cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs30388
title: Data from: Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

description: The mechanisms that determine patterns of species dispersal are important
 factors in the production and maintenance of biodiversity. Understanding
 these mechanisms helps to forecast the responses of species to
 environmental change. Here we used a comparative framework and genome-wide
 data obtained through RAD-seq to compare the patterns of connectivity
 among breeding colonies for five penguin species with shared ancestry,
 overlapping distributions, and differing ecological niches, allowing an
 examination of the intrinsic and extrinsic barriers governing dispersal
 patterns. Our findings show that at-sea range and oceanography underlie
 patterns of dispersal in these penguins. The pelagic niche of emperor
 (Aptenodytes forsteri), king (A. patagonicus), Adélie (Pygoscelis adeliae)
 and chinstrap (P. antarctica) penguins facilitates gene flow over
 thousands of kilometres. In contrast, the coastal niche of gentoo penguins
 (P. papua) limits dispersal, resulting in population divergences.
 Oceanographic fronts also act as dispersal barriers to some extent. We
 recommend that forecasts of extinction risk incorporate dispersal and that
 management units are defined by at-sea range and oceanography in species
 lacking genetic data.
description: Adelie penguins - VCF of
 SNP datasetAdelie.vcfChinstrap penguins - VCF of SNP datasetChinstrap.vcfGentoo penguins - VCF of full SNP datasetincludes outlier lociGentoos_all-SNPs.vcfGentoo penguins - VCF of neutral SNP datasetoutlier loci removedGentoos_neutral-SNPs.vcfGentoo penguins - nexus file for BFD*Input file of SNPs for BFD* species delimitationGentoos_input_for_BFD.nexGentoo penguins - phylip file for RAxMLPhylip alignment of SNPs for phylogenetic inference in RAxMLGentoos_input_for_RAxML.phyGentoos_input_for_SNAPP_set1XML input file for SNAPP analysis of gentoo penguins - set 1Gentoos_input_for_SNAPP_set2XML input file for SNAPP analysis - set 2
DOI: 10.5061/dryad.p5t5gh1
title: Data from: An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

description: [No abstract entered]
description: READMEREADME of Supplementary
 Archives and included files of Evangelista et al. 2019Evangelista_et_al_README_DRYAD.pdfSupplementary Archive 1Files included in Supplementary Archive 1, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_1.zipSupplementary Archive 2Files included in Supplementary Archive 2, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_2.zip
DOI: 10.5061/dryad.37g7v3v
title: Data from: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

description: Background: Crassulacean acid metabolism (CAM) enhances plant water-use
 efficiency through an inverse day/night pattern of stomatal
 closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved
 independently in over 35 plant lineages, accounting for ~ 6% of all higher
 plants. Agave species are highly heat- and drought-tolerant, and have been
 domesticated as model CAM crops for beverage, fiber, and biofuel
 production in semi-arid and arid regions. However, the genomic basis of
 evolutionary innovation of CAM in genus Agave is largely unknown. Results:
 Using an approach that integrated genomics, gene co-expression networks,
 comparative genomics and protein structure analyses, we investigated the
 molecular evolution of CAM as exemplified in Agave. Comparative genomics
 analyses among C3, C4 and CAM species revealed that core metabolic
 components required for CAM have ancient genomic origins traceable to
 non-vascular plants while regulatory proteins required for diel
 re-programming of metabolism have a more recent origin shared among C3, C4
 and CAM species. We showed that accelerated evolution of key functional
 domains in proteins responsible for primary metabolism and signaling,
 together with a diel re-programming of the transcription of genes involved
 in carbon fixation, carbohydrate processing, redox homeostasis, and
 circadian control is required for the evolution of CAM in Agave.
 Furthermore, we highlighted the potential candidates contributing to the
 adaptation of CAM functional modules. Conclusions: This work provides
 evidence of adaptive evolution of CAM related pathways. We showed that the
 core metabolic components required for CAM are shared by non-vascular
 plants, but regulatory proteins involved in re-reprogramming of carbon
 fixation and metabolite transportation appear more recently. We propose
 that the accelerated evolution of key proteins together with a diel
 re-programming of gene expression were required for CAM evolution from C3
 ancestors in Agave.
description: Supporting file
 1_Agam_transcript_LT200bpAgave americana
 transcript sequences of less than 200bpSupporting file
 2_Agam_representative_protein_sequenceRepresentative protein
 sequences of Agave americanaSupporting file
 3_Agde_representative_protein_sequenceRepresentative protein
 sequences of Agave desertiSupporting file
 4_Agte_representative_protein_sequenceRepresentative protein
 sequences of Agave tequilanaSupporting file
 5_ExpressionDataTime-course expression
 data of Agave americana for 15 samples collected with three biological
 replicates, including eight samples of the mature fourth fully expanded
 leaf collected at 3, 6, 9, 12, 15, 18, 21 and 24 hours after the beginning
 of the light period; three young leaf samples collected at diel time
 points of 6, 12 and 21 hours, respectively; and four non-leaf samples
 (i.e., meristem, rhizome, root or stem) collected at 3 hr after the
 beginning of the light period.
DOI: 10.5061/dryad.8m3h4
title: Data from: Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

description: Despite the demonstrated functional importance of gut microbes, our
 understanding of how animals regulate their metabolism in response to
 nutritionally beneficial symbionts remains limited. Here, we elucidate the
 functional importance of the African cotton stainer's (Dysdercus
 fasciatus) association with two actinobacterial gut symbionts and
 subsequently examine the insect's transcriptional response following
 symbiont elimination. In line with bioassays demonstrating the
 symbionts' contribution towards host fitness through the
 supplementation of B vitamins, comparative transcriptomic analyses of
 genes involved in import and processing of B vitamins revealed an
 upregulation of gene expression in aposymbiotic (symbiont-free) compared
 with symbiotic individuals; an expression pattern that is indicative of B
 vitamin deficiency in animals. Normal expression levels of these genes,
 however, can be restored by either artificial supplementation of B
 vitamins into the insect's diet or reinfection with the
 actinobacterial symbionts. Furthermore, the functional characterization of
 the differentially expressed thiamine transporter 2 through heterologous
 expression in Xenopus laevis oocytes confirms its role in cellular uptake
 of vitamin B1. These findings demonstrate that despite an extracellular
 localization, beneficial gut microbes can be integral to the host's
 metabolic homeostasis, reminiscent of bacteriome-localized intracellular
 mutualists.
description: Supplemental_data1_Transcript_contigsSupplemental_data2_Transcript_annotationTranscript annotation
DOI: 10.5061/dryad.82h0m
title: Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

description: Background: The extant squamates (&gt;9400 known species of lizards
 and snakes) are one of the most diverse and conspicuous radiations of
 terrestrial vertebrates, but no studies have attempted to reconstruct a
 phylogeny for the group with large-scale taxon sampling. Such an estimate
 is invaluable for comparative evolutionary studies, and to clarify their
 taxonomy. Here, we present the first large-scale phylogenetic estimate for
 Squamata. Results: The estimated phylogeny contains 4161 species
 representing all currently recognized families and subfamilies. The
 analysis is based on up to 12896 base pairs of sequence data per species
 (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF,
 c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes
 (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important
 confirmation for recent estimates of higher-level squamate phylogeny based
 on molecular data (but with more limited taxon sampling), estimates that
 are very different from previous morphology-based hypotheses. The tree
 also includes many relationships that differ from previous molecular
 estimates and many that differ from traditional taxonomy. Conclusions: We
 present a new large-scale phylogeny of squamate reptiles that should be a
 valuable resource for future comparative studies. We also present a
 revised classification of squamates at the family and subfamily level to
 bring the taxonomy more in line with the new phylogenetic hypothesis. This
 classification includes new, resurrected, and modified subfamilies within
 gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid
 snakes.
description: squam_shlMaximum-likelihood phylogeny containing 4162 species.squam_shl_namesMaximum-likelihood phylogeny containing 4162 species, with names changed to reflect the December, 2012 update of the Reptile Database (see Table S1).Squamata_10_28Matrix containing DNA sequences from 4162 species from 12 genes, with 12896 bp per species.Squamata_ModelsModel partition file for 12-gene matrix.
DOI: 10.5061/dryad.55t54
title: Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing

description: Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence
 data, but it is not specifically designed to generate data suitable for
 genetic mapping. Recently developed DNA library preparation methods for
 NGS have helped solve this problem, however, by combining the use of
 reduced representation libraries with DNA sample barcoding to generate
 genome-wide genotype data from a common set of genetic markers across a
 large number of samples. Here we use such a method, called
 genotyping-by-sequencing (GBS), to produce a data set for genetic mapping
 in an F1 population of apples (Malus x domestica) segregating for skin
 color. We show that GBS produces a relatively large, but extremely sparse,
 genotype matrix: over 270,000 SNPs were discovered, but most SNPs have too
 much missing data across samples to be useful for genetic mapping. After
 filtering for genotype quality and missing data, only 6% of the 85 million
 DNA sequence reads contributed to useful genotype calls. Despite this
 limitation, using existing software and a set of simple heuristics, we
 generated a final genotype matrix containing 3967 SNPs from 89 DNA samples
 from a single lane of Illumina HiSeq and used it to create a saturated
 genetic linkage map and to identify a known QTL underlying apple skin
 color. We therefore demonstrate that GBS is a cost effective method for
 generating genome-wide SNP data suitable for genetic mapping in a highly
 diverse and heterozygous agricultural species. We anticipate future
 improvements to the GBS analysis pipeline presented here that will enhance
 the utility of next-generation DNA sequence data for the purposes of
 genetic mapping across diverse species.
description: Gardner et al. dryad
 submissionGardner_dryad_submission.tar.gz
DOI: 10.5061/dryad.92p46
title: Data from: Conserved patterns of incomplete reporting in pre-vaccine era childhood diseases

description: Incomplete observation is an important yet often neglected feature of
 observational ecological timeseries. In particular, observational case
 report timeseries of childhood diseases have played an important role in
 the formulation of mechanistic dynamical models of populations and
 metapopulations. Yet to our knowledge, no comprehensive study of childhood
 disease reporting probabilities (commonly referred to as reporting rates)
 has been conducted to date. Here, we provide a detailed analysis of
 measles and whooping cough reporting probabilities in pre-vaccine United
 States cities and states, as well as measles in cities of England and
 Wales. Overall, we find the variability between locations and diseases
 greatly exceeds that between methods or time periods. We demonstrate a
 strong relationship within location between diseases and within disease
 between geographical areas. In addition, we find that demographic
 covariates such as ethnic composition and school attendance explain a
 non-trivial proportion of reporting probability variation. Overall, our
 findings show that disease reporting is both variable and non-random and
 that completeness of reporting is influenced by disease identity,
 geography and socioeconomic factors. We suggest that variations in
 incomplete observation can be accounted for and that doing so can reveal
 ecologically important features that are otherwise obscured.
description: GunningErhardtWearing2014Main file includes case reports, demographic rates, and IPUMS census microdata (large). R scripts are included to read in data. See README for more details.
DOI: 10.5061/dryad.h508g38
title: Data from: Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)

description: Investigating variation in gene flow across the genome between closely
 related species is important to understand how reproductive barriers shape
 genome divergence before speciation is complete. An efficient way to
 characterize differential gene flow is to study how the genetic
 interactions that take place in hybrid zones selectively filter gene
 exchange between species, leading to heterogeneous genome divergence. In
 the present study, genome-wide divergence and introgression patterns were
 investigated between two sole species, Solea senegalensis and Solea
 aegyptiaca, using restriction-associated DNA sequencing (RAD-Seq) to
 analyse samples taken from a transect spanning the hybrid zone. An
 integrative approach combining geographic and genomic clines methods with
 an analysis of individual locus introgression accounting for the
 demographic history of divergence was conducted. Our results showed that
 the two sole species have come into secondary contact postglacially, after
 experiencing a prolonged period (ca. 1.1 to 1.8 Myrs) of allopatric
 separation. Secondary contact resulted in the formation of a tension zone
 characterized by strong reproductive isolation, allowing introgression in
 only a minor fraction of the genome. We found multiple evidence for a
 preferential direction of introgression in the S. aegyptiaca genetic
 background, indicating a possible recent or ongoing movement of the hybrid
 zone. Deviant introgression signals found in the opposite direction
 suggested that S. senegalensis could have possibly undergone adaptive
 introgression that has not yet spread throughout the entire species range.
 Our study thus illustrates the varied outcomes of genetic interactions
 between divergent gene pools that recently met after a long history of
 divergence.
description: Souissi_Final_working_datasetThe SNP dataset used in all analysis except newhybrids analysis . The VCF file contains 10758 SNPs typed in 161 individuals.Only one single SNP for each pair of RAD loci associated with the same restriction site (i.e. within a distance less than 200 bp) was kept.locus_from_dadi_pop_final.vcfSouissi_AEG_SEN_JAFSThe JAFS dadi input file for Solea senegalensis and Solea aegyptiacaAEG_SEN.fsSouissi_DADI_input_to_generate_fsDataset from Souissi_VCF_dadi_analysis used as input in DADI to generate the FS filedadi_all_pop_final_edited.dataSouissi_VCF_DADI_analysisThe SNP dataset used in DADI analysis . The VCF file contains 10758 SNPs typed in 94 individuals.Only one single SNP for each pair of RAD loci associated with the same restriction site (i.e. within a distance less than 200 bp) was kept.Dadi_all_final.vcf
DOI: 10.5061/dryad.s706g
title: Data from: Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments

description: Studying the mechanisms that enable coral populations to inhabit spatially
 varying thermal environments can help evaluate how they will respond in
 time to the effects of global climate change and elucidate the
 evolutionary forces that enable or constrain adaptation. Inshore reefs in
 the Florida Keys experience higher temperatures than offshore reefs for
 prolonged periods during the summer. We conducted a common garden
 experiment with heat stress as our selective agent to test for local
 thermal adaptation in corals from inshore and offshore reefs. We show that
 inshore corals are more tolerant of a 6-week temperature stress than
 offshore corals. Compared with inshore corals, offshore corals in the 31
 °C treatment showed significantly elevated bleaching levels concomitant
 with a tendency towards reduced growth. In addition, dinoflagellate
 symbionts (Symbiodinium sp.) of offshore corals exhibited reduced
 photosynthetic efficiency. We did not detect differences in the
 frequencies of major (&gt;5%) haplotypes comprising Symbiodinium
 communities hosted by inshore and offshore corals, nor did we observe
 frequency shifts (‘shuffling’) in response to thermal stress. Instead,
 coral host populations showed significant genetic divergence between
 inshore and offshore reefs, suggesting that in Porites astreoides, the
 coral host might play a prominent role in holobiont thermotolerance. Our
 results demonstrate that coral populations inhabiting reefs &lt;10-km
 apart can exhibit substantial differences in their physiological response
 to thermal stress, which could impact their population dynamics under
 climate change.
description: Phenotypic
 DataThis file contains .csv
 files of raw trait measurements described in the paper (growth, bleaching,
 PAM) in addition to processed symbiont genotyping counts data (percent
 mapped reads and haplotype files). The accompanying R command file opens
 specific trait files and calls out columns in each to perform statistical
 analyses and generate figures as in the accompanying
 paper.TraitData.zipHost Genotyping Data (microsattelite genotypes)This file contains the raw data files for both the full genotyping dataset (including individuals with 3rd alleles) as well as a STRUCTURE input file that is a subset of the data containing only those individuals with diploid genotypes at all loci as described in the paper. The R command files are for completing ploidy modeling as described in supplementary file S1.CoralHostGenotyping.zipITS454rawreadsThis file contains raw .fna files from 454 sequencing of the ITS2 locus as described in the paper. Each file contains reads for a single sample and &gt; lines give the sample name for each file.White Balanced Photographs of Coral BleachingThis file contains pre- and post- experiment photographs of coral fragments that were analyzed to yield intensity measures indicative of bleaching as described in the paper.Bleachpics_CorelExposureCorrectwithWhite.zip
DOI: 10.5061/dryad.8n2b32q
title: Data from: Genomic divergence between Spanish Littorina saxatilis ecotypes unravels limited admixture and extensive parallelism associated with population history

description: The rough periwinkle, Littorina saxatilis, is a model system for studying
 parallel ecological speciation in microparapatry. Phenotypically parallel
 wave-adapted and crab-adapted ecotypes that hybridize within the middle
 shore are replicated along the northwestern coast of Spain, and have
 likely arisen from two separate glacial refugia. We tested whether greater
 geographic separation corresponding to reduced opportunity for
 contemporary or historical gene flow between parallel ecotypes resulted in
 less parallel genomic divergence. We sequenced double-digested
 restriction-associated DNA (ddRAD) libraries from individual snails from
 upper, mid, and low intertidal levels of three separate sites colonized
 from two separate refugia. FDIST analysis of 4256 SNP markers identified
 34.4% sharing of divergent loci between two geographically-close sites,
 however, these sites each shared only 9.9-15.1% of their divergent loci
 with a third more-distant site. STRUCTURE analysis revealed that genotypes
 from only three of 166 phenotypically intermediate mid-shore individuals
 appeared to result from recent hybridization suggesting that hybrids
 cannot be reliably identified using shell traits. Hierarchical AMOVA
 indicated that the primary source of genomic differentiation was
 geographic separation, but also revealed greater similarity of the same
 ecotype across the two geographically-close sites than previously
 estimated with dominant markers. These results from a model system for
 ecological speciation suggest that genomic parallelism is affected by the
 opportunity for historical or contemporary gene flow between populations.
description: Kess Galindo Boulding
 Lsaxatilis 2018 EE Analysis DataSample metadata with
 sampling site and transect for each sequenced individual, Stacks output
 and vcf files, Genepop and Structure input files for all, neutral, and
 outlier loci. AMOVA and FST results from Arlequin.Kess Galindo Boulding
 Lsaxatilis 2018 EE Upload Data.zip
DOI: 10.5061/dryad.98283
title: Data from: Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

description: Community characteristics reflect past ecological and evolutionary
 dynamics. Here, we investigate whether it is possible to obtain
 realistically shaped modelled communities – i.e., with phylogenetic trees
 and species abundance distributions shaped similarly to typical empirical
 bird and mammal communities – from neutral community models. To test the
 effect of gene flow, we contrasted two spatially explicit individual-based
 neutral models: one with protracted speciation, delayed by gene flow, and
 one with point mutation speciation, unaffected by gene flow. The former
 produced more realistic communities (shape of phylogenetic tree and
 species-abundance distribution), consistent with gene flow being a key
 process in macro-evolutionary dynamics. Earlier models struggled to
 capture the empirically observed branching tempo in phylogenetic trees, as
 measured by the gamma statistic. We show that the low gamma values typical
 of empirical trees can be obtained in models with protracted speciation,
 in pre-equilibrium communities developing from an initially abundant and
 widespread species. This was even more so in communities sampled
 incompletely, particularly if the unknown species are the youngest.
 Overall, our results demonstrate that the characteristics of empirical
 communities that we have studied can, to a large extent, be explained
 through a purely neutral model under pre-equilibrium conditions.
description: Simulated
 treesThis archive contains
 the simulated trees stored in parenthetic formatData.zip