic differentiation and introgression change through
 time. Across this range of divergences, we find that genome-wide
 differentiation increases but becomes no less heterogeneous. In contrast,
 we find that introgression heterogeneity decreases dramatically,
 suggesting that time helps isolated genomes ”congeal”. Thus, this work
 emphasizes the pivotal role that history plays in driving lineage
 divergence.
description: Assembly, variant, and
 cline data for paperThis package contains
 four sets of data: - cline_allele_frequencies: inferred allele frequencies
 at each SNP (filtered & unfiltered) at each contact zone - probes:
 probes used in exome capture for each contact zone - target_assemblies:
 annotated assemblies generated from exome capture data and used as
 pseudo-reference genome - variants: variant call format files (VCFs)
 generated by aligning read data from the contact zone to the
 PRGdatadryad.zip
DOI: 10.15468/dl.puvzhb
title: Occurrence Download

description: A dataset containing 14175 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cotinis mutabilis"
 ]
}

 The dataset includes 14175 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000395-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sf540
title: Data from: Discovery of a giant chameleon-like lizard (Anolis) on Hispaniola and its significance to understanding replicated adaptive radiations

description: We report a new chameleon-like Anolis species from Hispaniola that is
 ecomorphologically similar to congeners found only on Cuba. Lizards from
 both clades possess short limbs and a short tail and utilize relatively
 narrow perches, leading us to recognize a novel example of
 ecomorphological matching among islands in the well-known Greater
 Antillean anole radiation. This discovery supports the hypothesis that the
 assembly of island faunas can be substantially deterministic and
 highlights the continued potential for basic discovery to reveal new
 insights in well-studied groups. Restricted to a threatened band of
 midelevation transitional forest near the border of the Dominican Republic
 and Haiti, this new species appears to be highly endangered.
description: Data files for Mahler et
 al. 2016 AmNatThis data package
 contains raw data files associated with "Discovery of a giant
 chameleon-like lizard (Anolis) on Hispaniola and its significance to
 understanding replicated adaptive radiations" by Mahler and
 colleagues. These data comprise phylogenetic trees and XML files,
 phenotypic trait data, and GenBank and museum voucher information for
 individual specimens that were sequenced as part of this project. Note
 that all comparative analyses were conducted using only those species that
 overlap between the phylogeny and trait data sets (i.e., not all data in
 this package were featured in our paper). See the included file
 "README.txt" for information about each data
 file.Mahler_etal_2016_AmNat_DRYAD.zip
DOI: 10.5061/dryad.4f98t
title: Data from: Predicting ecological responses in a changing ocean: the effects of future climate uncertainty

description: Predicting how species will respond to climate change is a growing field
 in marine ecology, yet knowledge of how to incorporate the uncertainty
 from future climate data into these predictions remains a significant
 challenge. To help overcome it, this review separates climate uncertainty
 into its three components (scenario uncertainty, model uncertainty, and
 internal model variability) and identifies four criteria that constitute a
 thorough interpretation of an ecological response to climate change in
 relation to these parts (awareness, access, incorporation, communication).
 Through a literature review, the extent to which the marine ecology
 community has addressed these criteria in their predictions was assessed.
 Despite a high awareness of climate uncertainty, articles favoured the
 most severe emission scenario, and only a subset of climate models were
 used as input into ecological analyses. In the case of sea surface
 temperature, these models can have projections unrepresentative against a
 larger ensemble mean. Moreover, 91% of studies failed to incorporate the
 internal variability of a climate model into results. We explored the
 influence that the choice of emission scenario, climate model, and model
 realisation can have when predicting the future distribution of the
 pelagic fish, Electrona antarctica. Future distributions were highly
 influenced by the choice of climate model, and in some cases, internal
 variability was important in determining the direction and severity of the
 distribution change. Increased clarity and availability of processed
 climate data would facilitate more comprehensive explorations of climate
 uncertainty, and increase in the quality and standard of marine prediction
 studies.
description: processed CMIP5 SST
 projectionsThis file has projected
 annual mean Sea Surface Temperature (SST) averaged over the time period
 1981-2100. Data are taken from 15 CMIP5 climate models under two emission
 scenarios, RCP 4.5 and RCP 8.5. Where possible, multiple realisations of a
 climate model are included, as well as the mean output from these
 realisations. The present day baseline annual mean SST layer (1982-2001)
 is also available. Two spatial resolutions are available: 1x1 degree and
 0.25x0.25 degree created by a spline interpolation procedure in ArcGIS
 v.10.4.1. All original CMIP5 data are available at
 https://esgf-node.llnl.gov/projects/cmip5/. See README file for further
 information.SST_projections.zip
DOI: 10.5061/dryad.6k94r
title: Data from: Diversity and distribution of Wolbachia in relation to geography, host plant affiliation and life cycle of a heterogonic gall wasp

description: Background: The maternally inherited endosymbiont Wolbachia is widespread
 in arthropods and nematodes and can play an important role in the ecology
 and evolution of its host through reproductive manipulation. Here, we
 survey Wolbachia in Belonocnema treatae, a widely distributed North
 American cynipid gall forming wasp that exhibits regional host
 specialization on three species of oaks and alternation of sexually and
 aseuxlly reproducing generations. We investigated whether patterns of
 Wolbachia infection and diversity in B. treatae are associated with the
 insect's geographic distribution, host plant association, life cycle,
 and mitochondrial evolutionary history. Results: Screening of 463
 individuals from 23 populations including sexual and asexual generations
 from all three host plants across the southern U.S. showed an average
 infection rate of 56% with three common Wolbachia strains: wTre1-3 and an
 additional rare variant wTre4. Phylogenetic analysis based on wsp showed
 that these strains are unrelated and likely independently inherited. We
 found no difference in Wolbachia infection frequency among host plant
 associated populations or between the asexual and sexual generations, or
 between males and females of the sexual generation. Partially incomplete
 Wolbachia transmission rates might explain the occurrence of uninfected
 individuals. A parallel analysis of the mitochondrial cytochrome oxidase I
 gene in B. treatae showed high mtDNA haplotype diversity in both infected
 and uninfected populations suggesting an ancestral infection by Wolbachia
 as well as a clear split between eastern and western B. treatae mtDNA
 clades with a sequence divergence of &gt; 6%. The strain wTre1 was
 present almost exclusively in the western clade while wTre2 and wTre3
 occur almost exclusively in eastern populations. In contrast, the same
 strains co-occur as double-infection in Georgia and triple-infections in
 two populations in central Florida. Conclusions: The diversity of
 Wolbachia across geographically and genetically distinct populations of B.
 treatae and the co-occurrence of the same strains within three populations
 highlights the complex infection dynamics in this system. Moreover, the
 association of distinct Wolbachia strains with mitochondrial haplotypes of
 its host in populations infected by different Wolbachia strains suggests a
 potential role of the endosymbiont in reproductive isolation in B.
 treatae.
description: Mitochondrial
 sequencesMitochondrial sequences
 of 463 B. treatae individualsmtDNA
 Sequences.zipWolbachia
 SequencesSequences of 260
 Wolbachia infected B. treatae samplesCloning
 SequencesSequences files from 286
 cloned plasmids.sample
 overviewOverview of sample codes
 and Wolbachia infection status of all B. treatae
 individuals
DOI: 10.15468/dl.xrj4x5
title: Occurrence Download

description: A dataset containing 49303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-148.44 59.27,-118.08 59.27,-118.08 69.77,-148.44 69.77,-148.44 59.27))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 49303 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000394-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q9p4j
title: Data from: MonotomidGen – A matrix-based interactive key to the New World genera of Monotomidae (Coleoptera, Cucujoidea)

description: A matrix-based Lucid key is presented for the twelve genera of Monotomidae
 (Coleoptera: Cucujoidea) represented in the New World. A general overview
 is given for the features and technical specifications of an original
 interactive key for the identification of these genera. The list of
 terminal taxa included with the key provides a current summary of
 monotomid generic diversity for the Nearctic and Neotropical regions.
description: MonotomidGen Lucid Key
 FilesThis ZIP file includes
 all the deployed LUCID key files.MonotomidGen.zip
DOI: 10.5061/dryad.k86v1
title: Data from: New England cod collapse and the climate

description: To improve fishery management, there is an increasing need to understand
 the long-term consequences of natural and anthropogenic climate
 variability for ecological systems. New England’s iconic cod populations
 have been in decline for several decades and have recently reached
 unprecedented lows. We find that 17% of the overall decline in Gulf of
 Maine cod biomass since 1980 can be attributed to positive phases of the
 North Atlantic Oscillation (NAO). This is a consequence of three results:
 i) a 1-unit increase in the NAO winter index is associated with a 17%
 decrease in the spring biomass of age-1 cod the following year; ii) this
 NAO-driven decrease persists as the affected cohort matures; iii) fishing
 practices appear to exacerbate NAO’s direct biological effect such that,
 since 1913, a 1-unit increase in the NAO index lowers subsequent cod catch
 for up to 19 years. The Georges Bank cod stock displays similar patterns.
 Because we statistically detect a delay between the NAO and subsequent
 declines in adult biomass, our findings imply that observed current NAO
 conditions can be used in stock forecasts, providing lead time for
 adaptive policy. More broadly, our approach can inform forecasting efforts
 for other fish populations strongly affected by natural and anthropogenic
 climatic variation.
description: Meng_Oremus_Gaines_replicationThis zip file contains all code and data to replicate results in Meng, Oremus, Gaines, PLOS ONE, 2016
DOI: 10.5061/dryad.rp949
title: Data from: Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura

description: Robertsonian translocations resulting in fusions between sex chromosomes
 and autosomes shape karyotype evolution by creating new sex chromosomes
 from autosomes. These translocations can also reverse sex chromosomes back
 into autosomes, which is especially intriguing given the dramatic
 differences between autosomes and sex chromosomes. To study the genomic
 events following a Y chromosome reversal, we investigated an autosome-Y
 translocation in Drosophila pseudoobscura. The ancestral Y chromosome
 fused to a small autosome (the dot chromosome) approximately 10–15 Mya. We
 used single molecule real-time sequencing reads to assemble the D.
 pseudoobscura dot chromosome, including this Y-to-dot translocation. We
 find that the intervening sequence between the ancestral Y and the rest of
 the dot chromosome is only ∼78 Kb and is not repeat-dense, suggesting that
 the centromere now falls outside, rather than between, the fused
 chromosomes. The Y-to-dot region is 100 times smaller than the D.
 melanogaster Y chromosome, owing to changes in repeat landscape. However,
 we do not find a consistent reduction in intron sizes across the Y-to-dot
 region. Instead, deletions in intergenic regions and possibly a small
 ancestral Y chromosome size may explain the compact size of the Y-to-dot
 translocation.
description: dpse_falcon
 assemblyWe downloaded raw PacBio
 reads from
 ftp://ftp.hgsc.bcm.edu/Dpseudoobscura/Towards_finishing_the_D.pseudoobscura_genome/PacBio_Data/FastQ_files/ (these reads was generously granted by Drs. Stephen Schaeffer and Stephen Richards). We used the Falcon assembler v0.3.0 (https://github.com/PacificBiosciences/FALCON-integrate) to filter, correct and assemble reads. Then we polished the assembly using Quiver (SMRT Analysis v2.3.0)dpse_falcon.quiver.fastadpse_falcon gtfWe identified exon-introns junctions by mapping annotated transcripts (r3.03; Flybase) and transcripts of Y-linked genes from NCBI (gi|295126506|gb|GU937420.1|, gi|255764727|gb|EU595397.2|, gi|295126512|gb|GU937423.1|) to our assembly using exonerate 2.4.0. To complement these data, we mapped RNA-seq reads to our assembly using Tophat v2.0.13. We annotated transcripts, eliminated small redundant isoforms with cufflinks v2.2.2 .merged_de.gtfdpse expression and annotationWe mapped RNA-seq reads to our assembly using Tophat v2.0.13 and estimated expression level with cufflinks v2.2.2. We then searched for homologous genes using the predicted transcripts as BLAST queries to all D. melanogaster translations and transposon sequences (r6.07) with NCBIblast.expression and annotation.xlsx
DOI: 10.5061/dryad.12g7j
title: Data from: Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

description: The amphicarpic annual legume Amphicarpaea bracteata is unusual in
 producing aerial and subterranean cleistogamous flowers that always
 self-fertilize and, less commonly, aerial chasmogamous flowers that
 outcross. Although both morphologic and genetic variants are known in this
 highly selfing species, debate continues over whether this variation is
 continuous, reflecting the segregation of standing genetic variation, or
 discontinuous, reflecting distinct taxa that rarely intercross. We
 characterized SNP variation in 128 individuals in southern Wisconsin to
 assess within- and among-population variation at 3928 SNPs. We also
 assessed genotype and leaf morphology in an additional 76 individuals to
 connect phenotypic variation with genetic variation. Genetic variation
 maps onto three strongly divergent and highly inbred genetic groups
 showing little relation to site location. Each group has a distinct
 phenotype, but the divergence of these groups differs from the varietal
 divisions previously identified based on morphological characters. Like
 previous authors, we argue that the taxonomy of this species should be
 revised. Despite extensive sympatry, estimates of among-group migration
 rates are low, and hybrid individuals were at low frequency (&lt;2%)
 in our dataset. Restricted gene flow likely results from high selfing
 rates and partial reproductive incompatibility as evidenced by the
 U-shaped distribution of pairwise FST values reflecting “islands” of
 genomic divergence. These islands may be associated with hybrid
 incompatibility loci that arose in allopatry. The coexistence of lineages
 within sites may reflect density-dependent attack by species-specific
 strains of pathogenic fungi and/or root-nodulating bacteria specializing
 on distinct genotypes.
description: HRM melting
 temperaturesExcel spreadsheet with
 high resolution melt (HRM) temperatures for 8 loci and 90 Amphicarpaea
 bracteata samples (14 reference, 76 unknown). This data is used to assign
 samples to genotypic groups based on their melting temperature and the
 melting temperatures of reference samples with known
 genotypes.ambr_HRM_tm.xlsxleaf imagesAmphicarpaea bracteata leaf images for phenotypic analysisleaf_images.zip
DOI: 10.5061/dryad.tc722
title: Data from: Animal tracking meets migration genomics: transcriptomic analysis of a partially migratory bird species

description: Seasonal migration is a widespread phenomenon, which is found in many
 different lineages of animals. This spectacular behaviour allows animals
 to avoid seasonally adverse environmental conditions to exploit more
 favourable habitats. Migration has been intensively studied in birds,
 which display astonishing variation in migration strategies, thus
 providing a powerful system for studying the ecological and evolutionary
 processes that shape migratory behaviour. Despite intensive research, the
 genetic basis of migration remains largely unknown. Here we used
 state-of-the-art radio-tracking technology to characterize the migratory
 behaviour of a partially migratory population of European blackbirds
 (Turdus merula) in southern Germany. We compared gene expression of
 resident and migrant individuals using high-throughput transcriptomics in
 blood samples. Analyses of sequence variation revealed a non-significant
 genetic structure between blackbirds differing by their migratory
 phenotype. We detected only four differentially expressed genes between
 migrants and residents, which might be associated with hyperphagia,
 moulting, and enhanced DNA replication and transcription. The most
 pronounced changes in gene expression occurred between migratory birds
 depending on when, in relation to their date of departure, blood was
 collected. Overall, the differentially expressed genes detected in this
 analysis may play crucial roles in determining the decision to migrate, or
 in controlling the physiological processes required for the onset of
 migration. These results provide new insights into, and testable
 hypotheses for, the molecular mechanisms controlling the migratory
 phenotype and its underlying physiological mechanisms in blackbirds and
 other migratory bird species.
description: Blackbird_Blood_TranscriptomeMultifasta file containing the sequences of the blackbird transcriptome. The assembly was generated de novo using the program Trinity v20140717 (Grabherr et al. 2011) with the default k-mer size of 25 and a minimum contig length of 200 bp. To identify transcripts corresponding to coding genes, the obtained assembly was subjected to sequence similarity searches against a custom database containing the available bird proteins (chicken, duck, flycatcher, turkey and zebra finch; source: Ensembl release 77) and the well-annotated human and mouse protein datasets (Ensembl release 77).Blackbird_genotypesFiltered individuals’ genotypes stored in a VCF file generated by the Bayesian genetic variant detector FreeBayes v1.0.2 (Garrison & Marth), run with default parameters.
DOI: 10.5061/dryad.671bs
title: Data from: Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

description: Geographic isolation is suggested to be among the most important processes
 in the generation of cichlid fish diversity in East Africa’s Great lakes,
 both through isolation by distance and fluctuating connectivity caused by
 changing lake levels. However, even broad scale phylogeographic patterns
 are currently unknown in many non-cichlid littoral taxa from these
 systems. To begin to address this we generated restriction-site associated
 DNA sequence (RADseq) data to investigate phylogeographic structure
 throughout Lake Tanganyika in two broadly sympatric rocky shore catfish
 species from independent evolutionary radiations with differing
 behaviours: the mouth-brooding claroteine, Lophiobagrus cyclurus, and the
 brood-parasite mochokid, Synodontis multipunctatus. Our results indicated
 contrasting patterns between these species, with strong lake-wide
 phylogeographic signal in L. cyclurus including a deep divergence between
 the northern and southern lake basins. Further structuring of these
 populations was observed across a heterogeneous habitat over much smaller
 distances. Strong population growth was observed in L. cyclurus sampled
 from shallow shorelines, suggesting population growth associated with the
 colonization of new habitats following lake level rises. Conversely, S.
 multipunctatus, which occupies a broader depth range, showed little
 phylogeographic structure and lower rates of population growth. Our
 findings suggest that isolation by distance and/or habitat barriers may
 play a role in the divergence of non-cichlid fishes in Lake Tanganyika but
 this effect varies by species.
description: All_Synodontis_multipunctatus-alignmentAn alignment of RADseq data for Synodontis multipunctatusAll_Synodontis_multipunctatus.phymlAll_Lophiobagrus-alignmentAlignment of RADseq data for Lophiobagrus cyclurus and Lophiobagrus aquilusAll_Lophiobagrus.phymlStructure_input_Synodontis_multipunctatusStructure_input_LophiobagrusStructure input for Lophiobagrus cyclurus and Lophiobagrus aquilus