cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02qv3
title: Data from: Can RNA-Seq resolve the rapid radiation of advanced moths (Lepidoptera: Apoditrysia)? An exploratory study

description: Recent molecular phylogenetic studies of the insect order Lepidoptera have
 robustly resolved family-level divergences within most superfamilies, and
 most divergences among the relatively species-poor early-arising
 superfamilies. In sharp contrast, relationships among the superfamilies of
 more advanced moths and butterflies that comprise the mega-diverse clade
 Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This
 uncertainty, in turn, limits our ability to discern the origins, ages and
 evolutionary consequences of traits hypothesized to promote the
 spectacular diversification of Apoditrysia. Low support along the
 apoditrysian “backbone” probably reflects rapid diversification. If so, it
 may be feasible to strengthen resolution by radically increasing the gene
 sample, but case studies have been few. We explored the potential of
 next-generation sequencing to conclusively resolve apoditrysian
 relationships. We used transcriptome RNA-Seq to generate 1579 putatively
 orthologous gene sequences across a broad sample of 40 apoditrysians plus
 four outgroups, to which we added two taxa from previously published data.
 Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a
 strict filter that eliminated ortholog groups containing any apparent
 paralogs, yielded dramatic overall increase in bootstrap support for
 deeper nodes within Apoditrysia as compared to results from previous and
 concurrent 19-gene analyses. High support was restricted mainly to the
 huge subclade Obtectomera broadly defined, in which 11 of 12 nodes
 subtending multiple superfamilies had bootstrap support of 100%. The
 strongly supported nodes showed little conflict with groupings from
 previous studies, and were little affected by changes in taxon sampling,
 suggesting that they reflect true signal rather than artifacts of massive
 gene sampling. In contrast, strong support was seen at only 2 of 11 deeper
 nodes among the “lower”, non-obtectomeran apoditrysians. These represent a
 much harder phylogenetic problem, for which one path to resolution might
 include further increase in gene sampling, together with improved
 orthology assignments.
description: data_matrices_for_Bazinet_et_al_PLOS_ONE_2013The zip archive (data_matrices_for_Bazinet_et_al_PLOS_ONE_2013.zip) contains the following files: lep_16_taxa_19_genes_degen1.nex lep_16_taxa_741_genes_CONSENSUS_degen1.fasta lep_16_taxa_741_genes_REPRESENTATIVE_degen1.fasta lep_38_taxa_19_genes_degen1.nex lep_38_taxa_741_genes_CONSENSUS_degen1.fasta lep_38_taxa_741_genes_REPRESENTATIVE_degen1.fasta lep_45_taxa_19_genes_degen1.nex lep_46_taxa_741_genes_CONSENSUS_degen1.fasta lep_46_taxa_741_genes_REPRESENTATIVE_degen1.fasta These are the data matrices associated with the publication: Can RNA-Seq resolve the rapid radiation of advanced moths (Lepidoptera: Apoditrysia)? An exploratory study, Bazinet, Adam L., Cummings, Michael P., Mitter, Kim T., Mitter, Charles, to appear in PLOS ONE, 2013.
DOI: 10.5061/dryad.kj0tj
title: Data from: Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations

description: Next generation sequencing (NGS) technologies provide a rapid means to
 generate genomic resources for species exhibiting interesting ecological
 and evolutionary variation but for which such resources are scant or
 nonexistent. In the current report, we utilize 454 pyrosequencing to
 obtain transcriptome information for multiple individuals and tissue types
 from geographically disparate and ecologically differentiated populations
 of the perennial sunflower species Helianthus maximiliani. A total of
 850,275 raw reads were obtained averaging 355 bp in length. Reads were
 assembled, post processing, into 16,681 unique contigs with an N50 of 898
 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were
 annotated based on comparison to the Arabidopsis thaliana genome (TAIR10).
 Contigs were identified that exhibit high similarity to genes associated
 with natural variation in flowering time and freezing tolerance in other
 plant species and will facilitate future studies aimed at elucidating the
 molecular basis of clinal life history variation and adaptive
 differentiation in H. maximiliani. Large numbers of gene-associated simple
 sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) also
 were identified that can be deployed in mapping and population genomic
 analyses.
description: Hmax_trnscriptm_assmbly16,681 assembled contigs obtained from sequencing the Helianthus maximiliani transcriptome
DOI: 10.5061/dryad.45hh0
title: Data from: Genomics assisted ancestry deconvolution in grape

description: The genus Vitis (the grapevine) is a group of highly diverse, diploid
 woody perennial vines consisting of approximately 60 species from across
 the northern hemisphere. It is the world’s most valuable horticultural
 crop with ~8 million hectares planted, most of which is processed into
 wine. To gain insights into the use of wild Vitis species during the past
 century of interspecific grape breeding and to provide a foundation for
 marker-assisted breeding programmes, we present a principal components
 analysis (PCA) based ancestry estimation method to calculate admixture
 proportions of hybrid grapes in the United States Department of
 Agriculture grape germplasm collection using genome-wide polymorphism
 data. We find that grape breeders have backcrossed to both the
 domesticated V. vinifera and wild Vitis species and that reasonably
 accurate genome-wide ancestry estimation can be performed on interspecific
 Vitis hybrids using a panel of fewer than 50 ancestry informative markers
 (AIMs). We compare measures of ancestry informativeness used in selecting
 SNP panels for two-way admixture estimation, and verify the accuracy of
 our method on simulated populations of admixed offspring. Our method of
 ancestry deconvolution provides a first step towards selection at the seed
 or seedling stage for desirable admixture profiles, which will facilitate
 marker-assisted breeding that aims to introgress traits from wild Vitis
 species while retaining the desirable characteristics of elite V. vinifera
 cultivars.
description: 131021 Genomics assisted
 ancestry deconvolution in grapeGenome-wide SNP data for
 grapevine samples (Vitis) used for ancestry estimation. Sample IDs for
 individuals used as ancestral populations and interspecific hybrids.
 Scripts used for simulating interspecific hybrids using the genotype
 data.131021_Genomics_assisted_ancestry_deconvolution_in_grape.zip
DOI: 10.5061/dryad.3hc8s
title: Data from: Upstream analyses create problems with DNA-based species delimitation

description: Genetic-based delimitation of species typically involves a multistep
 process in which DNA data are analyzed with a series of different
 programs. Although the performance of the programs associated with each
 step has been evaluated separately, no analysis has considered how errors
 in the upstream assignment of individuals to putative species impacts the
 accuracy of species delimited in downstream analyses, such as those
 associated with the coalescent-based Bayesian program bpp. Here we show
 that because the minimal data requirements for accurate performance in
 each of the separate steps involved in the delimitation process differ,
 the reliability of inferences about species delimited from DNA sequences
 can be compromised. Our results provide important insights into the
 practice of species delimitation. Specifically, even if users exercise the
 practices advocated for DNA-based delimitation, there may very well be
 errors in individual-species association, and consequently uncertainty in
 the guide tree (both derived from upstream analyses that are prerequisites
 for analyses with bpp), which can lead to under or overestimation of
 biodiversity, even though the Bayesian program bpp itself may perform very
 well. These results highlight the usefulness of complementary data (i.e.,
 data in addition to genetic data), especially for the assignment of
 individuals to putative species, to improve the accuracy of species
 delimitation.
description: datafilesSupplementaryFigs&TableTable describing characteristics of loci used to simulate DNA data and figures for results that complement those in the printed text.
DOI: 10.5061/dryad.1v02q
title: Data from: How climate extremes—not means—define a species' geographic range boundary via a demographic tipping point

description: Species’ geographic range limits interest biologists and resource managers
 alike; however, scientists lack strong mechanistic understanding of the
 factors that set geographic range limits in the field, especially for
 animals. There exists a clear need for detailed case studies that link
 mechanisms to spatial dynamics and boundaries because such mechanisms
 allow us to predict whether climate change is likely to change a species’
 geographic range and, if so, how abundance in marginal populations
 compares to the core. The bagworm Thyridopteryx ephemeraeformis
 (Lepidoptera: Psychidae) is a major native pest of cedars, arborvitae,
 junipers, and other landscape trees throughout much of North America.
 Across dozens of bagworm populations spread over six degrees of latitude
 in the American Midwest, we find latitudinal declines in fecundity and egg
 and pupal survivorship as you proceed towards the northern range boundary.
 A spatial gradient of bagworm reproductive success emerges, which is
 associated with a progressive decline in local abundance and an increase
 in the risk of local population extinction near the species’ geographic
 range boundary. We develop a mathematical model, completely constrained by
 empirically estimated parameters, to explore the relative roles of
 reproductive asynchrony and stage-specific survivorship in generating the
 range limit for this species. We find that overwinter egg mortality is the
 biggest constraint on bagworm persistence beyond their northern range
 limit. Overwinter egg mortality is directly related to winter temperatures
 that fall below the bagworm eggs’ physiological limit. This threshold, in
 conjunction with latitudinal declines in fecundity and pupal survivorship,
 creates a non-linear response to climate extremes that sets the geographic
 boundary and provides a path for predicting northward range expansion
 under altered climate conditions. Our mechanistic modeling approach
 demonstrates how species’ sensitivity to climate extremes can create
 population tipping points not reflected in demographic responses to
 climate means, a distinction that is critical to successful ecological
 forecasting.
description: Shapefile of
 county-level bagworm occupancyShapefile of
 county-level bagworm occupancy constructed from Wollerman, E. H. 1971.
 Bagworm. United States Department of Agriculture Forest Pest Leaflet
 97.bagworm
 occupancy.zipAdult bagworm
 longevityData on adult bagworm
 longevity (in hours) by sexadult
 longevity.csvBagworm emergence
 phenologySummary data for bagworm
 emergence phenologyemergence
 phenology.xlsBagworm larval
 survivalBagworm larval
 survivorship as a function of latitudelarval
 survival.csvBagworm female mating
 successData on the proportion
 of females mated as a function of latitudeproportion of mated
 females.csvBagworm pupal
 survivalBagworm pupal
 survivorship as a function of latitudepupal
 survival.xlsx
DOI: 10.82294/dvnilywtb
title: COPUS. Territorio: Guainía. Sector: Cultura. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector cultura (educación informal) en el departamento de Guainía.
DOI: 10.5061/dryad.t91gr
title: Data from: Maternal and paternal contributions to pathogen resistance dependent on development stage in a whitefish (Salmonidae)

description: 1. It is often assumed that maternal and paternal contributions to
 offspring phenotype change over the lifetime of an individual. However,
 studies on parental effects typically suffer from the problems that
 heritabilities and maternal environmental effects are difficult to
 separate, and that both may depend on environmental factors and
 developmental stage 2. In order to experimentally disentangle maternal
 from paternal contributions and the likely effects of developmental stage
 from ecological effects, we sampled a natural population of the whitefish
 Coregonus palaea, used gametes for full-factorial in vitro fertilizations,
 raised over 10,000 of the resulting offspring singly at controlled
 conditions, and exposed them at different points during embryonic
 development to one of two strains of Pseudomonas fluorescens that differed
 in their virulence characteristics (only one caused mortality, while both
 delayed hatching and reduced growth) 3. Vulnerability to infection
 increased markedly over embryo development. This change coincided with a
 distinct shift in the importance of maternal to additive genetic effects
 on survival. Timing of exposure also affected the variance components for
 hatching time and larval length, but in a less consistent direction than
 the variance components for mortality. No significant genetic variation
 was found for any reaction norms across time points of exposure,
 indicating a uniformity among genotypes in how susceptibility changed over
 development. Phenotypes were also typically correlated across time points,
 which could constrain the evolution of the reaction norms 4. Our
 experiment demonstrates that the relative maternal and paternal
 contributions to susceptibility to an infection, and hence the
 evolutionary potential to respond to pathogen-induced selection, depends
 not only on the kind of pathogenic stress but also on the timing of the
 challenge.
description: Functional Ecology data
 file 1Embryo mortality and
 hatching timeFunctional Ecology data
 file 2Hatchling lenght and
 yolk sac dimensions
DOI: 10.5061/dryad.5m400
title: Data from: Brood parasites lay eggs matching the appearance of host clutches

description: Interspecific brood parasitism represents a prime example of the
 co-evolutionary arms race where each party has evolved strategies in
 response to the other. Here we investigated whether common cuckoos
 (Cuculus canorus) actively select nests within a host population to match
 the egg appearance of a particular host clutch. To achieve this goal, we
 quantified the degree of egg matching using the avian vision modelling
 approach. Randomization tests revealed that cuckoo eggs in naturally
 parasitized nests showed lower chromatic contrast to host eggs than those
 assigned randomly to other nests with egg-laying date similar to naturally
 parasitized clutches. Moreover, egg matching in terms of chromaticity was
 better in naturally parasitized nests than it would be in the nests of the
 nearest active non-parasitized neighbour. However, there was no indication
 of matching in achromatic spectral characteristics whatsoever. Thus, our
 results clearly indicate that cuckoos select certain host nests to
 increase matching of their own eggs with host clutches but only in
 chromatic characteristics. Our results implicate that the ability of
 cuckoos to actively choose host nests based on the eggshell appearance
 imposes a strong selection pressure on host egg recognition.
description: Reflectance
 data_matching2013_SupplReflectance spectra of
 the common cuckoo and great reed warbler eggs. Data were collected in the
 field in 2009.
DOI: 10.5061/dryad.f2330
title: Data from: Development of a Nasonia vitripennis outbred laboratory population for genetic analysis

description: The parasitoid wasp genus Nasonia has rapidly become a genetic model
 system for developmental and evolutionary biology. The release of its
 genome sequence led to the development of high-resolution genomic tools,
 for both interspecific and intraspecific research, which has resulted in
 great advances in understanding Nasonia biology. To further advance the
 utility of Nasonia vitripennis as a genetic model system and to be able to
 fully exploit the advantages of its fully sequenced and annotated genome,
 we developed a genetically variable and well-characterized experimental
 population. In this study, we describe the establishment of the
 genetically diverse HVRx laboratory population from strains collected from
 the field in the Netherlands. We established a maintenance method that
 retains genetic variation over generations of culturing in the laboratory.
 As a characterization of its genetic composition, we provide data on the
 standing genetic variation and estimate the effective population size (Ne)
 by microsatellite analysis. A genome-wide description of polymorphism is
 provided through pooled resequencing, which yielded 417 331 high-quality
 SNPs spanning all five Nasonia chromosomes. The HVRx population and its
 characterization are freely available as a community resource for
 investigators seeking to elucidate the genetic basis of complex trait
 variation using the Nasonia model system.
description: HVRx_VarScan_output_Chr1.vcfNasonia vitripennis HVRx outbred laboratory population SNP data - Chromosome 1. VarScan.v2.2.8 output according to the following rules: minimum consensus quality: 20; minimum count of minor allele: 2, minimum coverage: 8. Reads with mapping qualities less than 20 were discarded.HVRx_VarScan_output_Chr2.vcfNasonia vitripennis HVRx outbred laboratory population SNP data - Chromosome 2. VarScan.v2.2.8 output according to the following rules: minimum consensus quality: 20; minimum count of minor allele: 2, minimum coverage: 8. Reads with mapping qualities less than 20 were discarded.HVRx_VarScan_output_Chr3.vcfNasonia vitripennis HVRx outbred laboratory population SNP data - Chromosome 3. VarScan.v2.2.8 output according to the following rules: minimum consensus quality: 20; minimum count of minor allele: 2, minimum coverage: 8. Reads with mapping qualities less than 20 were discarded.HVRx_VarScan_output_Chr4.vcfNasonia vitripennis HVRx outbred laboratory population SNP data - Chromosome 4. VarScan.v2.2.8 output according to the following rules: minimum consensus quality: 20; minimum count of minor allele: 2, minimum coverage: 8. Reads with mapping qualities less than 20 were discarded.HVRx_VarScan_output_Chr5.vcfNasonia vitripennis HVRx outbred laboratory population SNP data - Chromosome 5. VarScan.v2.2.8 output according to the following rules: minimum consensus quality: 20; minimum count of minor allele: 2, minimum coverage: 8. Reads with mapping qualities less than 20 were discarded.
DOI: 10.5061/dryad.6v06v
title: Data from: Evolutionary origins and diversification of proteobacterial mutualists

description: Mutualistic bacteria infect most eukaryotic species in nearly every biome.
 Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote
 mutualisms: how do mutualist phenotypes originate in bacterial lineages
 and to what degree do mutualists traits drive or hinder bacterial
 diversification? Here, we reconstructed the phylogeny of the hyperdiverse
 phylum Proteobacteria to investigate the origins and evolutionary
 diversification of mutualistic bacterial phenotypes. Our ancestral state
 reconstructions (ASRs) inferred a range of 34–39 independent origins of
 mutualist phenotypes in Proteobacteria, revealing the surprising frequency
 with which host-beneficial traits have evolved in this phylum. We found
 proteobacterial mutualists to be more often derived from parasitic than
 from free-living ancestors, consistent with the untested paradigm that
 bacterial mutualists most often evolve from pathogens. Strikingly, we
 inferred that mutualists exhibit a negative net diversification rate
 (speciation minus extinction), which suggests that mutualism evolves
 primarily via transitions from other states rather than diversification
 within mutualist taxa. Moreover, our ASRs infer that proteobacterial
 mutualist lineages exhibit a paucity of reversals to parasitism or to
 free-living status. This evolutionary conservatism of mutualism is
 contrary to long-standing theory, which predicts that selection should
 often favour mutants in microbial mutualist populations that exploit or
 abandon more slowly evolving eukaryotic hosts.
description: TB2:S14910
 Consensus
 species tree from MrBayes 405taxa MrBayes analysis
 with sampled trees MrBayes input and output
 results for the concatenated genes to determine species tree of the
 proteobacteria and sampled posterior trees to provide sampling for
 phylogenetic uncertainty in ancestral state reconstruction.
 405taxa_mrbayes.tgz
  
 
 Diversitree
 analyses The diversitree analysis
 for ancestral state reconstruction Feb2013.p-value.3FreeRates.tar.gz   r8s analysis to rate smooth the tree to ultrametric To generate an ultrametric tree for diversitree a tree from the MrBayes posterior was rate smoothed with r8s r8s.tar.gz   BayesTraits input files BayesTraits input files for running BT. The actual running requires specifically setting BayesTraits.tar.gz  
description: Metadata collected for host association status from the
 literature.
DOI: 10.5061/dryad.138vs
title: Data from: Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an Artichoke

description: The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke
 or Sunchoke, was cultivated in eastern North America before European
 contact. As such, it represents one of the few taxa that can support an
 independent origin of domestication in this region. Its tubers were
 adopted as a source of food and forage when the species was transferred to
 the Old World in the early 1600s, and are still used today. Despite the
 cultural and economic importance of this tuber crop species, its origin is
 debated. Competing hypotheses implicate the occurrence of polyploidization
 with or without hybridization, and list the annual sunflower H. annuus and
 five distantly related perennial sunflower species as potential parents.
 Here, we test these scenarios by skimming the genomes of diverse
 populations of Jerusalem Artichoke and its putative progenitors. We
 identify relationships among Helianthus taxa using complete plastomes (151
 551 bp), partial mitochondrial genomes (196 853 bp) and 35S (8196 bp) and
 5S (514 bp) ribosomal DNA. Our results refute the possibility that
 Jerusalem Artichoke is of H. annuus ancestry. We provide the first genetic
 evidence that this species originated recursively from perennial
 sunflowers of central-eastern North America via hybridization between
 tetraploid Hairy Sunflower and diploid Sawtooth Sunflower.
description: Data_archiving_Bock_etal_2013_NewPhytologist