cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4vt08
title: Data from: Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

description: Sequence capture and restriction site associated DNA sequencing (RADseq)
 are popular methods for obtaining large numbers of loci for phylogenetic
 analysis. These methods are typically used to collect data at different
 evolutionary timescales; sequence capture is primarily used for obtaining
 conserved loci, whereas RADseq is designed for discovering single
 nucleotide polymorphisms (SNPs) suitable for population genetic or
 phylogeographic analyses. Phylogenetic questions that span both “recent”
 and “deep” timescales could benefit from either type of data, but studies
 that directly compare the two approaches are lacking. We compared
 phylogenies estimated from sequence capture and double digest RADseq
 (ddRADseq) data for North American phrynosomatid lizards, a species-rich
 and diverse group containing nine genera that began diversifying
 approximately 55 million years ago. Sequence capture resulted in 584 loci
 that provided a consistent and strong phylogeny using concatenation and
 species tree inference. However, the phylogeny estimated from the ddRADseq
 data was sensitive to the bioinformatics steps used for determining
 homology, detecting paralogs, and filtering missing data. The topological
 conflicts among the SNP trees were not restricted to any particular
 timescale, but instead were associated with short internal branches.
 Species tree analysis of the largest SNP assembly, which also included the
 most missing data, supported a topology that matched the sequence capture
 tree. This preferred phylogeny provides strong support for the paraphyly
 of the earless lizard genera Holbrookia and Cophosaurus, suggesting that
 the earless morphology either evolved twice, or that it evolved once and
 was subsequently lost in Callisaurus.
description: mtDNA
 alignmentNexus formatted file
 containing the partial (fragmented) mtDNA genome data.mtDNA.nexddRADseq dataCompressed folder containing all of the ddRADseq data assemblies in phylip format. Each *.phy file contains one concatenated alignment of the ddRADseq data. The folders are organized at three levels: 1) homology filter (80 or 90 or 95), 2) paralog filter (1 or 3), 3) minimum individuals (3, 4, 5, 6, 7, 8, 9, or 10).SNPdata_drayd.zipSequence capture data (all 584 captured loci)Sequence capture loci in nexus file format. Files are named according to locus name. Also includes a concatenated matrix of the 584 loci.nexus.zipSequence capture data (471 complete loci)A subset of the sequence capture loci that were captured for all species included in the study. The files are in nexus file format. Files are named according to locus name. Also included is a concatenated matrix of the 471 loci.nexus_471complete_loci.zip
DOI: 10.15468/dl.ht7pww
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Electroma vexillum (Reeve, 1857)"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040333-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8038
title: Data from: Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure

description: Over the past decades the use of molecular markers has revolutionized
 biology and led to the foundation of a new research discipline --
 phylogeography. Of particular interest has been the inference of
 population structure and biogeography. While initial studies focused on
 mtDNA as a molecular marker, it has become apparent that selection and
 genealogical lineage sorting could lead to erroneous inferences. As it is
 not clear to what extent these forces affect a given marker, it has become
 common practice to use the combined evidence from a set of molecular
 markers as an attempt to recover the signals that approximate the true
 underlying demography. Typically, the number of markers used is determined
 by either budget constraints or by statistical power required to recognize
 significant population differentiation. Using microsatellite markers from
 Drosophila and humans we show that even large numbers of loci (&gt;50)
 can frequently result in statistically well supported, but incorrect
 inference of population structure using the software BAPS. Most
 importantly, genomic features, such as chromosomal location, variability
 of the markers, or recombination rate, cannot explain this observation.
 Instead, it can be attributed to sampling variation among loci with
 different realizations of the stochastic lineage sorting. This phenomenon
 is particularly pronounced for low levels of population differentiation.
 Our results have important implications for ongoing studies of population
 differentiation, as we unambiguously demonstrate that statistical
 significance of population structure inferred from a random set of genetic
 markers cannot necessarily be taken as evidence for a reliable demographic
 inference.
description: Orozco-terWengel_dataMicrosatellite data for 21 natural populations of Drosophila melanogaster. The file is in MSA format (Dieringer D, Schlötterer C (2003) Microsatellite Analyser (Msa): A Platform Independent Analysis Tool for Large Microsatellite Data Sets. Molecular Ecology Notes 3, 167-169).
DOI: 10.5061/dryad.27h01
title: Data from: Identification of quantitative genetic components of fitness variation in farmed, hybrid and native salmon in the wild

description: Feral animals represent an important problem in many ecosystems due to
 interbreeding with wild conspecifics. Hybrid offspring from wild and
 domestic parents are often less adapted to local environment and
 ultimately, can reduce the fitness of the native population. This problem
 is an important concern in Norway, where each year, hundreds of thousands
 of farm Atlantic salmon escape from fish farms. Feral fish outnumber wild
 populations, leading to a possible loss of local adaptive genetic
 variation and erosion of genetic structure in wild populations. Studying
 the genetic factors underlying relative performance between wild and
 domesticated conspecific can help to better understand how domestication
 modifies the genetic background of populations, and how it may alter their
 ability to adapt to the natural environment. Here, based upon a
 large-scale release of wild, farm and wild x farm salmon crosses into a
 natural river system, a genome-wide quantitative trait locus (QTL) scan
 was performed on the offspring of 50 full-sib families, for traits related
 to fitness (length, weight, condition factor and survival). Six QTLs were
 detected as significant contributors to the phenotypic variation of the
 first three traits, explaining collectively between 9.8 and 14.8% of the
 phenotypic variation. The seventh QTL had a significant contribution to
 the variation in survival, and is regarded as a key factor to understand
 the fitness variability observed among salmon in the river. Interestingly,
 strong allelic correlation within one of the QTL regions in farmed salmon
 might reflect a recent selective sweep due to artificial selection.
description: phenotype_genotypeThe file contains 2474 lines, each corresponding to an individual in the study. Columns contain in turn: the individual's identification, (column 1) family (column 2), three measured traits : weight, length and CF (column 3,4 and 5 respectively), type: farm hybrid or wild (column 6), parents (column 7 and 8). The following columns are the SNP genotypes coded as 0101 0102 0201 or 0202.data_summary.txt
DOI: 10.5061/dryad.2307m
title: Data from: Body mass estimates of an exceptionally complete Stegosaurus (Ornithischia: Thyreophora): comparing volumetric and linear bivariate mass estimation methods

description: Body mass is a key biological variable, but difficult to assess from
 fossils. Various techniques exist for estimating body mass from skeletal
 parameters, but few studies have compared outputs from different methods.
 Here, we apply several mass estimation methods to an exceptionally
 complete skeleton of the dinosaur Stegosaurus. Applying a volumetric
 convex-hulling technique to a digital model of Stegosaurus, we estimate a
 mass of 1560 kg (95% prediction interval 1082–2256 kg) for this
 individual. By contrast, bivariate equations based on limb dimensions
 predict values between 2355 and 3751 kg and require implausible amounts of
 soft tissue and/or high body densities. When corrected for ontogenetic
 scaling, however, volumetric and linear equations are brought into close
 agreement. Our results raise concerns regarding the application of
 predictive equations to extinct taxa with no living analogues in terms of
 overall morphology and highlight the sensitivity of bivariate predictive
 equations to the ontogenetic status of the specimen. We emphasize the
 significance of rare, complete fossil skeletons in validating widely
 applied mass estimation equations based on incomplete skeletal material
 and stress the importance of accurately determining specimen age prior to
 further analyses.
description: Convex hull 3D
 filesDryad
 Submission.zip
DOI: 10.5061/dryad.kr3hf
title: Data from: Intraspecific genetic admixture and the morphological diversification of an estuarine fish population complex

description: The North-east American Rainbow smelt (Osmerus mordax) is composed of two
 glacial races first identified through the spatial distribution of two
 distinct mtDNA lineages. Contemporary breeding populations of smelt in the
 St. Lawrence estuary comprise contrasting mixtures of both lineages,
 suggesting that the two races came into secondary contact in this estuary.
 The overall objective of this study was to assess the role of
 intraspecific genetic admixture in the morphological diversification of
 the estuarine rainbow smelt population complex. The morphology of
 mixed-ancestry populations varied as a function of the relative
 contribution of the two races to estuarine populations, supporting the
 hypothesis of genetic admixture. Populations comprising both ancestral
 mtDNA races did not exhibit intermediate morphologies relative to pure
 populations but rather exhibited many traits that exceeded the parental
 trait values, consistent with the hypothesis of transgressive segregation.
 Evidence for genetic admixture at the level of the nuclear gene pool,
 however, provided only partial support for this hypothesis. Variation at
 nuclear AFLP markers revealed clear evidence of the two corresponding
 mtDNA glacial races. The admixture of the two races at the nuclear level
 is only pronounced in mixed-ancestry populations dominated by one of the
 mtDNA lineages, the same populations showing the greatest degree of
 morphological diversification and population structure. In contrast,
 mixed-ancestry populations dominated by the alternate mtDNA lineage showed
 little evidence of introgression of the nuclear genome, little
 morphological diversification and little contemporary population genetic
 structure. These results only partially support the hypothesis of
 transgressive segregation and may be the result of the differential
 effects of natural selection acting on admixed genomes from different
 sources.
description: Smelt AFLP data - Dodson
 et al. 2015 (PlosONE)This file contains AFLP
 genotypes (29 loci) for 447 Rainbow smelt (Osmerus mordax). One sheet
 contains the data, one sheet establishes the correspondence between Site
 numbers in the publication (Table 2 and Figure 2) and codes used for
 indiividual genotypes.DodsonAl_PlosONE15_AFLPdata.xlsxDodsonAl_PlosONE15_MorphoDataThis files contains morphological data. One sheet contains the data itself, one sheet establishes the correspondence between sampling sites in Figure 1 and Table 1 with the codes used in the datasheet; one sheet details the meaning of trait variables. These traits are also presented in the DodsonAl_PlosONE15_DescriptionVariables.pdf file
DOI: 10.5061/dryad.n1d61
title: Data from: Phanerozoic diversity and neutral theory

description: Although Phanerozoic increases in the global richness, local richness, and
 evenness of marine invertebrates are well documented, a common explanation
 for these patterns has been difficult to identify. Evidence is presented
 here from marine invertebrate communities that there is a Phanerozoic
 increase in the fundamental biodiversity number (θ), which describes
 diversity and relative abundance distributions in neutral ecological
 theory. If marine ecosystems behave according to the rules of Hubbell’s
 Neutral Theory of Biodiversity and Biogeography, the Phanerozoic increase
 in θ suggests three possible mechanisms for the parallel increases in
 global richness, local richness, and evenness: (1) an increase in the
 per-individual probability of speciation, (2) an increase in the area
 occupied by marine metacommunities, and (3) an increase in the density
 (per-area abundance) of marine organisms. Because speciation rates have
 declined over time and because there is no clear evidence for an increase
 in metacommunity area through the Phanerozoic, the most likely of these is
 an increase in the spatial density of marine invertebrates over the
 Phanerozoic, an interpretation supported by previous studies of fossil
 abundance. This, coupled with a Phanerozoic rise in body size, suggests
 that an increase in primary productivity through time is the primary cause
 of Phanerozoic increases in θ, global richness, local richness, local
 evenness, abundance, and body size.
description: appendix1List of Paleobiology Database collections used in this study, including collection number, age, paleolatitude, paleolongitude, sedimentary environment, country, state, tectonic plate, lithification state, lithology, reference number, and collection size.Estimates of theta for all data sets in this studyColumns include data set number, number of specimens, number of species, theta, geologic age, lithification state, lithology, and sedimentary environment.appendix2.txt
DOI: 10.5061/dryad.71tg4
title: Data from: Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

description: Wood decay mechanisms in Agaricomycotina have been traditionally separated
 in two categories termed white and brown rot. Recently the accuracy of
 such a dichotomy has been questioned. Here, we present the genome
 sequences of the white rot fungus Cylindrobasidium torrendii and the brown
 rot fungus Fistulina hepatica both members of Agaricales, combining
 comparative genomics and wood decay experiments. Cylindrobasidium
 torrendii is closely related to the white-rot root pathogen Armillaria
 mellea, while F. hepatica is related to Schizophyllum commune, which has
 been reported to cause white rot. Our results suggest that C. torrendii
 and S. commune are intermediate between white-rot and brown-rot fungi, but
 at the same time they show characteristics of decay that resembles soft
 rot. Both species cause weak wood decay and degrade all wood components
 but leave the middle lamella intact. Their gene content related to lignin
 degradation is reduced, similar to brown-rot fungi, but both have
 maintained a rich array of genes related to carbohydrate degradation,
 similar to white-rot fungi. These characteristics appear to have evolved
 from white-rot ancestors with stronger ligninolytic ability. Fistulina
 hepatica shows characteristics of brown rot both in terms of wood decay
 genes found in its genome and the decay that it causes. However, genes
 related to cellulose degradation are still present, which is a
 plesiomorphic characteristic shared with its white-rot ancestors. Four
 wood degradation-related genes, homologs of which are frequently lost in
 brown-rot fungi, show signs of pseudogenization in the genome of F.
 hepatica. These results suggest that transition towards a brown rot
 lifestyle could be an ongoing process in F. hepatica. Our results
 reinforce the idea that wood decay mechanisms are more diverse than
 initially thought and that the dichotomous separation of wood decay
 mechanisms in Agaricomycotina into white rot and brown rot should be
 revisited.
description: 26 genes - species
 phylogeny - original alignmentsThis folder contains all
 the original alignments for each one of the 26 genes prior to exclusion of
 poorly aligned areas26GenesDatasets_SpeciesPhylogeny.zip26GenesDatasets_Aligned+GblocksThe folder contains the alignment of each one of the 26 genes used for the species phylogeny after GBlocks26Genes_MLandBrBayes_filesfinal analyzed files and tree files for both MrBayes and RAxMLWood_decay_phylogeneticsthe folder includes the wood decay protein datasets and their phylogenetic analysesreconciled_treesthe folder contains the reconciled trees using Notung.Pseudogenization_related_phylogeniesthe folder contains the phylogenies of DyP, GH74, GH5-7, GH74 with the inclusion of the predicted proteins from potential pseudogenes. It also contains the phylogenies of the protein clusters of genes upstream and downstream of the potential pseudogenes.
DOI: 10.15468/dl.nappdx
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spinus cucullatus"
 ]
}

 The dataset includes 251 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001628-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d4500
title: Data from: Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle

description: Analysis of DNA from archaeological remains is a valuable tool to
 interpret the history of ancient animal populations. So far most studies
 of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal
 lineages, but only partially the relationships of current breeds and
 ancient populations. In this study we explore the feasibility of nuclear
 DNA analysis. DNA was extracted from 1000-years old cattle bone collected
 from Ferento, an archaeological site in central Italy. Amplification of 15
 microsatellite FAO-recommended markers with PCR products yielded genotypes
 for four markers. Expected heterozygosity was comparable with values of
 modern breeds, but observed heterozygosity was underestimated due to
 allelic loss. Genetic distances suggested a position intermediate between
 (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the
 Iberian, North-European and Central-European cattle, but also a clear
 relationship with two central-Italian breeds, Chianina and Romagnola. This
 suggests that these breeds are derived from medieval cattle living in the
 same area. Our results illustrate the potential of ancient DNA for
 reconstructing the history of local cattle husbandry.
description: microsatellite
 genotypeFirst sheet contains the
 breed code, second sheet contains the breed- cluster abbraviations, third
 sheet contains the genotype for 4 microsatellite genotype dataset, fourth
 sheet contains the 30 microsatellite genotype dataset
DOI: 10.5061/dryad.bj042
title: Data from: Reduced crossover interference and increased ZMM-independent recombination in the absence of Tel1/ATM

description: Meiotic recombination involves the repair of double-strand break (DSB)
 precursors as crossovers (COs) or noncrossovers (NCOs). The proper number
 and distribution of COs is critical for successful chromosome segregation
 and formation of viable gametes. In budding yeast the majority of COs
 occurs through a pathway dependent on the ZMM proteins
 (Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3), which form foci at CO-committed
 sites. Here we show that the DNA-damage-response kinase Tel1/ATM limits
 ZMM-independent recombination. By whole-genome mapping of recombination
 products, we find that lack of Tel1 results in higher recombination and
 reduced CO interference. Yet the number of Zip3 foci in tel1Δ cells is
 similar to wild type, and these foci show normal interference. Analysis of
 recombination in a tel1Δ zip3Δ double mutant indicates that COs are less
 dependent on Zip3 in the absence of Tel1. Together these results reveal
 that in the absence of Tel1, a significant proportion of COs occurs
 through a non-ZMM-dependent pathway, contributing to a CO landscape with
 poor interference. We also see a significant change in the distribution of
 all detectable recombination products in the absence of Tel1, Sgs1, Zip3,
 or Msh4, providing evidence for altered DSB distribution. These results
 support the previous finding that DSB interference depends on Tel1, and
 further suggest an additional level of DSB interference created through
 local repression of DSBs around CO-designated sites.
description: PGENETICS_TEL1_ReCombine_dataProcessed sequencing and microarray data from analysis of meiotic recombination in Saccharomyces cerevisiae. Genotypes analyzed are wild type, tel1, sgs1, zip3, msh4, tel1 zip3, and sgs1 zip3.Simulation scriptsPython scripts used to simulate crossover and DSB interference in Figure 6B.simulation.zip
DOI: 10.5061/dryad.dt682
title: Data from: A mid-Oligocene (Whitneyan) rhinocerotid from northeastern California

description: Rhinoceroses were important in North American mammal faunas from the late
 middle Eocene to the Miocene, but the group’s poor sampling outside the
 High Plains and eastern Rocky Mountain regions during their early
 evolution significantly hinders understanding of their biogeography. This
 limited geographic sampling is particularly true of early–middle Oligocene
 time, with the vast majority of Whitneyan localities occurring in the
 White River Badlands of South Dakota. Thus, any rhinocerotid from outside
 the High Plains during this period is significant. We describe two new
 rhinocerotid specimens from the middle Oligocene Steamboat Formation of
 the northeastern Warner Mountains of California. Although the Steamboat
 Formation is well known for fossil plants, this is the first report of
 mammalian fossils from the area: an isolated lower molar recovered in 1974
 but not previously described or illustrated, and a mandibular fragment
 recovered approximately 20 years later and bearing two molar teeth, most
 likely pertaining to the same taxon and horizon. The lack of distinctive
 morphological characters suggests both fossils be conservatively referred
 to Rhinocerotidae incertae sedis. Based on published tooth measurement
 data, Trigonias osborni represents the closest size match, but that
 species is currently only known from the Chadronian. Similarly, the
 Whitneyan taxon Diceratherium tridactylum is approximately the right size,
 but is currently only known from the High Plains and its presence in
 California would expand its geographic range substantially. Of greatest
 importance here is that sediments of the eastern Warner Mountains may
 represent a largely unexplored locale for early–middle Oligocene fossil
 vertebrates, and may yield important future finds.
description: SuppInfo Bright et al.,
 2015 - Mid-Oligocene rhinocerotidPhotogrammetric 3D
 reconstructions of tooth fossils UCMP226229 and UCMP121793, created using
 Agisoft PhotoScan Standard edition v0.9 and Adobe Acrobat 8 Professional.
 Adobe Acrobat Reader v8 or higher is needed to view 3D
 content.SuppInfoBright2015-Mid-OligoceneRhinocerotid.pdf