cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fq684
title: Data from: Do saline taxa evolve faster? comparing relative rates of molecular evolution between freshwater and marine eukaryotes

description: The major branches of life diversified in the marine realm, and numerous
 taxa have since transitioned between marine and freshwaters. Previous
 studies have demonstrated higher rates of molecular evolution in
 crustaceans inhabiting continental saline habitats as compared with
 freshwaters, but it is unclear whether this trend is pervasive or whether
 it applies to the marine environment. We employ the phylogenetic
 comparative method to investigate relative molecular evolutionary rates
 between 148 pairs of marine or continental saline vs. freshwater lineages
 representing disparate eukaryote groups, including bony fish,
 elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and
 other eukaryotes, using available protein-coding and non-coding genes.
 Overall, we observed no consistent pattern in nucleotide substitution
 rates linked to habitat across all genes and taxa. However, we observed
 some trends of higher evolutionary rates within protein-coding genes in
 freshwater taxa—the comparisons mainly involving bony fish—compared with
 their marine relatives. The results suggest no systematic differences in
 substitution rate between marine and freshwater organisms.
description: Input and output files
 for rates analysis, organised by source studyFiles include nucleotide
 alignments, newick format tree files, PAML control files, and PAML output
 files, organised by source study of the genetic/phylogenetic data and by
 gene. Nucleotide sequences were obtained from GenBank and aligned, or
 obtained from the source study authors directly (where noted in the
 Supplementary Material 2) but were further modified for analysis conducted
 in this study. Thus, the alignments do not necessarily reflect the
 original source study alignments.Mitterboeck et al. 2016_Dryad
 data.rar
DOI: 10.5061/dryad.p6m94
title: Data from: Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes

description: Strong spatial sorting of genetic variation in contiguous populations is
 often explained by local adaptation or secondary contact following
 allopatric divergence. A third explanation, spatial sorting by stochastic
 effects of range expansion, has been considered less often though
 theoretical models suggest it should be widespread, if ephemeral. In a
 study designed to delimit species within a clade of venomous coralsnakes,
 we identified an unusual pattern within the Texas coral snake (Micrurus
 tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages
 over a portion of its range, but weak sorting of these lineages elsewhere.
 We tested three alternative hypotheses to explain this pattern—local
 adaptation, secondary contact following allopatric divergence, and range
 expansion. Collectively, near panmixia of nuclear DNA, the signal of range
 expansion associated sampling drift, expansion origins in the Gulf Coast
 of Mexico, and species distribution modeling suggest that the spatial
 sorting of divergent mtDNA lineages within M. tener has resulted from
 genetic surfing of standing mtDNA variation—not local adaptation or
 allopatric divergence. Our findings highlight the potential for the
 stochastic effects of recent range expansion to mislead estimations of
 population divergence made from mtDNA, which may be exacerbated in systems
 with low vagility, ancestral mtDNA polymorphism, and male-biased
 dispersal.
description: mtDNA_concatenated_alignmentConcatenated mitochondrial alignment used in Mr Bayes and partial Mantel test analysesmtDNA_concatenated_Mr_Bayes.nexmtDNA_BEAST_ebspMitochondrial alignments used in Extended Bayesian Skyline Plot analysesmtDNA_IMa2_analysisMitochondrial alignments used in IMa2 analysesnucDNA_RADseq_STACKS_data_MicrurusNuclear SNP data associated with STACKS output (includes STRUCTURE and PHYLIP files used in multiple analyses). Both 25% and 50% missing individuals/SNP datasets are included.nucDNA_RAxML_SNP_analysisNuclear SNP alignments and trees from RAxML analyses.Micrurus_input_psi_statistic_4027_SNPsInput file for directionality index analysis of nuclear SNPs.SDM-tener-fulvius-locality_dataLocality data used for SDM modelling.SDM_tener-fulvius-localities.xlsxMantel_test_matricesDissimilarity matrices used to conduct Mantel tests.Partial_Mantel_matrices.zip
DOI: 10.5061/dryad.nn8kv
title: Data from: Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals

description: As climate change challenges organismal fitness by creating a
 phenotype–environment mismatch, phenotypic plasticity generated by
 epigenetic mechanisms (e.g., DNA methylation) can provide a temporal
 buffer for genetic adaptation. Epigenetic mechanisms may be crucial for
 sessile benthic marine organisms, such as reef-building corals, where
 ocean acidification (OA) and warming reflect in strong negative responses.
 We tested the potential for scleractinian corals to exhibit phenotypic
 plasticity associated with a change in DNA methylation in response to OA.
 Clonal coral fragments of the environmentally sensitive Pocillopora
 damicornis and more environmentally robust Montipora capitata were exposed
 to fluctuating ambient pH (7.9–7.65) and low pH (7.6–7.35) conditions in
 common garden tanks for ~6 weeks. M. capitata responded weakly, or
 acclimated more quickly, to OA, with no difference in calcification,
 minimal separation of metabolomic profiles, and no change in DNA
 methylation between treatments. Conversely, P. damicornis exhibited
 diminished calcification at low pH, stronger separation in metabolomic
 profiles, and responsiveness of DNA methylation to treatment. Our data
 suggest corals differ in their temporal dynamics and sensitivity for
 environmentally triggered real-time epigenetic reprogramming. The
 generation of potentially heritable plasticity via environmental induction
 of DNA methylation provides an avenue for assisted evolution applications
 in corals under rapid climate change.
description: Full analysis and data
 repository for Putnam et al Evolutionary Applications
 2016All Analysis Script,
 Data, and Output files to reproduce results and figures for Putnam et al
 Evolutionary Applications 2016Coral_DNAMethylation_Plasticity_zipped.zip
DOI: 10.5061/dryad.rn539
title: Data from: A new solitary free-living species of the genus Sphenopus (Cnidaria: Anthozoa: Zoantharia: Sphenopidae) from Okinawa-jima Island, Japan

description: A new species of free-living solitary zoantharian is described from
 Okinawa, Japan. Sphenopus exilis sp. n. occurs on silty seafloors in Kin
 Bay and Oura Bay on the east coast of Okinawa-jima Island. Sphenopus
 exilis sp. n. is easily distinguished from other Sphenopus species by its
 small polyp size and slender shape, although there were relatively few
 differences between Sphenopus exilis sp. n. and S. marsupialis in the
 molecular phylogenetic analyses. Currently, very little is known about the
 ecology and diversity of Sphenopus species. Thus, reviewing each species
 carefully via combined morphological and molecular analyses by using newly
 obtained specimens from type localities is required to clearly understand
 and distinguish the species within the genus Sphenopus.
description: Table
 1_ReCnidae types and sizes
 in different tissue sections of the holotype of Sphenopus exilis sp.
 n.Fig. 2
 re2olyps of Sphenopus
 exilis sp. n. A. In situ image of S. exilis sp. n., polyp with no black
 patterns, from the type locality in Kin Bay, Okinawa, Japan on 29 October
 2011. B. Polyps of NSMT-Co1576 & NSMT-Co1577 from Kin Bay,
 Okinawa-jima Island, Japan. The white circle points to the holotype. C. In
 situ image of NSMT-Co1578 from Oura Bay, Okinawa-jima Island, Japan, on 13
 November 2012. Faint black patterns and bands appear on the oral disc and
 the tentacles. D. Polyps of lot number NSMT-Co1578 showing phenotypic
 variation with black stripes on the upper part of the polyps. Scale bars:
 1 cm.Fig. 3Morphological features
 of Sphenopus exilis sp. n. A. Cross section of holotype NSMT-Co1576
 through the actinopharynx showing the mesenterial arrangement and dense
 sand encrustations. B. Well-developed mesogleal sphincter muscles visible
 on a hand-cut longitudinal section of the holotype NSMT-Co1576. C.
 Comparison of polyp shape between S. exilis sp. n. NSMT-Co1577 and S.
 marsupialis (from Brunei, refer to Reimer et al. 2012).Fig4Maximum likelihood tree
 of nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) region
 for newly obtained sequences from Sphenopus exilis sp. n. in this study
 along with previously published GenBank sequences of family Sphenopidae.
 Bootstrap values of ML &gt;60% are shown at respective nodes. Nodes
 supported by Bayesian posterior probabilities &gt;0.90 are marked with
 asterisks. Species names’ of sequences obtained from GenBank follow with
 accession numbers. The subtree shown in b) shows only the clade formed by
 genus Sphenopus, Palythoa mizigama and P. umbrosa, delineated by the gray
 square in a).
DOI: 10.5061/dryad.f4857
title: Data from: Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

description: Acropyga ants are a widespread clade of small subterranean formicines that
 live in obligate symbiotic associations with root mealybugs. We generated
 a data set of 944 loci of ultraconserved elements (UCEs) to reconstruct
 the phylogeny of 41 representatives of 23 Acropyga species using both
 concatenation and species-tree approaches. We investigated the
 biogeographic history of the genus through divergence dating analyses and
 ancestral range reconstructions. We also explored the evolution of the
 Acropyga-mealybug mutualism using ancestral state reconstruction methods.
 We recovered a highly supported species phylogeny for Acropyga with both
 concatenation and species-tree analyses. The age for crown-group Acropyga
 is estimated to be around 30 Ma. The geographic origin of the genus
 remains uncertain, although phylogenetic affinities within the subfamily
 Formicinae point to a Paleotropical ancestor. Two main Acropyga lineages
 are recovered with mutually exclusive distributions in the Old World and
 New World. Within the Old World clade, a Palearctic and African lineage is
 suggested as sister to the remaining species. Ancestral state
 reconstructions indicate that Old World species have diversified mainly in
 close association with xenococcines from the genus Eumyrmococcus, although
 present-day associations also involve other mealybug genera. In contrast,
 New World Acropyga predominantly evolved with Neochavesia until a recent
 (10-15 Ma) switch to rhizoecid mealybug partners (genus Rhizoecus). The
 striking mandibular variation in Acropyga evolved most likely from a
 5-toothed ancestor. Our results provide an initial evolutionary framework
 for extended investigations of potential co-evolutionary interactions
 between these ants and their mealybug partners.
description: Data matrix:
 Acropyga_UCE-944-matrixRAxML_Acropyga_UCE-944.nexRAxML Besttree generated from Acropyga_UCE-944-matrixRAxML_Besttree_Acropyga_UCE-944.treData matrix: Acropyga_UCE-100-best-matrix used for BEAST analysesBEAST_Acropyga_UCE-100.nexBEAST chronogram generated from Acropyga_UCE-100-matrix.BEAST_Acropyga_UCE-100.treBEAST xml file used for analysis of Acropyga_UCE-100-matrixBEAST_Acropyga_UCE-100.xml
DOI: 10.5061/dryad.qf2t8
title: Data from: Allele-specific transcriptome and methylome analysis reveals stable inheritance and cis-regulation of DNA methylation in Nasonia

description: Gene expression divergence between closely related species could be
 attributed to both cis- and trans- DNA sequence changes during evolution,
 but it is unclear how the evolutionary dynamics of epigenetic marks are
 regulated. In eutherian mammals, biparental DNA methylation marks are
 erased and reset during gametogenesis, resulting in paternal or maternal
 imprints which lead to genomic imprinting. Whether DNA methylation
 reprogramming exists in insects is not known. Wasps of the genus Nasonia
 are non-social parasitoids that are emerging as a model for studies of
 epigenetic processes in insects. In this study, we quantified
 allele-specific expression and methylation genome-wide in Nasonia
 vitripennis and Nasonia giraulti and their reciprocal F1 hybrids. No
 parent-of-origin effect in allelic expression was found for &gt;8,000
 covered genes, suggesting a lack of genomic imprinting in adult Nasonia.
 As we expected, both significant cis- and trans- effects are responsible
 for the expression divergence between N. vitripennis and N. giraulti.
 Surprisingly, all 178 differentially methylated genes are also
 differentially methylated between the two alleles in F1 hybrid offspring,
 recapitulating the parental methylation status with nearly 100% fidelity,
 indicating the presence of strong cis-elements driving the target of gene
 body methylation. In addition, we discovered that total and
 allele-specific expression is positively correlated with allele-specific
 methylation in a subset of the differentially methylated genes. The 100%
 cis-regulation in F1 hybrids suggests the methylation machinery is
 conserved and DNA methylation is targeted by cis features in Nasonia. The
 lack of genomic imprinting and parent-of-origin differentially methylated
 regions in Nasonia, together with the stable inheritance of methylation
 status between generations suggest either a cis regulatory motif for
 methylation at the DNA level or highly stable inheritance of an epigenetic
 signal in Nasonia.
description: Data for Main Figures
 and Supporting FiguresThis file contains
 datasheets for Fig 1, Fig 2, Fig 3, Fig 4, Fig 5, S2 Fig, S3 Fig, S4 Fig,
 S5 Fig and S6 Fig.NasoniaSSDataFinalPLOSBio.xlsx
DOI: 10.15468/dl.bzhavw
title: Occurrence Download

description: A dataset containing 21979397 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Southern African Bird Atlas Project 2"
 ]
}

 The dataset includes 21979397 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001437-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bq68f
title: Data from: Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States

description: The integration of ecological niche modelling into phylogeographic
 analyses has allowed for the identification and testing of potential
 refugia under a hypothesis-based framework, where the expected patterns of
 higher genetic diversity in refugial populations and evidence of range
 expansion of nonrefugial populations are corroborated with empirical data.
 In this study, we focus on a montane-restricted cryophilic harvestman,
 Sclerobunus robustus, distributed throughout the heterogeneous Southern
 Rocky Mountains and Intermontane Plateau of southwestern North America. We
 identified hypothetical refugia using ecological niche models (ENMs)
 across three time periods, corroborated these refugia with population
 genetic methods using double-digest RAD-seq data and conducted
 population-level phylogenetic and divergence dating analyses. ENMs
 identify two large temporally persistent regions in the mid-latitude
 highlands. Genetic patterns support these two hypothesized refugia with
 higher genetic diversity within refugial populations and evidence for
 range expansion in populations found outside hypothesized refugia.
 Phylogenetic analyses identify five to six genetically divergent,
 geographically cohesive clades of S. robustus. Divergence dating analyses
 suggest that these separate refugia date to the Pliocene and that
 divergence between clades pre-dates the late Pleistocene glacial cycles,
 while diversification within clades was likely driven by these cycles.
 Population genetic analyses reveal effects of both isolation by distance
 (IBD) and isolation by environment (IBE), with IBD more important in the
 continuous mountainous portion of the distribution, while IBE was stronger
 in the populations inhabiting the isolated sky islands of the south. Using
 model-based coalescent approaches, we find support for postdivergence
 migration between clades from separate refugia.
description: Environmental distance
 matrixThe environmental
 distance matrix used in assessing isolation by
 environment.EnvironmentalDistance.csvm16_ConcatenatedLociConcatenated matrix of loci from the m16 pyRAD analysism16_PCA_StructureStructure from the m16 pyRAD analysis file used for PCA.m16_SNPsSNPs file from the m16 pyRAD analysism32_ConcatenatedLociConcatenated matrix of loci from the m32 pyRAD analysism32_PCA_StructureStructure from the m32 pyRAD analysis file used for PCA.m32_SNPsSNPs file from the m32 pyRAD analysis
DOI: 10.5061/dryad.12
title: Data from: Surprising complexity of the ancestral apoptosis network

description: Apoptosis, one of the main types of programmed cell death, is regulated
 and performed by a complex protein network. Studies in model organisms,
 mostly in the nematode C. elegans, identified a relatively simple
 apoptotic network consisting of only a few proteins. However, analysis of
 several recently sequenced invertebrate genomes, ranging from the
 cnidarian sea anemone Nematostella vectensis, representing one of the
 morphologically simplest metazoans, to the deuterostomes sea urchin and
 amphioxus, contradicts the current paradigm of a simple ancestral network
 that expanded in vertebrates. Results Here we show that the
 apoptosome-forming CED-4/Apaf-1 protein, present in single copy in
 vertebrate, nematode, and insect genomes, had multiple paralogs in the
 cnidarian-bilaterian ancestor. Different members of this ancestral Apaf-1
 family lead to the extant proteins in nematodes/insects and in
 deuterostomes, explaining significant functional differences between
 proteins that until now were believed to be orthologous. Similarly, the
 evolution of the Bcl-2 and caspase protein families appears surprisingly
 complex and apparently included significant gene loss in nematodes and
 insects and expansions in deuterostomes. Conclusion The emerging picture
 of the evolution of the apoptosis network is one of a succession of
 lineage-specific expansions and losses, which combined with the limited
 number of "apoptotic" protein families, resulted in apparent
 similarities between networks in different organisms that mask an
 underlying complex evolutionary history. Similar results are beginning to
 surface for other regulatory networks, contradicting the intuitive notion
 that regulatory networks evolved in a linear way, from simple to complex.
description: Apoptosis
 DataZip file containing 107
 filesapoptosis_data.zipSequences and AlignmentsZip file containing 11 filessequences_and_alignments.zipAdditional Table 2Protein sequences for Figure 2 (phylogeny and domain organization of CED-4/Apaf-1 homologs)godzik_additional_table_2.docAdditional Table 3Protein sequences for Figure 3 (phylogeny of the multi-motif Bcl-2 family)godzik_additional_table_3.docAdditional Table 4Protein sequences for Additional Figure 4 (phylogeny of the caspase family)godzik_additional_table_4.docAdditional Figure 4phylogeny of the caspase familygodzik_additional_figure_4.eps
DOI: 10.5061/dryad.k9b6f
title: Data from: High throughput method for analysis of repeat number for 28 phase variable loci of Campylobacter jejuni strain NCTC11168

description: Mutations in simple sequence repeat tracts are a major mechanism of phase
 variation in several bacterial species including Campylobacter jejuni.
 Changes in repeat number of tracts located within the reading frame can
 produce a high frequency of reversible switches in gene expression between
 ON and OFF states. The genome of C. jejuni strain NCTC11168 contains 29
 loci with polyG/polyC tracts of seven or more repeats. This protocol
 outlines a method—the 28-locus-CJ11168 PV-analysis assay—for rapidly
 determining ON/OFF states of 28 of these phase-variable loci in a large
 number of individual colonies from C. jejuni strain NCTC11168. The method
 combines a series of multiplex PCR assays with a fragment analysis assay
 and automated extraction of fragment length, repeat number and expression
 state. This high throughput, multiplex assay has utility for detecting
 shifts in phase variation states within and between populations over time
 and for exploring the effects of phase variation on adaptation to
 differing selective pressures. Application of this method to analysis of
 the 28 polyG/polyC tracts in 90 C. jejuni colonies detected a 2.5-fold
 increase in slippage products as tracts lengthened from G8 to G11 but no
 difference between tracts of similar length indicating that flanking
 sequence does not influence slippage rates. Comparison of this observed
 slippage to previously measured mutation rates for G8 and G11 tracts in C.
 jejuni indicates that PCR amplification of a DNA sample will over-estimate
 phase variation frequencies by 20-35-fold. An important output of the
 28-locus-CJ11168 PV-analysis assay is combinatorial expression states that
 cannot be determined by other methods. This method can be adapted to
 analysis of phase variation in other C. jejuni strains and in a diverse
 range of bacterial species.
description: LangoScholey_Archive
 _MapPicture showing a map of
 the files in this archiveLangoScholey_Archive_Map.pngPSAnalyse_0_99This folder contains all the files required for running of the program PSAnalyseLangoScoley_Control_Sequence_FilesThis folder contains the control sequences for the specific variants used for the analysesLangoScholey_Test_Sequence_FilesThis folder contains the test sequences used to validate the assayReadMeThis file is a description of the contents of the archiveLangoScholey_28_Locus_CJ_11168_PV_Assay_20160222.txt