cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j5g7m
title: Data from: Fruit flies medicate offspring after seeing parasites

description: Hosts have numerous defenses against parasites, of which behavioral immune
 responses are an important but under-appreciated component. Here we
 describe a behavioral immune response Drosophila melanogaster utilizes
 against endoparasitoid wasps. We found that when flies see wasps they
 switch to laying eggs in alcohol-laden food sources that protect hatched
 larvae from infection. This oviposition behavior change, mediated by
 neuropeptide F, is retained long after wasps are removed. Flies respond to
 diverse female larval endoparasitoids but not to pupal endoparasitoids or
 males, showing they maintain specific wasp search images. Furthermore, the
 response evolved multiple times across the genus Drosophila. Our data
 reveal a behavioral immune response based on anticipatory medication of
 offspring, and outline a non-associative memory paradigm based on innate
 parasite recognition by the host.
description: Schlenke_EgglayPaperRawdataThis Excel file contains all the raw data associated with the paper (except for brain scan images), assembled in sheets by figure.Schlenke_Rawdata.xlsxNPF_brainstainsThis zip file contains the z-stack confocal microscopy image data from Drosophila melanogaster brains stained with anti-NPF antibody.NPF_stains.zip
DOI: 10.5061/dryad.2c20k
title: Data from: Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source

description: The introduction of invasive species to new locations (that is, biological
 invasions) can have major impact on biodiversity, agriculture and public
 health. As such, determining the routes and modality of introductions with
 genetic data has become a fundamental goal in molecular ecology. To assist
 with this goal, new statistical methods and frameworks have been
 developed, such as approximate Bayesian computation (ABC) for inferring
 invasion history. Here, we present a model of invasion accounting for
 multiple introductions from a single source (MISS), a heretofore largely
 unexplored model. We simulate microsatellite data to evaluate the power of
 ABC to distinguish between single and multiple introductions from the same
 source, under a range of demographic parameters. We also apply ABC to
 microsatellite data from three invasions of bumblebee in New Zealand. In
 addition, we assess the performance of several methods of summary
 statistics selection. Our simulated results suggested good ability to
 distinguish between one- and two-wave models over much but not all of the
 parameter space tested, independent of summary statistics used. Globally,
 parameter estimation was good except for bottleneck timing. For one of the
 bumblebee species, we clearly rejected the MISS model, while for the other
 two we found inconclusive results. Since a second wave may provide genetic
 reinforcement to initial colonists, help relieve inbreeding among
 founders, or increase the hazard of the invasion, its detection may be
 crucial for managing invasions; we suggest that the MISS model could be
 considered as a potential model in future theoretical and empirical
 studies of invasions.
description: ABC_parameters_ref_tableThe attached tar zip contains our ABC reference tables, the parameter files for creating simulations, a power analysis script, and summary statistics calculated on the observed Bombus samples. See the Readme file for details.dryad_Benazzo_et_al.tar
DOI: 10.5061/dryad.84jr7
title: Data from: Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing

description: Next generation sequencing (NGS) methodologies have proven useful in
 deciphering the food items of generalist predators, but have yet to be
 applied to gelatinous animal gut and tentacle content. NGS can potentially
 supplement traditional methods of visual identification. Chrysaora
 quinquecirrha (Atlantic sea nettle) has progressively become more abundant
 in Mid-Atlantic United States’ estuaries including Barnegat Bay (New
 Jersey), potentially having detrimental effects on both marine organisms
 and human enterprises. Full characterization of this predator's diet
 is essential for a comprehensive understanding of its impact on the food
 web and its management. Here we tested the efficacy of NGS for prey item
 determination in the Atlantic sea nettle. We implemented a NGS “shotgun”
 approach to randomly sequence DNA fragments isolated from gut lavages and
 gastric pouch/tentacle picks of 8 and 84 sea nettles, respectively. These
 results were verified by visual identification and co-occurring plankton
 tows. Over 550,000 contigs were assembled from ~110 million paired-end
 reads. Of these, 100 contigs were confidently assigned to 23 different
 taxa, including soft bodied organisms previously undocumented as prey
 species, including copepods, fish, ctenophores, anemones, amphipods,
 barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms,
 gastropods, bivalves, and hemichordates. Our results not only indicate
 that a “shotgun” NGS approach can supplement visual identification
 methods, but targeted enrichment of a specific amplicon/gene is not a
 prerequisite for identifying Atlantic sea nettle prey items.
description: Table S1 Gastric Lavage
 Build SummaryGastric Lavage Build
 SummaryTable S2 Gastric
 Pouch/Tentacle Pick Build SummaryGastric Pouch/Tentacle
 Pick Build SummaryTable S2 Gastric Pouch.Tentacle
 Pick Build Summary.xlsxTable S3 Combined
 Gastric Lavage Build + Gastric Pouch/Tentacle Pick
 SummaryCombined Gastric Lavage
 Build + Gastric Pouch/Tentacle Pick SummaryTable S3 Combined Gastric
 Lavage Build + Gastric Pouch.Tentacle Pick
 Summary.xlsxTable S4 MEGAN
 assignmentsMEGAN
 assignmentsCombined Gastric Lavage
 Build + Gastric Pouch.Tentacle Pick Contig Blast
 Hits.xmlCombined Gastric Lavage
 Build + Gastric Pouch.Tentacle Pick Contig Blast Hits: xml
 fileCombined Gastric Lavage
 Build + Gastric Pouch/Tentacle Pick Contigs.faCombined Gastric Lavage
 Build + Gastric Pouch/Tentacle Pick Contigs: fasta fileCombined Gastric Lavage Build +
 Gastric Pouch.Tentacle Pick
 Contigs.fa.zipGastric Lavage
 Contigs.faGastric Lavage Contig:
 fasta fileGastric Pouch/Tentacle
 Pick Contigs.faGastric Pouch/Tentacle
 Pick Contigs: fasta fileGastric Pouch.Tentacle Pick
 Contigs.fa.zip
DOI: 10.5061/dryad.m86k3
title: Data from: Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni

description: Campylobacter is among the most common worldwide causes of bacterial
 gastroenteritis. This organism is part of the commensal microbiota of
 numerous host species, including livestock, and these animals constitute
 potential sources of human infection. Molecular typing approaches,
 especially multi-locus sequence typing (MLST), have been used to attribute
 the source of human campylobacteriosis by quantifying the relative
 abundance of alleles, at 7 MLST loci, among isolates from animal
 reservoirs and human infection, implicating chicken as a major infection
 source. The increasing availability of bacterial genomes provides data on
 allelic variation at loci across the genome, providing the potential to
 improve the discriminatory power of data for source attribution. Here we
 present a source attribution approach based on the identification of novel
 epidemiological markers among a reference pan-genome list of 1810 genes
 identified through gene-by-gene comparison of 884 genomes of C. jejuni
 isolates from animal reservoirs, the environment and clinical cases.
 Fifteen loci, involved in metabolic activities, protein modification,
 signal transduction and stress response, or coding for hypothetical
 proteins, were selected as host-segregating markers and used to attribute
 the source of 42 French and 281 UK clinical C. jejuni isolates. Consistent
 with previous studies of British campylobacteriosis, analyses performed
 using STRUCTURE software, attributed 56.8% of British clinical cases to
 chicken, emphasizing the importance of this host reservoir as an infection
 source in the UK. However, among French clinical isolates, approximately
 equal proportions of isolates were attributed to chicken and ruminant
 reservoirs suggesting possible differences in the relative importance of
 animal host reservoirs and indicating a benefit for further national-scale
 attribution modelling to account for differences in production, behaviour
 and food consumption.
description: contigsWhole genome sequencing reads for the 212 French Campylobacter jejuni isolates referred to in the associated publication.
DOI: 10.5061/dryad.1q9g7
title: Data from: A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

description: Understanding the mechanisms responsible for phenotypic diversification
 within and among species ultimately rests with linking naturally occurring
 mutations to functionally and ecologically significant traits. Colour
 polymorphisms are of great interest in this context because discrete
 colour patterns within a population are often controlled by just a few
 genes in a common environment. We investigated how and why phenotypic
 diversity arose and persists in the Zosterops borbonicus white-eye of
 Reunion (Mascarene archipelago), a colour polymorphic songbird in which
 all highland populations contain individuals belonging to either a brown
 or a grey plumage morph. Using extensive phenotypic and genomic data, we
 demonstrate that this melanin-based colour polymorphism is controlled by a
 single locus on chromosome 1 with two large-effect alleles, which was not
 previously described as affecting hair or feather colour. Differences
 between colour morphs appear to rely upon complex cis-regulatory variation
 that either prevents the synthesis of pheomelanin in grey feathers, or
 increases its production in brown ones. We used coalescent analyses to
 show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele
 spread quickly once it arose from a new mutation. Since colour morphs are
 always found in mixture, this implies that the selected allele does not go
 to fixation, but instead reaches an intermediate frequency, as would be
 expected under balancing selection.
description: Data for
 microsatellites, spectrophotometry and melanins dosageThis file contains 1)
 microsatellites data in GENPOP format, 2) morphometric data for birds
 included in the pedigree analysis, 3) Spectrophotometry measurements and
 4) Results from the dosage of melanins for 12 individuals. Localities
 coordinates are also provided.All_data_microsats_spectro_melanindosage.xlsxUnfiltered VCF file for 42 individualsSNPs calls for individual GBS data from the same three localities as in Pooled RAD-seq. Colors and localities for each individuals are provided in a separate excel file.Highlands_dataset.recode.vcfInformation about individuals included in the GBS VCF fileMorph and localities for each individual included in the GBS study.Localities_Morphs_individuals_VCF.xlsx
DOI: 10.5061/dryad.5vn76
title: Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling

description: Climate-mediated changes in hybridization will dramatically alter the
 genetic diversity, adaptive capacity and evolutionary trajectory of
 interbreeding species. Our ability to predict the consequences of such
 changes will be key to future conservation and management decisions. Here
 we tested through simulations how recent warming (over a 32-year period)
 is affecting the geographic extent of a climate-mediated developmental
 threshold implicated in maintaining a butterfly hybrid zone (Papilio
 glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These
 simulations predict a 68 km shift of this hybrid zone. To empirically test
 this prediction, we assessed genetic and phenotypic changes using
 contemporary and museum collections and document a 40 km northward shift
 of this hybrid zone. Interactions between the two species appear
 relatively unchanged during hybrid zone movement. We found no change in
 the frequency of hybridization and regions of the genome that experience
 little to no introgression moved largely in concert with the shifting
 hybrid zone. Model predictions based on climate scenarios predict this
 hybrid zone will continue to move northward, but with substantial spatial
 heterogeneity in the velocity (55-144 km/1°C), shape, and contiguity of
 movement. Our findings suggest that the presence of non-climatic barriers
 (e.g., genetic incompatibilities) and/or non-linear responses to climatic
 gradients may preserve species boundaries as the species shift. Further,
 we show that variation in the “geography” of hybrid zone movement could
 result in evolutionary responses that differ for geographically distinct
 populations spanning hybrid zones and thus have implications for the
 conservation and management of genetic diversity.
description: RAD data processing
 filesCline_analysisSTRUCTUREUSA_mapSimulation ModelingMetadata_for_specimensREADME
DOI: 10.5061/dryad.b23d7k8
title: Data from: The early composition and evolution of the turtle shell (Reptilia, Testudinata)

description: The shell of the oldest true turtle (Testudinata) branch
 (Proterochersidae) from the Late Triassic (Norian) of Poland and Germany
 was built in its anterior and posterior part from an osteodermal mosaic
 which developed several million years after the plastron, neurals, and
 costal bones. The most detailed description of the shell composition in
 proterochersids thus far is provided together with a review of the shell
 composition in other Triassic pantestudinates, the scenario of early
 evolution of the turtle shell is proposed based on new data, and the
 possible adaptive meaning of the observed evolutionary changes is
 discussed. These observations are consistent with the trend of shell
 simplification previously reported in turtles. Several aspects of
 proterochersid shell anatomy are intermediate between O. semitestacea and
 more derived turtles, supporting their stem phylogenetic position. Three
 additional ossifications were sutured to xiphiplastra and pelvis in
 Proterochersis spp. and at least in some individuals the nuchal bone was
 paired. The peripherals, suprapygals, and pygal bone are most likely of
 osteodermal origin and homologous to the proterochersid shell mosaic.
description: Movie
 S1SMNS 17755a: CT scan,
 dorsal-ventralMovie
 S2SMNS 17755a: CT scan,
 lateral-medialMovie
 S3SMNS 17755a: CT scan,
 anterior-posteriorMovie
 S4ZPAL V.39/22: CT scan,
 ventral-dorsalMovie
 S5ZPAL V.39/22: CT scan,
 medial-lateralMovie
 S6ZPAL V.39/22: CT scan,
 anterior-posteriorMovie
 S7ZPAL V.39/22: Volumetric
 renderModel
 S1ZPAL V.39/22: 3D
 renderModel
 S2ZPAL V.39/22: 3D model
 (PDF)MatrixUpdated matrix for
 phylogenetic analysesMatrixUpdated matrix for
 phylogenetic analysesSzczygielski & Sulej
 - supplementMaterial descriptions,
 tables, extended discussion, supplementary figures, character list,
 character matrix, phylogenetic trees, lists of synapomorphies, and
 referencesSzczygielski & Sulej
 - supplementMaterial descriptions,
 tables, extended discussion, supplementary figures, character list,
 character matrix, phylogenetic trees, lists of synapomorphies, and
 references
DOI: 10.5061/dryad.jf7cr
title: Data from: Accounting for genetic differences among unknown parents in microevolutionary studies: how to include genetic groups in quantitative genetic animal models

description: Quantifying and predicting microevolutionary responses to environmental
 change requires unbiased estimation of quantitative genetic parameters in
 wild populations. ‘Animal models’, which utilize pedigree data to separate
 genetic and environmental effects on phenotypes, provide powerful means to
 estimate key parameters and have revolutionized quantitative genetic
 analyses of wild populations. However, pedigrees collected in wild
 populations commonly contain many individuals with unknown parents. When
 unknown parents are non-randomly associated with genetic values for focal
 traits, animal model parameter estimates can be severely biased. Yet, such
 bias has not previously been highlighted and statistical methods designed
 to minimize such biases have not been implemented in evolutionary ecology.
 We first illustrate how the occurrence of non-random unknown parents in
 population pedigrees can substantially bias animal model predictions of
 breeding values and estimates of additive genetic variance, and create
 spurious temporal trends in predicted breeding values in the absence of
 local selection. We then introduce ‘genetic group’ methods, which were
 developed in agricultural science, and explain how these methods can
 minimize bias in quantitative genetic parameter estimates stemming from
 genetic heterogeneity among individuals with unknown parents. We summarize
 the conceptual foundations of genetic group animal models and provide
 extensive, step-by-step tutorials that demonstrate how to fit such models
 in a variety of software programs. Furthermore, we provide new functions
 in r that extend current software capabilities and provide a standardized
 approach across software programs to implement genetic group methods.
 Beyond simply alleviating bias, genetic group animal models can directly
 estimate new parameters pertaining to key biological processes. We discuss
 one such example, where genetic group methods potentially allow the
 microevolutionary consequences of local selection to be distinguished from
 effects of immigration and resulting gene flow. We highlight some
 remaining limitations of genetic group models and discuss opportunities
 for further development and application in evolutionary ecology. We
 suggest that genetic group methods should no longer be overlooked by
 evolutionary ecologists, but should become standard components of the
 toolkit for animal model analyses of wild population data sets.
description: Tutorial and files
 associated with the Wolak & Reid 'How To' paper in Journal
 of Animal Ecology.Contains MCMCglmm,
 WOMBAT, and ASReml (standalone) analysis files and model output
 files.WolakAndReid_GenGroupHowTo_tutorials.tar
DOI: 10.5061/dryad.457br
title: Data from: Sequence-based association analysis reveals an MGST1 eQTL with pleiotropic effects on bovine milk composition

description: [No abstract entered]
description: GWAS_pop_dataChromosome 5 Illumina BovineHD genotypes and phenotypes for the milk fat percentage GWAS population.RNAseq_pop_imputed_seq_dataChromsome 5 imputed sequence and gene expression data used for eQTL mappingRNAseq_pop_imputed_seq_data_with_gap_varsChromsome 5 imputed sequence and gene expression data used for eQTL mapping - with reference gap variantsLarge_pop_imputed_seqChromsome 5 imputed sequence and phenotype data used for milk composition association mappingRNAseq_pop_del_haplotypeGene expression (phenotypes), pedigree, and diplotype (haplotype pair) data for analysis of the CNV-proxy haplotypeZipped library of Supplementary files 1-12A zipped collection of all manuscript supplementary files in their native format (ie. not *.pdf)Supplementary_files.zip
DOI: 10.5061/dryad.s7dj0
title: Data from: Evolutionary diversification of reef corals: a comparison of the molecular and fossil records

description: Understanding historical patterns of diversity dynamics is of paramount
 importance for many evolutionary questions. The fossil record has long
 been the only source of information on patterns of diversification, but
 the molecular record, derived from time-calibrated phylogenies, is
 becoming an important additional resource. Both fossil and molecular
 approaches have shortcomings and biases. These have been well studied for
 fossil data but much less so for molecular data and empirical comparisons
 between approaches are lacking. Here we compare the patterns of
 diversification derived from fossil and molecular data in scleractinian
 reef coral species. We also assess the robustness of molecular
 diversification rates to poor taxon sampling. We find that the temporal
 pattern of molecular diversification rates is robust to incomplete
 sampling when rates are calculated per interval. The major obstacle of
 molecular methods is that rate estimates are distorted because
 diversification rates can never be negative, whereas the fossil record
 suffers from incomplete preservation and inconsistent taxonomy.
 Nevertheless, the molecular pattern of diversification is comparable to
 the pattern we observe in the fossil record, with the timing of major
 diversification pulses coinciding in each dataset. For example, both agree
 that the end-Triassic coral extinction was a catastrophic bottleneck in
 scleractinian evolution.
description: Simpsonetal_coral_species_rangesgensp = Genus species, FAD_stage = Stage name of first occurrence, LAD_stage = Stage name of last occurrence, FAD_MYA = Time of first occurrence (mya) from middle of stage, LAD_MYA = Time of last occurrence (mya) from top of stage. This data is derived from occurrence data downloaded from the Paleobiology Database (http://paleodb.org) on 17 March 2011. See paper for details of the download.Scler-Cytb_COI_August2010_combined.trees.tar80000 time-calibrated molecular phylogenies for a 144-taxon set using two mitochondrial genes, CO1 and Cytochrome B, which were downloaded from GenBank (see Suplementary Table 1 for taxa and accession numbers), including 10 outgroup species. Produced in BEAST 1.5.2
DOI: 10.5061/dryad.n856c
title: Data from: High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex

description: Identifying homology between sex chromosomes of different species is
 essential to understanding the evolution of sex determination. Here, we
 show that the identity of a homomorphic sex chromosome pair can be
 established using a linkage map, without information on offspring sex. By
 comparing sex-specific maps of the European tree frog Hyla arborea, we
 find that the sex chromosome (linkage group 1) shows a threefold
 difference in marker number between the male and female maps. In contrast,
 the number of markers on each autosome is similar between the two maps. We
 also find strongly conserved synteny between H. arborea and Xenopus
 tropicalis across 200 million years of evolution, suggesting that the rate
 of chromosomal rearrangement in anurans is low. Finally, we show that
 recombination in males is greatly reduced at the centers of large
 chromosomes, consistent with previous cytogenetic findings. Our research
 shows the importance of high-density linkage maps for studies of
 recombination, chromosomal rearrangement and the genetic architecture of
 ecologically or economically important traits.
description: Hyla arborea
 genomeDraft genome assembly
 for a male H. arborea from Lavigny, Switzerland, in gzipped fasta format.
 Assembled from 5x-depth 100bp PE Illumina reads with Abyss-PE (k=44),
 scaffolded with SSPACE. Whole-genome and RNAseq reads for this individual
 are available on NCBI SRA.Harb1.0.fa.gz