cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1s15q
title: Data from: Wing shape variation associated with mimicry in butterflies

description: Mimetic resemblance in unpalatable butterflies has been studied by
 evolutionary biologists for over a century, but has largely focused on the
 convergence in wing color patterns. In Heliconius numata, discrete
 color-pattern morphs closely resemble co-mimics in the distantly-related
 genus Melinaea. We examine the possibility that the shape of the butterfly
 wing also shows adaptive convergence. First, simple measures of forewing
 dimensions were taken of individuals in a cross between H. numata morphs,
 and showed quantitative differences between two of the segregating morphs,
 F. elegans and F. silvana. Second, landmark-based geometric morphometric
 and elliptical Fourier outline analyses were used to more fully
 characterize these shape differences. Extension of these techniques to
 specimens from natural populations suggested that, while many of the
 coexisting morphs could not be discriminated by shape, the differences we
 identified between F. elegans and F. silvana hold in the wild.
 Interestingly, despite extensive overlap, the shape variation between
 these two morphs is paralleled in their respective Melinaea co-mimics. Our
 study therefore suggests that wing-shape variation is associated with
 mimetic resemblance, and raises the intriguing possibility that the
 supergene responsible for controlling the major switch in color pattern
 between morphs also contributes to wing shape differences in H. numata.
description: WING paper Data for
 repositoryWing measurements taken
 for the preparation of the Evolution manuscript. This Excel file contains
 10 sheets. A brief discription may be found in rows below the data in each
 sheet.
DOI: 10.5061/dryad.7163d
title: Data from: Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

description: Little is known about the genetic basis differentiating resident and
 anadromous forms found in many salmonid species. Using a medium-density
 SNP array, we documented genomic diversity and divergence at 2336
 genetically mapped loci among three pairs of North American anadromous and
 freshwater Atlantic salmon populations. Our results show that across the
 genome, freshwater populations have lower diversity and a smaller
 proportion of private polymorphism relative to anadromous populations.
 Moreover, differentiation was more pronounced among freshwater than among
 anadromous populations at multiple spatial scales, suggesting a large
 effect of genetic drift in these isolated freshwater populations. Using
 nonhierarchical and hierarchical genome scans, we identified hundreds of
 markers spread across the genome that are potentially under divergent
 selection between anadromous and freshwater populations, but few outlier
 loci were repeatedly found in all three freshwater–anadromous comparisons.
 Similarly, a sliding window analysis revealed numerous regions of high
 divergence that were nonparallel among the three comparisons. These last
 results show little evidence for the parallel evolution of alleles
 selected for in freshwater populations, but suggest nonparallel adaptive
 divergence at many loci of small effects distributed through the genome.
 Overall, this study emphasizes the important role of genetic drift in
 driving genome-wide reduction in diversity and divergence in freshwater
 Atlantic salmon populations and suggests a complex multigenic basis of
 adaptation to resident and anadromous strategies with little parallelism.
description: 203individuals_2716SNPsContains the genotypes of the 203 Atlantic salmon individuals from Québec, Canada, analysed in this study at 2716 SNPs.
DOI: 10.5061/dryad.qn57t
title: Data from: Ancient host shifts followed by host conservatism in a group of ant parasitoids

description: While ant colonies serve as host to a diverse array of myrmecophiles, few
 parasitoids are able to exploit this vast resource. A notable exception is
 the wasp family Eucharitidae, which is the only family of insects known to
 exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae
 species attack five subfamilies across the ant phylogeny. Our goal is to
 uncover the pattern of eucharitid diversification, including timing of key
 evolutionary events, biogeographic patterns and potential cophylogeny with
 ant hosts. We present the most comprehensive molecular phylogeny of
 Eucharitidae to date, including 44 of the 53 genera and fossil-calibrated
 estimates of divergence dates. Eucharitidae arose approximately 50 Ma
 after their hosts, during the time when the major ant lineages were
 already established and diversifying. We incorporate host association data
 to test for congruence between eucharitid and ant phylogenies and find
 that their evolutionary histories are more similar than expected at
 random. After a series of initial host shifts, clades within Eucharitidae
 maintained their host affinity. Even after multiple dispersal events to
 the New World and extensive speciation within biogeographic regions,
 eucharitids remain parasitic on the same ant subfamilies as their Old
 World relatives, suggesting host conservatism despite access to a diverse
 novel ant fauna.
description: Murray_et_al_2013_alignment_and_best_tree.nexNexus format sequence alignment of 237 taxa and 5 gene regions followed by the maximum clade credibility dated phylogeny.Murray_et_al_2013_ASRcoding_48taxa.txtSubset of entire dataset containing a list of 48 eucharitid taxa with their corresponding subfamily associations. This coding scheme was used for Bayesian and parsimony ancestral state reconstruction.Murray_et_al_2013_ASR_48taxa.txtMurray_et_al_2013_Supplementary.pdfThis is the supplementary information published along with the manuscript. Contains table of taxon localities of all OTUs used in matrix, dated phylogeny, ant host records, and other data.
DOI: 10.5061/dryad.8h7k1
title: Data from: Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study

description: Characterizing the trophic relationships between large herbivores and the
 outstanding plant diversity in rainforest is a major challenge because of
 their elusiveness. This is crucial to understand the role of these
 herbivores in the functioning of the rainforest ecosystems. We tested a
 non-invasive approach based on the high-throughput sequencing of
 environmental samples using small plant plastid sequences (the trnL P6
 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to
 investigate the diet of the largest neotropical herbivore, the lowland
 tapir. Sequencing was performed on plant DNA extracted from tapir faeces
 collected at the Nouragues station, a protected area of French Guiana. In
 spite of a limited sampling, our approach reliably provided information
 about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4%
 of the plant families and genera identified thanks to the trnL P6 loop,
 respectively, matched with taxa already known to be consumed by tapirs.
 With this approach we were able to show that two families and eight new
 genera are also consumed by the lowland tapir. The taxonomic resolution of
 this method is limited to the plant family and genera. Complementary
 barcodes, such as a small portion of ITS1, can be used to efficiently
 narrow identifications down to the species in some problematic families.
 We will discuss the remaining limitations of this approach and how useful
 it is at this stage to unravel the diet of elusive rainforest herbivores
 and better understand their role as engineers of the ecosystem.
description: tapir_gh_uniqThis file presents the number of occurrences of each sequence (the trnL P6 loop) in the different faecal samples from tapirs.The sequences have been generated by the Illumina technology (Illumina/Solexa Genome Analyzer IIx).The sequences are sorted starting with the most repeated ones among all the samples. Data collection: Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier , Cécile Richard-Hansen Contact author: Fabrice Hibert (fabricenz@gmail.com)tapir_itsSap_uniqThis fasta file presents the number of occurrences of each sequence (the first internal transcribed spacer (ITS1) of nuclear ribosomal DNA, for the Sapotaceae ) in the different faecal samples from tapirs.The sequences have been generated by the Illumina technology (Illumina/Solexa Genome Analyzer IIx).The sequences are sorted starting with the most repeated ones among all the samples. Data collection: Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier , Cécile Richard-Hansen Contact author: Fabrice Hibert (fabricenz@gmail.com)tapir_gh_filteredtapir_itsSap_filtered
DOI: 10.5061/dryad.65v85
title: Data from: Population-specific recombination sites within the human MHC region

description: Genetic rearrangement by recombination is one of the major driving forces
 for genome evolution and recombination are known to occur in non-random,
 discreet recombination sites within the genome. Mapping of recombination
 sites have proved difficult particularly in the human MHC region that is
 complicated by both population variation and highly polymorphic HLA genes.
 To overcome these problems, HLA typed individuals from three
 representative populations: Asian, European and African were used to
 generate phased HLA haplotypes. Extended haplotype homozygosity (EHH)
 plots constructed from the phased haplotype data revealed discreet EHH
 drops corresponding to recombination events and these signatures were
 observed to be different for each population. Surprisingly, the majority
 of recombination sites detected are unique to each population rather than
 being common. Unique recombination sites account for 56.8% (21/37 of total
 sites) in the Asian cohort, 50.0% (15/30 sites) in Europeans and 63.2%
 (24/38 sites) in Africans. Validation carried out at a known sperm typing
 recombination site of 45kb (HLA-F Telomeric) showed that EHH was an
 efficient method to narrow the recombination region to 826bp and this was
 further refined to 660bp by re-sequencing. This approach significantly
 enhanced mapping of the genomic architecture within the human MHC will be
 useful in studies to identify disease risk genes.
description: Genotype Data withn MHC
 in CHSG Population (PED file)mhc_genotype_CHSG.pedGenotype Data withn MHC in CHSG Population (MAP file)mhc_genotype_CHSG.map
DOI: 10.5061/dryad.rd240
title: Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape

description: Elucidating the spatial dynamic and core constituents of the microbial
 communities found in association with arthropod hosts is of crucial
 importance for insects that may vector human or agricultural pathogens.
 The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the
 human bed bug, has made a recent resurgence in North America, as well as
 worldwide, potentially owing to increased travel, climate change and
 resistance to insecticides. A comprehensive survey of the bed bug
 microbiome has not been performed to date, nor has an assessment of the
 spatial dynamics of its microbiome. Here we present a survey of internal
 and external bed bug microbial communities by amplifying the V4–V6
 hypervariable region of the 16S rDNA gene region followed by 454 Titanium
 sequencing using 31 individuals from eight distinct collection locations
 obtained from residences in Cincinnati, OH. Across all samples, 97% of the
 microbial community is made up of two dominant OTUs, previously identified
 as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from
 the Enterobacteriaceae. Microbial communities varied among host locations
 for measures of community diversity and exhibited structure according to
 collection location. This broad survey represents the most in-depth
 assessment, to date, of the microbes that associate with bed bugs.
description: 16SCimexlectualrius
DOI: 10.5061/dryad.f1t15
title: Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

description: Over half of all vertebrates are “fishes”, which exhibit enormous
 diversity in morphology, physiology, behavior, reproductive biology, and
 ecology. Investigation of fundamental areas of vertebrate biology depend
 critically on a robust phylogeny of fishes, yet evolutionary relationships
 among the major actinopterygian and sarcopterygian lineages have not been
 conclusively resolved. Although a consensus phylogeny of teleosts has been
 emerging recently, it has been based on analyses of various subsets of
 actinopterygian taxa, but not on a full sample of all bony fishes. Here we
 conducted a comprehensive phylogenetic study on an unprecedented
 combination of broad taxonomic sampling of actinopterygian and
 sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular
 data set of 21 independent loci. These data yielded a resolved
 phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally
 monophyletic Sarcopterygii and Actinopterygii, as currently understood,
 with polypteriforms as the first diverging lineage within Actinopterygii;
 2) a monophyletic group containing gars and bowfin (= Holostei) as sister
 group to Teleostei; and 3) the earliest diverging lineage among teleosts
 being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating
 analysis employing a set of 24 newly applied fossil calibrations reveals
 divergence times that are more consistent with paleontological estimates
 than previous studies. Establishing a new phylogenetic pattern with
 accurate divergence dates for bony fishes illustrates several areas where
 the fossil record is incomplete and provides critical new insights on
 diversification of this important vertebrate group.
description: sequence
 alignmentbuildv7_submit.nex
DOI: 10.15468/2tpwj4
title: Rediscovery of the genus Atyopsis Chace, 1983 (Decapoda: Atyidae) in mainland India following a 72 - year gap

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kunjulakshmi, Kozhikkaparambil, Santos, Maclean Antony, Prakash, Sanjeevi (2025): Rediscovery of the genus Atyopsis Chace, 1983 (Decapoda: Atyidae) in mainland India following a 72 - year gap. Zootaxa 5722 (4): 570-582, DOI: 10.11646/zootaxa.5722.4.7, URL: https://doi.org/10.11646/zootaxa.5722.4.7AbstractThis study resolves a longstanding uncertainty surrounding the presence of the genus Atyopsis from mainland India, based on recent collections from the Mulki (Karnataka) and Bhubaneswar (Odisha) regions of western and eastern India. Originally reported 72 years ago as Atya moluccensis by Tiwari (1951), the report lacks morphological validation. This combined with absence in subsequent records has led to scepticism regarding the genuine occurrence of the genus in India’s mainland freshwater ecosystems. In the present study, we report on the rediscovery of Atyopsis, and identified the species as Atyopsis spinipes, thereby reaffirming and validating the presence of the genus after seven decades. Atyopsis spinipes can be easily distinguished from its congener A. moluccensis, based on the shape and armature of the rostrum and the proportions of the endopod of first pleopod in males. This finding underscores the need for continued systematic surveys to shed light on the understudied shrimp fauna of India’s freshwater ecosystems.
DOI: 10.5061/dryad.475
title: Data from: Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate

description: As a first step toward population and quantitative genetic analysis of
 neurotransmitter receptors in Drosophila melanogaster, we describe the
 parameters of nucleotide variation in three serotonin receptors and their
 association with pupal heart rate. Thirteen kilobases of DNA including the
 complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216
 highly inbred lines extracted from two North American populations in
 California and North Carolina. Nucleotide and amino acid polymorphism is
 in the normal range for Drosophila genes and proteins, and linkage
 disequilibrium decays rapidly such that haplotype blocks are typically
 only a few SNPs long. However, intron 1 of 5-HT1A consists of two
 haplotypes that are at significantly different frequencies in the two
 populations. Neither this region of the gene nor any of the common amino
 acid polymorphisms in the three loci associate with either heart rate or
 heart rate variability. A cluster of SNPs in intron 2 of 5-HT1A, including
 a triallelic site, do show a highly significant interaction between
 genotype, sex, and population. While it is likely that a combination of
 weak, complex selection pressures and population structure has helped
 shape variation in the serotonin receptors of Drosophila, much larger
 sampling strategies than are currently adopted in evolutionary genetics
 will be required to disentangle these effects.
description: Supplementary Table
 4Sequences of 5-HT1A and
 5-HT1B alleles5HT1A_B.txtSupplementary Table 5Sequences of 5-HT2 alleles5HT2.txtSupplementary Figure 1Plots of Association for each term in the full Mixed ModelNDG_SF1.pdfSupplementary Table 1List of Primers used in PCR amplification and SequencingNDG_ST1.pdfSupplementary Table 2Parameters of Nucleotide Variation by Exon and IntronNDG_ST2.pdfSupplementary Table 3Association statistics for each trait by siteNDG_ST3.xlsSupplementary Table 6Polymorphisms and LinesRawData.xls
DOI: 10.5061/dryad.7c7q0
title: Data from: Complete genome sequences provide a case study for the evaluation of gene-tree thinking

description: Complete genome sequences from a genus of Gammaproteobacteria, Shewanella,
 are used to generate a genome-wide exploration of the gene-tree
 species-tree dichotomy. A number of datasets were constructed and analyses
 were attempted. Single genes were chosen from 243 regions of collinear
 gene homology (128 of these 243 chosen genes are from the core Shewanella
 genome and 162 of 243 have the complete taxon sampling) from a previous
 study (Dikow, 2011) and subjected to phylogenetic analysis both
 individually and concatenated. In addition, three of the 243 sets of
 collinear genes from the core Shewanella genome were also chosen
 (comprising 15, 17, and 23 genes each) to be analysed in detail, this time
 to maximize the expectation of gene concordance. Analysis of these 55
 genes in maximum parsimony (MP) and maximum likelihood (ML) produced 164
 unique topologies (out of 166 resulting topologies). No genes from within
 collinear regions were congruent with one another, and none of these 164
 topologies matches the result from concatenation. This result is
 particularly striking given that we chose collinear sets of genes.
 Analyses in MP and ML of 243 genes distributed across the genome produced
 567 unique topologies (out of 571 resulting topologies for those 162 genes
 with complete taxon sampling). These results are discussed in light of
 recent works focused on incongruence. The gene as a phylogenetic unit is
 also discussed. It is our conclusion that molecular systematics has been
 reliant on the gene as a unit without a critical eye on the distinction
 between gene homology and character homology.
description: Dikow&Smith_treesPhylogenetic trees presented in the paperone gene per lcbfasta files for the "one gene per LCB" datasetlcb 27fasta files for genes in LCB27lcb 156fasta files for genes in LCB 156lcb 175fasta files for genes in LCB 175
DOI: 10.5061/dryad.42gc4
title: Data from: The complete sequence of the mitochondrial genome of Butomus umbellatus - a member of an early branching lineage of monocotyledons

description: In order to study the evolution of mitochondrial genomes in the early
 branching lineages of the monocotyledons, i.e., the Acorales and
 Alismatales, we are sequencing complete genomes from a suite of key taxa.
 As a starting point the present paper describes the mitochondrial genome
 of Butomus umbellatus (Butomaceae) based on next-generation sequencing
 data. The genome was assembled into a circular molecule, 450,826 bp in
 length. Coding sequences cover only 8.2% of the genome and include 28
 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA
 genes and a 16S rRNA gene are transferred from the plastid genome.
 However, the total amount of recognized plastid sequences in the
 mitochondrial genome is only 1.5% and the amount of DNA transferred from
 the nucleus is also low. RNA editing is abundant and a total of 557 edited
 sites are predicted in the protein coding genes. Compared to the 40
 angiosperm mitochondrial genomes sequenced to date, the GC content of the
 Butomus genome is uniquely high (49.1%). The overall similarity between
 the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest
 relative yet sequenced, is low (less than 20%), and the two genomes differ
 in size by a factor 2. Gene order is also largely unconserved. However,
 based on its phylogenetic position within the core alismatids Butomus will
 serve as a good reference point for subsequent studies in the early
 branching lineages of the monocotyledons.
description: Butomus umbellatus
 mitochodrial reads454 FLX standard reads
 in fasta format from a mitochondrial fraction obtained from one individual
 of Butomus umbellatus (collected in the field).MID08
DOI: 10.5061/dryad.q1d7f
title: Data from: Prevention of ventilator-associated pneumonia in intensive care units: an international online survey

description: Background: On average 7% of patients admitted to intensive-care units
 (ICUs) suffer from a potentially preventable ventilator-associated
 pneumonia (VAP). Our objective was to survey attitudes and practices of
 ICUs doctors in the field of VAP prevention. Methods: A questionnaire was
 made available online in 6 languages from April, 1st to September 1st,
 2012 and disseminated through international and national ICU societies. We
 investigated reported practices as regards (1) established clinical
 guidelines for VAP prevention, and (2) measurement of process and
 outcomes, under the assumption “if you cannot measure it, you cannot
 improve it”; as well as attitudes towards the implementation of a
 measurement system. Weighted estimations for Europe were computed based on
 countries for which at least 10 completed replies were available, using
 total country population as a weight. Data from other countries were
 pooled together. Detailed country-specific results are presented as an
 online supplement. Results: A total of 1730 replies were received from 77
 countries; 1281 from 16 countries were used to compute weighted European
 estimates, as follows: care for intubated patients, combined with a
 measure of compliance to this guideline at least once a year, was reported
 by 57% of the respondents (95% CI: 54-60) for hand hygiene, 28% (95% CI:
 24-33) for systematic daily interruption of sedation and weaning protocol,
 and 27% (95%: 23-30) for oral care with chlorhexidine. Only 20% (95% CI:
 17-22) were able to provide an estimation of outcome data (VAP rate) in
 their ICU, still 93% (95% CI: 91-94) agreed that “Monitoring of
 VAP-related measures stimulates quality improvement”. Results for 449
 respondents from 61 countries not included in the European estimates are
 broadly comparable. Conclusions: This study shows a low compliance with
 VAP prevention practices, as reported by ICU doctors in Europe and
 elsewhere, and identifies priorities for improvement
description: icu_survey_repository_s9Each record is a reply to the online survey.
DOI: 10.6084/m9.figshare.31158364
title: CSA for ratios of intervertebral equine cervical spine.

description: CSA at the intervertebral level of the equine caudal cervical spine is measures by three observers in normal and affected horses.