cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m5k62
title: Data from: Bayesian causal inference explains movement coordination to auditory beats

description: Many everyday skilled actions depend on moving in time with signals that
 are embedded in complex auditory streams (e.g. musical performance,
 dancing or simply holding a conversation). Such behaviour is apparently
 effortless; however, it is not known how humans combine auditory signals
 to support movement production and coordination. Here, we test how
 participants synchronize their movements when there are potentially
 conflicting auditory targets to guide their actions. Participants tapped
 their fingers in time with two simultaneously presented metronomes of
 equal tempo, but differing in phase and temporal regularity.
 Synchronization therefore depended on integrating the two timing cues into
 a single-event estimate or treating the cues as independent and thereby
 selecting one signal over the other. We show that a Bayesian inference
 process explains the situations in which participants choose to integrate
 or separate signals, and predicts motor timing errors. Simulations of this
 causal inference process demonstrate that this model provides a better
 description of the data than other plausible models. Our findings suggest
 that humans exploit a Bayesian inference process to control movement
 timing in situations where the origin of auditory signals needs to be
 resolved.
description: Experimental and
 Simulated AsynchroniesMatlab data continuing
 experimental asynchronies, pooled across participants, for each condition.
 Corresponding simulated asynchronies are also provided. Probability
 distribution values from KDE fitting are provided for both the
 experimental and simulated asynchronies.exp_and_sim_data_for_repo_140414.mat
DOI: 10.5061/dryad.76r4c
title: Data from: Asymmetric mismatch in strain-specific genital morphology causes increased harm to Drosophila females

description: Although several evolutionary forces have been proposed to contribute to
 genital morphological diversification, it is unclear which might act early
 during the evolution of novel structural traits. We test the hypothesis
 that mismatch between interacting male and female secondary sexual
 structures gives rise to increased harm to females, consistent with the
 outcome predicted from a history of sexual conflict. We mate Drosophila
 sechellia females to males from a collection of D. mauritiana-D. sechellia
 interspecific genetic introgression lines that possess quantitative
 morphological variation in the posterior lobe of the genital arch, an
 external genital structure that can cause wounds to the female abdomen
 during mating. We find that males with smaller posterior lobes, and those
 that possess lobes with similarities in shape to D. mauritiana, cause more
 severe wounding compared to either D. sechellia males with strain-specific
 morphologies or introgression males that possess larger lobes or lobes
 with more pronounced D. sechellia features. These results suggest a
 possible history of sexual conflict during the evolution of the posterior
 lobe in D. sechellia, but also suggest a potential contribution of
 divergence in sensory recognition mechanisms to posterior lobe evolution.
description: Posterior lobe
 coordinatesPosterior lobe outline
 x,y coordinatesPOSTERIOR_LOBE_XY_COORDS.zipWounding dataTab-delimited text file with wounding measures and associated data.WOUNDS.txt
DOI: 10.5061/dryad.d380g
title: Data from: Joined at the hip: linked characters and the problem of missing data in studies of disparity

description: Paleontological investigations into morphological diversity, or disparity,
 are often confronted with large amounts of missing data. We illustrate how
 missing discrete data effects disparity using a novel simulation for
 removing data based on parameters from published datasets that contain
 both extinct and extant taxa. We develop an algorithm that assesses the
 distribution of missing characters in extinct taxa, and simulates data
 loss by applying that distribution to extant taxa. We term this technique
 ‘linkage’. We compare differences in disparity metrics and ordination
 spaces produced by linkage and random character removal. When we
 incorporated linkage among characters, disparity metrics declined and
 ordination spaces shrank at a slower rate with increasing missing data,
 indicating that correlations among characters govern the sensitivity of
 disparity analysis. We also present and test a new disparity method that
 uses the linkage algorithm to correct for the bias caused by missing data.
 We equalized proportions of missing data among time bins before
 calculating disparity, and found that estimates of disparity changed when
 missing data were taken into account. By removing the bias of missing
 data, we can gain new insights into the morphological evolution of
 organisms and highlight the detrimental effects of missing data on
 disparity analysis.
description: AnalyzeDataContains the functions to run the correction factor and data removal scripts.CorrectionFunctions.SourceThe source file read by AnalyzeData that contains all the functions for calculating the correction factor.Ordination-Disparity.SourceThe source file read by AnalyzeData that contains all the functions for calculating the ordination spaces and disparity analysis following data removal.Luo2007ExampleAn example data file to use with the correction factor script. Data from Luo et al. 2007.PCOMatrixExampleAn example PCO data file that the correction factor outputs. To be used with the t-test function.LuoMatrixExtantExample extant dataset used in the data removal component of the study.LuoMatrixExtinctExample extinct dataset used in the linkage data removal component of the study.LuoMatrixExtinctRandomExample extinct dataset used in the random data removal component of the study.PCO_AllDifferences between original and 'data removed' ordination spaces for all taxa datasets.Linkage_AllDisparity metric outputs following linkage data removal for all taxa datasets.Random_AllDisparity metric outputs following random data removal for all taxa datasets.Disparity_TTestT-test results for mammals and pterosaurs for all disparity metrics. The test examines disparity differences between adjacent time bins.FunctionDocumentationInstructions on how to use the R scripts. Contains detailed information on each function used by correction factor.
DOI: 10.5061/dryad.v1908
title: Data from: Tree of sex: a database of sexual systems

description: The vast majority of eukaryotic organisms reproduce sexually, yet the
 nature of the sexual system and the mechanism of sex determination often
 vary remarkably, even among closely related species. Some species of
 animals and plants change sex across their lifespan, some contain
 hermaphrodites as well as males and females, some determine sex with
 highly differentiated chromosomes, while others determine sex according to
 their environment. Testing evolutionary hypotheses regarding the causes
 and consequences of this diversity requires interspecific data placed in a
 phylogenetic context. Such comparative studies have been hampered by the
 lack of accessible data listing sexual systems and sex determination
 mechanisms across the eukaryotic tree of life. Here, we describe a
 database developed to facilitate access to sexual system and sex
 chromosome information, with data on sexual systems from 11038 plant, 709
 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian,
 and 11556 invertebrate species.
description: Plant Data -
 FinalPlant data on sexual
 system and chromosome numbers, based on published literature (19 May 2014
 freeze). Zip file includes database, with expanded references in a
 separate file and personal communications.plant.data19may2014.zipInvertebrate Data - FinalInvertebrate data on sexual system and chromosome numbers, based on published literature (19 May 2014 freeze).invert.data-may19.csvVertebrate Data - FinalVertebrate data on sexual system and chromosome numbers, based on published literature (19 May 2014 freeze).vert.data-may19.csv
DOI: 10.25824/redu/7xipwi
title: Calculation of thermal conductivity at solid fluid interfaces via molecular simulations

description: This repository contains the simulation data and input scripts used in the paper Thermal Conductivity at Solid Fluid interfaces: Molecular simulation and Effective Modeling. All files are provided to enable full reproducibility of the molecular dynamics simulations used to compute the thermal conductivity of silica–methane slit pore systems. The data include the initial molecular configurations and the LAMMPS input script used to perform the NVE ensemble simulations.
DOI: 10.5061/dryad.pf013
title: Data from: Experimental evolution of external immune defenses in the red flour beetle

description: The red flour beetle, Tribolium castaneum, secretes quinones that control
 the microbial flora in the surrounding environment. These secretions act
 as an external immune defence that provides protection against pathogens.
 At high concentrations, however, these secretions are harmful to the host
 itself, and selection may thus have optimized the level of expression
 under natural conditions. Here, we show that the expression of external
 immunity responded to selection during experimental evolution within a few
 generations. At the same time, one component of internal immune defence
 (phenoloxidase activity) was compromised in beetles selected for either
 high or low external defences. Intriguingly, offspring protection against
 a natural pathogen was reduced in flour obtained from beetle lines
 selected for low amounts of secretions. Altogether, this suggests that
 external and internal immune defences work together efficiently under
 natural conditions, whereas every manipulation on the side of external
 immune defence comes with costs to the internal immune defence.
description: Joop et al.
 2014_JEBIncluding raw data on
 quinone seection, PPO activity, quinone flux, number offspring, bacterial
 inhibition and survival in the presence and absence of microsporidia
 and/or quinones, using the red flour beetle, Tribolium
 castaneum.
DOI: 10.15468/dl.6h96t6
title: Occurrence Download

description: A dataset containing 901704 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Country is Denmark",
 "DatasetKey is Danish Mycological Society, fungal records database",
 "OccurrenceStatus is Present",
 "Year 2010-2026"
 ]
}

 The dataset includes 901704 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001588-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4g832
title: Data from: Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)

description: In species differentiation, characters do not usually diverge
 synchronously and there are also processes that effectively shuffle
 character states present in lineages descendant from a common ancestor.
 Species are thus expected to show some degree of incongruence among
 characters, and we argue that taxonomic delimitation actually benefits
 from integrative approaches and objective strategies dealing with
 character conflict. We illustrate the potential of exploiting conflict for
 species delimitation in a study-case of ground beetles of the subgenus
 Carabus (Mesocarabus), where traditional taxonomy fails to accurately
 delimit species. The molecular phylogenies of four mitochondrial and three
 nuclear genes, cladistic analysis of the aedeagus, ecological niche
 divergence, and morphometry of pronotal shape in altogether more than 500
 specimens of Mesocarabus, show that none of these character sets are fully
 congruent with each other. For these data, a three-steps operational
 strategy is proposed for species delimitation by (1) delineating candidate
 species based on the integration of incongruence among conclusive lines of
 evidence, (2) corroborating candidate species with inconclusive lines of
 evidence, and (3) refining a final species proposal based on an integrated
 characterization of candidate species based on the evolutionary analysis
 of incongruence. This procedure provided a general understanding of the
 reticulate process of hybridization and introgression acting on
 Mesocarabus and generated the hypothesis of seven Mesocarabus species,
 including two putative hybrid lineages. Our work emphasizes the importance
 of incorporating critical analyses of character and phylogenetic conflict
 to infer both the evolutionary history and species boundaries through an
 integrative taxonomic approach.
description: Sequence Alignment 9 DNA
 fragments MesocarabusSequence_Alignment_9DNA_Fragments_Mesocarabus.nexMITochondrial_combined_dataset_BEAST_imputRIBosomal_combined_dataset_BEAST_imputHUWE1_BEAST_imputLSUa_BEAST_imputLSUb_ITS2_BEAST_imputPronotum_outlines_Harmonics_297_Mesocarabus
DOI: 10.5061/dryad.6cq0n
title: Data from: Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum

description: To study the genetic architecture of anther exsertion, a trait under
 stabilizing selection in wild radish, artificial selection on anther
 exsertion was applied for 11 generations. Two replicate lines each of
 increased and decreased exsertion plus two randomly-mated controls were
 included. Full pedigree information is available from generation five. To
 estimate correlated responses to selection, 571 plants from all lines and
 matrilines were grown in the greenhouse and a number of floral, growth,
 and phenology traits were measured. To create an outbred F2 mapping
 population, all possible crosses among the two high and two low exsertion
 lines were made, using a multiple-family design to capture the genetic
 variance still present after 11 generations of selection. Six floral
 traits were measured on 40 parents, 240 F1, and 4,868 F2 offspring.
 Opportunities for reuse of these data include traits not previously
 analyzed, other analyses, especially using the pedigree and fitness data,
 and seeds from all generations and photos of flowers in the later
 generations are available.
description: ArtificialSelectionExsertionTrait and pedigree information for 8 or 9 generations of selectionCorrelatedResponsesData for many traits after 5 or 6 generations of selection2001FieldFlowerMeasFloral traits measured repeatedly across the life of the plantsQTLParentalMeasurementsTrait measurements for the parental generation of the mapping populationQTLF1measurementsMapping F1 measurementsQTL F2 MeasurementsMapping F2 measurements
DOI: 10.5061/dryad.rf0d1
title: Data from: Parallel signatures of selection in temporally-isolated lineages of pink salmon

description: Studying the effect of similar environments on diverse genetic backgrounds
 has long been a goal of evolutionary biologists with studies typically
 relying on experimental approaches. Pink salmon, a highly-abundant and
 widely-ranging salmonid, provide a naturally-occurring opportunity to
 study the effects of similar environments on divergent genetic backgrounds
 due to a strict two-year semelparous life-history. The species is composed
 of two reproductively-isolated lineages with overlapping ranges that share
 the same spawning and rearing environments in alternate years. We used
 restriction site-associated DNA (RAD) sequencing to discover and genotype
 approximately 8,000 SNP loci in three population pairs of even- and
 odd-year pink salmon along a latitudinal gradient in North America. We
 found greater differentiation within the odd-year than the even-year
 lineage and greater differentiation in the southern pair from Puget Sound
 than in the northern Alaskan population pairs. We identified 15 SNPs
 reflecting signatures of parallel selection using both a
 differentiation-based method (BAYESCAN) and an environmental correlation
 method (BAYENV). These SNPs represent genomic regions that may be
 particularly informative in understanding adaptive evolution in pink
 salmon and exploring how differing genetic backgrounds within a species
 respond to selection from the same natural environment.
description: Seeb et al. parallel
 selection genotypesGenotypes from RAD
 sequencing for 8036 SNPs.
DOI: 10.5061/dryad.vg7sr
title: Data from: Multidimensional (co)evolutionary stability

description: The complexity of biotic and abiotic environmental conditions is such that
 the fitness of individuals is likely to depend on multiple traits. Using a
 synthetic framework of phenotypic evolution that draws from adaptive
 dynamics and quantitative genetics approaches, we explore how the number
 of traits under selection influences convergence stability and
 evolutionary stability in models for coevolution in multidimensional
 phenotype spaces. Our results allow us to identify three different effects
 of trait dimensionality on stability. First are (i) a “combinatorial
 effect”: without epistasis and genetic correlations, a higher number of
 trait dimensions offers more opportunities for equilibria to be unstable;
 and (ii) epistatic interactions, that is, fitness interactions between
 traits, which tend to destabilize evolutionary equilibria; this effect
 increases with the dimension of phenotype space. These first two effects
 influence both convergence stability and evolutionary stability, while
 (iii) genetic correlations (due, e.g., to pleiotropy or linkage
 disequilibrium) can affect only convergence stability. We illustrate the
 general prediction that increased dimensionality destabilizes evolutionary
 equilibria using examples drawn from well-studied classical models of
 frequency-dependent competition for resources, adaptation to a spatially
 heterogeneous environment, and antagonistic coevolution. In addition, our
 analyses show that increased dimensionality can favor diversification, for
 example, in the form of local adaptation, as well as evolutionary escape.
description: Simulation codes and
 scripts to plot the figures.Debarre-etal_2014_amnat.zip
DOI: 10.5061/dryad.50tp1
title: Data from: Effects of genetic similarity on the life history strategy of co-infecting trematodes: are parasites capable of intra-host kin recognition?

description: For conspecific parasites sharing the same host, kin recognition can be
 advantageous when the fitness of one individual depends on what another
 does; yet, evidence of kin recognition among parasites remains limited.
 Some trematodes, like Coitocaecum parvum, have plastic life cycles
 including two alternative life-history strategies. The parasite can wait
 for its intermediate host to be eaten by a fish definitive host, thus
 completing the classical three-host life cycle, or mature precociously and
 produce eggs while still inside its intermediate host as a facultative
 shortcut. Two different amphipod species are used as intermediate hosts by
 C. parvum, one small and highly mobile and the other larger, sedentary,
 and burrow dwelling. Amphipods often harbour two or more C. parvum
 individuals, all capable of using one or the other developmental strategy,
 thus creating potential conflicts or cooperation opportunities over
 transmission routes. This model was used to test the kin recognition
 hypothesis according to which cooperation between two conspecific
 individuals relies on the individuals' ability to evaluate their
 degree of genetic similarity. First, data showed that levels of intrahost
 genetic similarity between co-infecting C. parvum individuals differed
 between host species. Second, genetic similarity between parasites sharing
 the same host was strongly linked to their likelihood of adopting
 identical developmental strategies. Two nonexclusive hypotheses that could
 explain this pattern are discussed: kin recognition and cooperation
 between genetically similar parasites and/or matching genotypes involving
 parasite genotype–host compatibility filters.
description: P. excavatum Pair-wise
 Rousset's distance between individual parasitesP. fluviatilis_Pair-wise
 Rousset's distance between individual parasites
DOI: 10.5061/dryad.39mc5
title: Data from: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models

description: Background: Molecular clock methodologies allow for the estimation of
 divergence times across a variety of organisms; this can be particularly
 useful for groups lacking robust fossil histories, such as microbial
 eukaryotes with few distinguishing morphological traits. Here we have used
 a Bayesian molecular clock method under three distinct clock models to
 estimate divergence times within oomycetes, a group of fungal-like
 eukaryotes that are ubiquitous in the environment and include a number of
 devastating pathogenic species. The earliest fossil evidence for oomycetes
 comes from the Lower Devonian (~400 Ma), however the taxonomic affinities
 of these fossils are unclear. Results: Complete genome sequences were used
 to identify orthologous proteins among oomycetes, diatoms, and a brown
 alga, with a focus on conserved regulators of gene expression such as DNA
 and histone modifiers and transcription factors. Our molecular clock
 estimates place the origin of oomycetes by at least the mid-Paleozoic
 (~430-400 Ma), with the divergence between two major lineages, the
 peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190
 Ma). Divergence times estimated under the three clock models were similar,
 although only the strict and random local clock models produced reliable
 estimates for most parameters. Conclusions: Our molecular timescale
 suggests that modern pathogenic oomycetes diverged well after the origin
 of their respective hosts, indicating that environmental conditions or
 perhaps horizontal gene transfer events, rather than host availability,
 may have driven lineage diversification. Our findings also suggest that
 the last common ancestor of oomycetes possessed a full complement of
 eukaryotic regulatory proteins, including those involved in histone
 modification, RNA interference, and tRNA and rRNA methylation;
 interestingly no match to canonical DNA methyltransferases could be
 identified in the oomycete genomes studied here.
description: StrictClockGamma_50milBeast .xml file for Strict Clock analysis with 50 million generationsUCLDClockGamma_50milBeast .xml file for UCLD analysis with 50 million generationsRandomClockGamma_50milBeast .xml file for Random Clock analysis with 50 million generations
DOI: 10.5061/dryad.tt36g
title: Data from: Trophic convergence drives morphological convergence in marine tetrapods

description: Marine tetrapod clades (e.g. seals, whales) independently adapted to
 marine life through the Mesozoic and Caenozoic, and provide iconic
 examples of convergent evolution. Apparent morphological convergence is
 often explained as the result of adaptation to similar ecological niches.
 However, quantitative tests of this hypothesis are uncommon. We use
 dietary data to classify the feeding ecology of extant marine tetrapods
 and identify patterns in skull and tooth morphology that discriminate
 trophic groups across clades. Mapping these patterns onto phylogeny
 reveals coordinated evolutionary shifts in diet and morphology in
 different marine tetrapod lineages. Similarities in morphology between
 species with similar diets—even across large phylogenetic distances—are
 consistent with previous hypotheses that shared functional constraints
 drive convergent evolution in marine tetrapods.
description: Kelley and Motani
 Supplementary Material for Proceedings B.Contents: Table S1: Diet
 data and sources, Figure S1: Skull measurements, Table S2: Specimens used
 in this study, Figure S2: Phylogenetic distribution of diets, Table S3-S6:
 LDA results Figure S3: LDA score biplotsKelley Convergence
 Supplementary Material for Proceedings
 B..docxKelley and Motani Tree
 S1Tree S1: Tree used in
 this study: Marine Tetrapods Updated.nexMarine Tetrapods
 Updated.nex