cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b87j
title: Data from: Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies

description: 1. Observed patterns in the fossil record reflect not just
 macroevolutionary dynamics, but preservation patterns. Sampling rates
 themselves vary not simply over time or among major taxonomic groups, but
 within time intervals over geography and environment, and among species
 within clades. Large databases of presences of taxa in fossil-bearing
 collections allow us to quantify variation in per-collection sampling
 rates among species within a clade. We do this separately not just for
 different time/stratigraphic intervals, but also for different geographic
 or ecologic units within time/stratigraphic intervals. We then re-assess
 per-million-year sampling rates given the distributions of per-collection
 sampling rates 2. We use simple distribution models (geometric and
 lognormal) to assess general models of per-locality sampling rate
 distributions given occurrences among appropriate fossiliferous
 localities. We break these down not simply by time-period, but by general
 biogeographic units in order to accommodate variation over space as well
 as among species. 3. We apply these methods to occurrence data for
 Meso-Cenozoic mammals drawn from the Paleobiology Database and the New and
 Old Worlds fossil mammal database. We find that all models of distributed
 rates do vastly better than the best uniform sampling rates, and that the
 lognormal in particular does an excellent job of summarizing sampling
 rates. We also show that the lognormal distributions vary fairly
 substantially among biogeographic units of the same age. 4. As an example
 of the utility of these rates, we assess the most likely divergence times
 for basal (Eocene-Oligocene) carnivoramorphan mammals from North America
 and Eurasia using both stratigraphic and morphological data. The results
 allow for unsampled taxa or unsampled portions of sampled lineages to be
 in either continent and also allow for the variation in sampling rates
 among species. We contrast five models using stratigraphic likelihoods in
 different ways to summarize how they might affect macroevolutionary
 inferences.
description: Fossil Mammal
 Occurrences and LocalitiesPBDB and NOW locality
 numbers by substages; mammal species by locality
 numbers.Dryad
 Upload.xlsxPaleoDB
 RefsSampling Rate Variation
 OSX 0Program for assessing
 distributions of per-collection sampling rates.
DOI: 10.5061/dryad.6sg4q
title: Data from: Mating preferences do not maintain the tailspot polymorphism in the platyfish, Xiphophorus variatus

description: Negative assortative, or disassortative, mating describes the scenario
 when individuals tend to mate with dissimilar phenotypes more often than
 by random chance alone. This form of nonrandom mating has the power to
 select for the maintenance of polymorphism in conspicuous traits, for
 example, when females prefer mates that have a different trait value than
 their own. The livebearing variable platyfish, Xiphophorus variatus,
 exhibits high polymorphism for a melanic pigmentation trait called
 tailspots, which results in variation in a conspicuous visual cue.
 Livebearers often exhibit female mating preferences based on morphological
 traits and disassortative mating has been suggested in a related species.
 Whether mating choice contributes to the maintenance of tailspot variation
 has never been tested. Here, we examined mating preferences of wild-caught
 females for pairs of male stimuli differing in their tailspot pattern.
 Females showed no evidence for either assortative or disassortative
 association preferences, spending equal time with males of different
 patterns. These results corroborate data on natural mating patterns in X.
 variatus, suggesting that mate choice for tailspots is either nonexistent
 or at least insufficient to account for the maintenance of tailspot
 variation.
description: Culumber&Rosenthal_anyFishprojectThis zip file contains the project files (tps, path, and texture files) used in making animations for the associated manuscript.
DOI: 10.5061/dryad.1c14t
title: Data from: Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)

description: The major histocompatibility complex (MHC), an important component of the
 vertebrate immune system, provides an important suite of genes to examine
 the role of genetic diversity at non-neutral loci for population
 persistence. We contrasted patterns of diversity at the two classical MHC
 loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC
 class II (DAB), and neutral microsatellite loci across 70 populations
 spanning the species range from Washington State to Japan. There was no
 correlation in allelic richness or heterozygosity between MHC loci or
 between MHC loci and microsatellites. The two unlinked MHC loci may be
 responding to different selective pressures; the distribution of FST
 values for the two loci was uncorrelated, and evidence for both balancing
 and directional selection on alleles and lineages of DAB and UBA was
 observed in populations throughout the species range but rarely on both
 loci within a population. These results suggest that fluctuating selection
 has resulted in the divergence of MHC loci in contemporary populations.
description: GenotypesExcel tables containing the two digit genotypes (as used for Genepop) for MHC UBA, MHC DAB and the neutral microsatellites (Oki1a, Oki1b, Oki6, Oki29, Omy77, One8, Ots2, Ots3, Ots107, and Ots108) used to evaluate population diversity and patterns of selection in sockeye salmon. Tissue samples were collected over multiple years as indicated in each table. ID# corresponds to the population numbers given in Table 1 in the manuscript. The number of individuals sampled in each year is given along with the number of individuals with each genotype. The two digit allele designations for the published names for each DAB (Miller et al. 2001) and UBA (McClelland et al. 2011) allele are defined below the main table for each locus; published names correspond to those given in Figure 2 and throughout the text. For questions regarding genotype data please contact Dr. Kristi Miller (Kristi.Miller@dfo-mpo.gc.ca).
DOI: 10.5061/dryad.r5k63
title: Data from: Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades

description: The Leguminosae, the third-largest angiosperm family, has a global
 distribution and high ecological and economic importance. We examine how
 the legume systematic research community might join forces to produce a
 comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500
 species of legumes and then translate it into a phylogeny-based
 classification. We review the current state of knowledge of legume
 phylogeny and highlight where problems lie, for example in taxon sampling
 and phylogenetic resolution. We review approaches from bioinformatics and
 next-generation sequencing, which can facilitate the production of better
 phylogenetic estimates. Finally, we examine how morphology can be
 incorporated into legume phylogeny to address issues in comparative
 biology and classification. Our goal is to stimulate the research needed
 to improve our knowledge of legume phylogeny and evolution; the approaches
 that we discuss may also be relevant to other species-rich angiosperm
 clades.
description: Alignment and
 phylogenetic treesSequence alignment and
 trees for three-locus phylogenetic analysis of legume
 species.lpwg.tz
DOI: 10.5061/dryad.d3mb4
title: Data from: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

description: Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all
 living vertebrates. Despite their dominant role in aquatic ecosystems, the
 evolutionary history and tempo of acanthomorph diversification is poorly
 understood. We investigate the pattern of lineage diversification in
 acanthomorphs by using a well-resolved time-calibrated phylogeny inferred
 from a nuclear gene supermatrix that includes 520 acanthomorph species and
 37 fossil age constraints. This phylogeny provides resolution for what has
 been classically referred to as the “bush at the top” of the teleost tree,
 and indicates acanthomorphs originated in the Early Cretaceous.
 Paleontological evidence suggests acanthomorphs exhibit a pulse of
 morphological diversification following the end Cretaceous mass
 extinction; however, the role of this event on the accumulation of living
 acanthomorph diversity remains unclear. Lineage diversification rates
 through time exhibit no shifts associated with the end Cretaceous mass
 extinction, but there is a global decrease in lineage diversification
 rates 50 Ma that occurs during a period when morphological disparity among
 fossil acanthomorphs increases sharply. Analysis of clade-specific shifts
 in diversification rates reveal that the hyperdiversity of living
 acanthomorphs is highlighted by several rapidly radiating lineages
 including tunas, gobies, blennies, snailfishes, and Afro-American
 cichlids. These lineages with high diversification rates are not
 associated with a single habitat type, such as coral reefs, indicating
 there is no single explanation for the success of acanthomorphs, as
 exceptional bouts of diversification have occurred across a wide array of
 marine and freshwater habitats.
description: Alignment of 10 nuclear
 genes in nexus formatAligned DNA sequence
 data of 10 nuclear genes, interleaved. Taxa missing from individual genes
 are scored as missing data, e.g., "?"Near_et_al.nex
DOI: 10.5061/dryad.1tm84
title: Data from: Predicting novel trophic interactions in a non-native world

description: Humans are altering the global distributional ranges of plants, while
 their co-evolved herbivores are frequently left behind. Native herbivores
 often colonise non-native plants, potentially reducing invasion success or
 causing economic loss to introduced agricultural crops. We developed a
 predictive model to forecast novel interactions and verified it with a
 data set containing hundreds of observed novel plant–insect interactions.
 Using a food network of 900 native European butterfly and moth species and
 1944 native plants, we built an herbivore host-use model. By extrapolating
 host use from the native herbivore–plant food network, we accurately
 forecasted the observed novel use of 459 non-native plant species by
 native herbivores. Patterns that governed herbivore host breadth on
 co-evolved native plants were equally important in determining non-native
 hosts. Our results make the forecasting of novel herbivore communities
 feasible in order to better understand the fate and impact of introduced
 plants.
description: predicting novel host
 use codeR code for analysis of
 host use in food web of plants and Lepidoptera herbivores. Assessment of
 transferability only novel hosts.plant_informationnames and status of German plants in host use analysisLepidoptera informationtaxonomic information on Lepidoptera in host use analysisinteraction data on plants and Lepidoptera in BWmatrix of interactions of plants and Lepidopteran herbivoresmatrix_species_20120901.txtplant phylogenya Newick tree readable in R package "ape". A supertree of all plants found in Baden-Wuerttemburg, Germany. Constructed using Phylomatic with branch lengths constrained to those recorded in Wikstrom et al 2001plant_phylo_2010_11_30.tre
DOI: 10.5061/dryad.gf18v
title: Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

description: Understanding life history traits is an important first step in
 formulating effective conservation and management strategies. The use of
 artificial propagation and supplementation as such a strategy can have
 numerous effects on the supplemented natural populations and minimizing
 life history divergence is crucial in minimizing these effects. Here, we
 use single nucleotide polymorphism (SNP) genotypes for large-scale
 parentage analysis and pedigree reconstruction in a hatchery population of
 steelhead, the anadromous form of rainbow trout. Nearly complete sampling
 of the broodstock for several consecutive years in two hatchery programmes
 allowed inference about multiple aspects of life history. Reconstruction
 of cohort age distribution revealed a strong component of fish that spawn
 at 2 years of age, in contrast to programme goals and distinct from
 naturally spawning steelhead in the region, which raises a significant
 conservation concern. The first estimates of variance in family size for
 steelhead in this region can be used to calculate effective population
 size and probabilities of inbreeding, and estimation of iteroparity rate
 indicates that it is reduced by hatchery production. Finally, correlations
 between family members in the day of spawning revealed for the first time
 a strongly heritable component to this important life history trait in
 steelhead and demonstrated the potential for selection to alter life
 history traits rapidly in response to changes in environmental conditions.
 Taken together, these results demonstrate the extraordinary promise of
 SNP-based pedigree reconstruction for providing biological inference in
 high-fecundity organisms that is not easily achievable with traditional
 physical tags.
description: Russian River 2007-2011
 SNPPITinputRR07-11_SNPPITinput.txtSNP genotypes Russian River 2007-2011Two column format SNP genotypes from two hatcheries (WSH and CVFF) in the Russian River.DA_RussianRiver2007-11.txt
DOI: 10.5061/dryad.mr221
title: Data from: Molecular phylogeny of the burying beetles (Coleoptera: Silphidae: Nicrophorinae)

description: Burying beetles (Silphidae: Nicrophorus) are well-known for their
 monopolization of small vertebrate carcasses in subterranean crypts and
 complex biparental care behaviors. They have been the focus of intense
 behavioral, ecological, and conservation research since the 1980s yet no
 thorough phylogenetic estimate for the group exists. Herein, we infer
 relationships, test past hypotheses of relationships, and test
 biogeographic scenarios among 55 of the subfamily Nicrophorinae’s
 currently valid and extant 72 species. Two mitochondrial genes, COI and
 COII, and two nuclear genes, the D2 region of 28S, and the protein coding
 gene CAD, provided 3,971 nucleotides for 58 nicrophorine and 5 outgroup
 specimens. Ten partitions, with each modeled by GTR + I + G, were used for
 a 100 M generation MrBayes analysis and maximum likelihood bootstrapping
 with Garli. The inferred Bayesian phylogeny was mostly well-resolved with
 only three weak branches of biogeographic relevance. The common ancestor
 of the subfamily and of the genus Nicrophorus was reconstructed as Old
 World with four separate transitions to the New World and four reverse
 colonizations of the Old World from the New. Divergence dating from
 analysis with BEAST indicate the genus Nicrophorus originated in the
 Cretaceous, 127–99 Ma. Most prior, pre-cladistic hypotheses of
 relationships were strongly rejected while most modern hypotheses were
 largely congruent with monophyletic groups in our estimated phylogeny. Our
 results reject a recent hypothesis that Nicrophorus morio Gebler, 1817
 (NEW STATUS as valid species) is a subspecies of N. germanicus (L., 1758).
 Two subgenera of Nicrophorus are recognized:
 NecroxenusSemenov-Tian-Shanskij, 1933, and NicrophorusFabricius, 1775.
description: Nicrophorinae locality
 and specimen dataSee ReadMe
 file.Nicrophorinae-Sikes-2013-04-10.csv
DOI: 10.5061/dryad.1fb3d
title: Data from: Integrative taxonomy of the freshwater worm Rhyacodrilus falciformis s.l. (Clitellata: Naididae), with the description of a new species

description: The genetic and morphological variation within Rhyacodrilus falciformis
 Bretscher, 1901 (Clitellata: Naididae) in Europe was explored using an
 integrative approach, with three unlinked genetic markers [the
 mitochondrial cytochrome c oxidase subunit I (COI), the nuclear histone 3
 (H3) and internal transcribed spacer region (ITS)] combined with
 morphology, to investigate whether this taxon constitutes a single or
 several species. Using Automatic Barcode Gap Discovery on the COI data
 set, the specimens were divided into seven clusters, used as hypothetical
 species that were further tested with the other data sources. Single-gene
 trees were estimated for all three markers, using coalescence analysis and
 they were in many parts incongruent with each other. Only one of the
 clusters was supported by all trees; it was also morphologically
 differentiated from the other clusters by the shape of its modified penial
 chaetae. This group consists of two specimens from the Crotot Cave in
 south-eastern France, and morphologically they fit a previously described
 but invalid variety, ‘pigueti’, which is here described as a new species,
 Rhyacodrilus pigueti Achurra & Martinsson sp. n. The study
 highlights the fact that a single data source (e.g. COI barcodes) seldom
 provides a sufficient basis for taxonomic decisions such as species
 delimitation.
description: BEAST input file for
 COICOI.fasta.xmlBEAST input file for H3H3.fasta.log.txtBEAST input file for ITSITS.fasta.xmlBEAST log file for COICOI.fasta.log.txtBEAST log file for H3H3.fasta.log.txtBEAST log file for ITSITS.fasta.log.txt
DOI: 10.5061/dryad.4365v
title: Data from: Sex ratio and density affect sexual selection in a sex-role reversed fish

description: Understanding how demographic processes influence mating systems is
 important to decode ecological influences on sexual selection in nature.
 We manipulated sex ratio and density in experimental populations of the
 sex-role reversed pipefish Syngnathus typhle. We quantified sexual
 selection using the Bateman gradient (ß′ss), the opportunity for selection
 (I), and sexual selection (Is), and the maximum standardized sexual
 selection differential (s′max). We also measured selection on body length
 using standardized selection differentials (s′) and mating differentials
 (m′), and tested whether the observed I and Is differ from values obtained
 by simulating random mating. We found that I, Is, and s′max, but not ß′ss,
 were higher for females under female- than male-bias and the opposite for
 males, but density did not affect these measures. However, higher density
 decreased sexual selection (m′ but not s′) on female length, but selection
 on body length was not affected by sex ratio. Finally, Is but not I was
 higher than expected from random mating, and only for females under female
 bias. This study demonstrates that both sex ratio and density affect
 sexual selection and that disentangling interrelated demographic processes
 is essential to a more complete understanding of mating behavior and the
 evolution of mating systems.
description: Sim_data_mbData from simulated random mating under male biasSim_data_fbData from simulated random mating under female biasSex.sel.measuresMesures of sexual selection calculated per replicate for each treatment and sex.matingandreproductivesuccessmating and reproductive success and standardized length for all individuals
DOI: 10.5061/dryad.503tf
title: Data from: Patterns of cranial ontogeny in lacertid lizards: morphological and allometric disparity

description: We explored the ontogenetic dynamics of the morphological and allometric
 disparity in the cranium shapes of twelve lacertid lizard species. The
 analysed species (Darevskia praticola, Dinarolacerta mosorensis,
 Iberolacerta horvathi, Lacerta agilis, L. trilineata, L. viridis, Podarcis
 erhardii, P. melisellensis, P. muralis, P. sicula, P. taurica and Zootoca
 vivipara) can be classified into different ecomorphs: terrestrial lizards
 that inhabit vegetated habitats (habitats with lush or sparse vegetation),
 saxicolous and shrub-climbing lizards. We observed that there was an
 overall increase in the morphological disparity (MD) during the ontogeny
 of the lacertid lizards. The ventral cranium, which is involved in the
 mechanics of jaw movement and feeding, showed higher levels of MD, an
 ontogenetic shift in the morphospace planes and more variable allometric
 patterns than more conserved dorsal crania. With respect to ecology, the
 allometric trajectories of the shrub-climbing species tended to cluster
 together, whereas the allometric trajectories of the saxicolous species
 were highly dispersed. Our results indicate that the ontogenetic patterns
 of morphological and allometric disparity in the lacertid lizards are
 modified by ecology and functional constraints and that the identical
 mechanisms that lead to intraspecific morphological variation also produce
 morphological divergence at higher taxonomic levels.
description: Lacertidae dorsal
 symRaw shape coordinates
 and log centroid size values, with species, age/sex and habitat preference
 classifiers, for dorsal craniumLacertidae ventral
 symRaw shape coordinates
 and log centroid size values, with species, age/sex and habitat preference
 classifiers, for ventral craniumLAcertidae dorz
 procrustes SheetsProcrustes coordinates
 and CS values, with species, age/sex and habitat preference classifiers,
 for dorsal cranium, for use in IMP series software (Sheets,
 2000)Lacertidae vent
 procrustes SheetsProcrustes coordinates
 and CS values, with species, age/sex and habitat preference classifiers,
 for ventral cranium, for use in IMP series software (Sheets,
 2000)LAE349~1.treesFour alternative trees, for testing phylogenetic signal via MorphoJ
DOI: 10.5061/dryad.164dg
title: Data from: Differential introgression in a mosaic hybrid zone reveals candidate barrier genes

description: Hybrid zones act as genomic sieves; although globally advantageous alleles
 will spread throughout the zone and neutral alleles can be freely
 exchanged between species, introgression will be restricted for genes that
 contribute to reproductive barriers or local adaptation. Seminal fluid
 proteins (SFPs) are known to contribute to reproductive barriers in
 insects and have been proposed as candidate barrier genes in the
 hybridizing field crickets G. pennsylvanicus and G. firmus. Here, we have
 used 125 SNPs to characterize patterns of differential introgression and
 to identify genes that may contribute to prezygotic barriers between these
 species. Using a transcriptome scan of the male cricket accessory gland
 (the site of SFP synthesis), we identified genes with major allele
 frequency differences between the species. We then compared patterns of
 introgression for genes encoding seminal fluid proteins with patterns for
 genes expressed in the same tissue that do not encode SFPs. We find no
 evidence that seminal fluid proteins have reduced gene exchange across the
 cricket hybrid zone. However, a number of genes exhibit dramatically
 reduced introgression, and many of these genes encode proteins with
 functional roles consistent with known barriers.
description: SNP genotyping assay
 designSequenom MassArray Assay
 Design for multiplexed SNP genotypingDryad1.docxGenomic clinesFigure S1.pdf