cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fc30r431
title: Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

description: In phylogenetic analyses of molecular sequence data, partitioning involves
 estimating independent models of molecular evolution for different sets of
 sites in a sequence alignment. Choosing an appropriate partitioning scheme
 is an important step in most analyses because it can affect the accuracy
 of phylogenetic reconstruction. Despite this, partitioning schemes are
 often chosen without explicit statistical justification. Here, we describe
 two new objective methods for the combined selection of best-fit
 partitioning schemes and nucleotide substitution models. These methods
 allow millions of partitioning schemes to be compared in realistic
 timeframes, and so permit the objective selection of partitioning schemes
 even for large multi-locus DNA datasets. We demonstrate that these methods
 significantly outperform previous approaches, including the ad hoc
 selection of partitioning schemes (e.g. partitioning by gene or codon
 position), and a recently proposed hierarchical clustering method. We have
 implemented these methods in an open-source program, PartitionFinder. This
 program allows users to select partitioning schemes and substitution
 models using a range of information-theoretic metrics (e.g. the BIC, AIC,
 and AICc). We hope that PartitionFinder will encourage the objective
 selection of partitioning schemes, and thus lead to improvements in
 phylogenetic analyses. PartitionFinder is written in Python and runs under
 Mac OSX 10.4 and above. The program, source code, and a detailed manual
 are freely available from .
description: Table_3_Li_2008This file contains all of the input and output files for table 3 in the paper. Including Li et al's alignment file, and partitioning files for all of the different schemes in table 3 of the paper. It also contains the mac-compiled version of RaxML that I used for the analysis, although any version of raxML should work.Table_1_and_2_datasetsThere are 10 subfolders, each of which contains a dataset and a partitionfinder.cfg file. The datasets are described in table 1 of the paper, and the results are in table 2. The files in the folders should reproduce all of the results in table 2. All analyses are were run with PartitionFinder v0.9. To download this particular version (which is guaranteed to work with these files, while later versions might not be) follow this link: . Later versions of PartitionFinder are available here: .
DOI: 10.5061/dryad.87b01fq0
title: Data from: Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

description: BACKGROUND: The morphological peculiarities of turtles have, for a long
 time, impeded their accurate placement in the phylogeny of amniotes.
 Molecular data used to address this major evolutionary question have so
 far been limited to a handful of markers and/or taxa. These studies have
 supported conflicting topologies, positioning turtles as either the sister
 group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes),
 to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale
 data have been shown to be useful in resolving other debated phylogenies,
 but no such adequate dataset is yet available for amniotes. RESULTS: In
 this study, we used next-generation sequencing to obtain seven new
 transcriptomes from the blood, liver, or jaws from four turtles, a caiman,
 a lizard, and a lungfish. We used a phylogenomic dataset based on 248
 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve
 the origins of turtles. Maximum likelihood and Bayesian concatenation
 analyses and species tree approaches performed under the most realistic
 models of the nucleotide and amino acid substitution processes
 unambiguously support turtles as a sister group to birds and crocodiles.
 The use of more simplistic models of nucleotide substitution for both
 concatenation and species tree reconstruction methods leads to the
 artefactual grouping of turtles and crocodiles, most likely because of
 substitution saturation at third codon positions. Relaxed molecular clock
 methods estimate the divergence between turtles and archosaurs around 255
 million years ago. The most recent common ancestor of living turtles,
 corresponding to the split between Pleurodira and Cryptodira, is estimated
 to have occurred around 157 million years ago, in the Upper Jurassic
 period. This is a more recent estimate than previously reported, and
 questions the interpretation of controversial Lower Jurassic fossils as
 being part of the extant turtles radiation. CONCLUSIONS: These results
 provide a phylogenetic framework and timescale with which to interpret the
 evolution of the peculiar morphological, developmental, and molecular
 features of turtles within the amniotes.
description: Chiari_amnios248genes_nt.nexNucleotides (codons) concatenation of 248 genes for 16 vertebrate taxa.Chiari_amnios248genes_aa.nexAmino acids concatenation of 248 genes for 16 vertebrate taxa.
DOI: 10.5061/dryad.m0r5qv24
title: Data from: Disruption of gene expression in hybrids of the fire ants Solenopsis invicta and Solenopsis richteri

description: Transcriptome analysis is a powerful tool for unveiling the distribution
 and magnitude of genetic incompatibilities between hybridizing taxa. The
 nature of such incompatibilities is closely associated with the
 evolutionary histories of the parental species and may differ across
 tissues and between the sexes. In eusocial insects, the presence of castes
 that experience divergent selection regimes may result in additional
 distinct patterns of caste-specific hybrid incompatibilities. We analyzed
 levels of expression of &gt;14,000 genes in two life stages of each
 caste and sex in the fire ants S. invicta and S. richteri and in their
 hybrids. We found strong contributions of both developmental stage and
 caste to gene expression patterns. Hybrid incompatibilities were
 surprisingly modest: only 32 genes were mis-expressed, indicating low
 levels of disruption in gene regulation in hybrids. The castes differed in
 numbers of mis-expressed genes, with males and workers each mis-expressing
 at least seven times as many genes as queens. Interestingly, homologues of
 many of the mis-expressed genes have been implicated in behavioral
 variation in Drosophila melanogaster. General expression profiles of
 hybrids were more similar to those of S. richteri than S. invicta,
 presumably because S. richteri trans-regulatory elements tend to be
 dominant to those of S. invicta and/or because there is an overall bias in
 the genetic composition of the hybrids towards S. richteri. Altogether,
 our results suggest that selection acting on each caste may contribute
 differently to interspecific divergence and speciation in this group of
 ants.
description: Gene expression levels
 in fire antsAnalysis of gene
 expression levels in workers, queens and males of the fire ants S.
 invicta, S. richteri and their hybrids, at the larval, pupal and adult
 stages (see also Ometto et al. 2011 Mol Biol Evol 28:1381–1392). Samples
 were collected in the field in 2005 and 2007. All collected colonies were
 returned to the laboratory and maintained in a rearing room under standard
 conditions. Gene expression of each sample (n=140) was measured through
 microarray hybridizations. Next, we estimated the relative expression of
 each clone for each node (caste/species/stage; n = 27), and the
 significance of the differential expression of such clones among nodes,
 using the Bayesian approach implemented in the program Bayesian Analysis
 of Gene Expression Levels (BAGEL; Meiklejohn and Townsend 2006 Brief
 Bioinformatics 6:318–330). Three-letter labels (one for each node)
 identify species (i = S. invicta; r = S. richteri; h = S. invicta X S.
 richteri), caste (W = workers; Q = queens; M = males), and developmental
 stage (l = larvae; p = pupae; a = adults).SupplementaryTableS2.txt.zip
DOI: 10.5061/dryad.5vp21b10
title: Data from: Accurate estimation of substitution rates with neighbour-dependent models in a phylogenetic context

description: Most models and algorithms developed to perform statistical inference from
 DNA data make the assumption that substitution processes affecting
 distinct nucleotide sites are stochastically independent. This assumption
 ensures both mathematical and computational tractability, but is in
 disagreement with observed data in many situations -- one well-known
 example being CpG dinucleotide hypermutability in mammalian genomes. In
 this paper, we consider the class of RN95+YpR substitution models, which
 allows neighbour-dependent effects -- including CpG hypermutability -- to
 be taken into account, through transitions between pyrimidine-purine
 dinucleotides. We show that it is possible to adapt inference methods
 originally developed under the assumption of independence between sites to
 RN95+YpR models, using a mathematically rigorous framework provided by
 specific structural properties of this class of models. We assess how
 efficient this approach is at inferring the CpG hypermutability rate from
 aligned DNA sequences. The method is tested on simulated data and compared
 against several alternatives; the results suggest that it delivers a high
 degree of accuracy at a low computational cost. We then apply our method
 to an alignment of ten DNA sequences from primate species. Model
 comparisons within the RN95+YpR class show the importance of taking into
 account neighbour-dependent effects. An application of the method to the
 detection of hypomethylated islands is discussed.
description: appendixENm001Sequence of the ENm001 region of the ENCODE Pilot Project (position 115,810,521 to position 117,687,946 on chromosome 7) from the hg19 version of the human genome, together with aligned sequences from nine other primate species (Chimpanzee, Gorilla, Orang-utan, Macaque, Baboon, Marmoset, Tarsier, Gray mouse lemur, Galago) as available from the Galaxy web tool (http://galaxy.psu.edu/).ENm001_ARPortion of ENm001 made from "Ancestral" repeated elements, according to the RepeatMasker annotations on the human sequence from the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) Pieces of the alignment corresponding to simple repeats, low complexity regions, members of the Alu family, and RNA elements that diverged less than 25% and L1 elements that diverged less than 20% from the reference RepBase sequence, were removed.
DOI: 10.5061/dryad.mb0cd1bs
title: Data from: Adaptive value of phenological traits in stressful environments: predictions based on seed production and laboratory natural selection

description: Phenological traits often show variation within and among natural
 populations of annual plants. Nevertheless, the adaptive value of
 post-anthesis traits is seldom tested. In this study, we estimated the
 adaptive values of pre- and post-anthesis traits in two stressful
 environments (water stress and interspecific competition), using the
 selfing annual species Arabidopsis thaliana. By estimating seed production
 and by performing laboratory natural selection (LNS), we assessed the
 strength and nature (directional, disruptive and stabilizing) of selection
 acting on phenological traits in A. thaliana under the two tested stress
 conditions, each with four intensities. Both the type of stress and its
 intensity affected the strength and nature of selection, as did genetic
 constraints among phenological traits. Under water stress, both
 experimental approaches demonstrated directional selection for a shorter
 life cycle, although bolting time imposes a genetic constraint on the
 length of the interval between bolting and anthesis. Under interspecific
 competition, results from the two experimental approaches showed
 discrepancies. Estimation of seed production predicted directional
 selection toward early pre-anthesis traits and long post-anthesis periods.
 In contrast, the LNS approach suggested neutrality for all phenological
 traits. This study opens questions on adaptation in complex natural
 environment where many selective pressures act simultaneously.
description: FITNESS_estimationLNS_phenotypes
DOI: 10.5061/dryad.996cr8f0
title: Data from: Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

description: Extensive phenotypic variation is a common feature among village chickens
 found throughout much of the developing world, and in traditional chicken
 breeds that have been artificially selected for traits such as plumage
 variety. We present here an assessment of traditional and village chicken
 populations, for fine mapping of Mendelian traits using genome-wide
 single-nucleotide polymorphism (SNP) genotyping while providing
 information on their genetic structure and diversity. Bayesian clustering
 analysis reveals two main genetic backgrounds in traditional breeds,
 Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage
 disequilibrium (LD) reveals useful LD (r2greater than or equal to0.3) in
 both traditional and village chickens at pairwise marker distances of
 ~10 Kb; while haplotype block analysis indicates a median block size of
 11–12 Kb. Association mapping yielded refined mapping intervals for duplex
 comb (Gga 2:38.55–38.89 Mb) and rose comb (Gga 7:18.41–22.09 Mb)
 phenotypes in traditional breeds. Combined mapping information from
 traditional breeds and Chilean village chicken allows the oocyan phenotype
 to be fine mapped to two small regions (Gga 1:67.25–67.28 Mb, Gga
 1:67.28–67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe
 pigmentation phenotype supports previous findings that the trait is
 sex-linked and polygenic. A critical assessment of the number of SNPs
 required to map simple traits indicate that between 90 and 110K SNPs are
 required for full genome-wide analysis of haplotype block
 structure/ancestry, and for association mapping in both traditional and
 village chickens. Our results demonstrate the importance and uniqueness of
 phenotypic diversity and genetic structure of traditional chicken breeds
 for fine-scale mapping of Mendelian traits in the species, with village
 chicken populations providing further opportunities to enhance mapping
 resolutions.
description: dryad_genoGenotype data following genotyping on the Illumina 57k SNP chip for chicken. Data is provided in a format compatible with GenABEL for R.dryad_phenoPhenotype file for the accompanying genotype file. Present in a format compatible for use with GenABEL for R.
DOI: 10.5061/dryad.6n3d6109
title: Data from: Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations

description: Two commonly used techniques for estimating the effect of genes on traits
 in wild populations are the candidate gene approach and quantitative
 genetic analyses. However, whether these two approaches measure the same
 underlying processes remains unresolved. Here we use these two methods to
 test if they are alternative or complementary approaches to understanding
 genetic variation in the timing of reproduction – a key trait involved in
 adaptation to climate change - in wild tit populations. Our analyses of
 the candidate gene Clock show weak correlates with timing variables in
 blue tits, but no association in great tits, confirming earlier results.
 Quantitative genetic analyses revealed very low levels of both direct
 (female) and indirect (male) additive genetic variation in timing traits
 for both species, in contrast to previous studies on these traits, and
 much lower than generally assumed. Hence, neither method suggests strong
 genetic effects on timing of breeding in birds and further work should
 seek to assess the generality of these conclusions. We discuss how
 differences in the genetic control of traits, species life-history and
 confounding environmental variables may determine how useful integrating
 these two techniques is to understand phenotypic variation in wild
 populations.
description: BTpedFull blue tit pedigree.
 This dataset comprises 3,090 individual blue tits and a total of 4,024
 breeding events between 2001 and 2008.GTpedFull great tit pedigree.
 Our full dataset for great tits comprises 12,724 individuals and a total
 of 19,395 breeding events between 1947 and 2008.
DOI: 10.5061/dryad.m6r6hc12
title: Data from: Is your phylogeny informative? Measuring the power of comparative methods

description: Phylogenetic comparative methods may fail to produce meaningful results
 when either the underlying model is inappropriate or the data contain
 insufficient information to inform the inference. The ability to measure
 the statistical power of these methods has become crucial to ensure that
 data quantity keeps pace with growing model complexity. Through
 simulations, we show that commonly applied model choice methods based on
 information criteria can have remarkably high error rates; this can be a
 problem because methods to estimate the uncertainty or power are not
 widely known or applied. Furthermore, the power of comparative methods can
 depend significantly on the structure of the data. We describe a Monte
 Carlo based method which addresses both of these challenges, and show how
 this approach both quantifies and substantially reduces errors relative to
 information criteria. The method also produces meaningful confidence
 intervals for model parameters. We illustrate how the power to distinguish
 different models, such as varying levels of selection, varies both with
 number of taxa and structure of the phylogeny. We provide an open-source
 implementation in the pmc (“Phylogenetic Monte Carlo”) package for the R
 programming language. We hope such power analysis becomes a routine part
 of model comparison in comparative methods.
description: pmcAn R package containing
 functions to perform the method described in the package, manual for these
 functions, and a vignette demonstrating how the package is used to
 replicate the results of this study.
DOI: 10.5061/dryad.vj86fq35
title: Data from: Response to selection on cold tolerance is constrained by inbreeding

description: The evolutionary potential of any given population is of fundamental
 importance for its longer-term prospects. Modern land-use practices often
 result in small and isolated populations, increasing extinction risk
 through reduced genetic diversity caused by inbreeding or drift.
 Concomitant genetic erosion may further interfere with a population’s
 evolutionary potential. In this study we investigate the consequences of
 inbreeding on evolutionary potential (the ability to increase cold
 resistance) in the tropical butterfly Bicyclus anynana. We applied
 artificial selection to chill-coma recovery time, starting from three
 levels of inbreeding (outbred control, one or two full-sib matings). Ten
 generations of selection produced highly divergent phenotypes, with the
 lines selected for increased cold tolerance showing by ca. 28% shorter
 recovery times after cold exposure relative to unselected controls.
 Correlated responses to selection in 10 life history and stress resistance
 traits were essentially absent. Inbred lines showed a weaker response to
 selection, thus indicating a reduced evolutionary potential. Inbreeding
 depression was still measurable in some traits after the course of
 selection. Traits more closely related to fitness showed a clear fitness
 rebound, suggesting a trait-specific impact of purging. Our findings have
 important implications for the longer-term survival of small populations
 in fragmented landscapes.
description: selectionSelection on cold tolerancereproductive traitsFecundity, egg hatching successdevelopmental traitslarval time, pupal time, pupal mass, growth ratecold and heat stresscold and heat tolerance after selectionlongevity and survivallongevity control, longevity after cold shock and survival after heat shock
DOI: 10.15468/zf263j
title: Davis & Elkins College Herbarium - Fungi

description: The Davis &amp; Elkins College Herbarium (DEWV) contains over 10,000 vouchers of macrofungi of West Virginia. This is an ongoing project documenting the distribution and diversity of macrofungi in the state. The project has yielded several new state records, including the discovery of species that have not previously been scientifically described. The herbarium also contains approximately 2,000 vascular plants.
DOI: 10.5061/dryad.4nr4cf37
title: Data from: Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria)

description: Disparity, or morphological diversity, is often quantified by evolutionary
 biologists investigating the macroevolutionary history of clades over
 geological timescales. Disparity is typically quantified using proxies for
 morphology, such as measurements, discrete anatomical characters, or
 geometric morphometrics. If different proxies produce differing results,
 then the accurate quantification of disparity in deep time may be
 problematic. However, despite this, few studies have attempted to examine
 disparity of a single clade using multiple morphological proxies. Here, as
 a case study for this question, we examine the disparity of the volant
 Mesozoic fossil reptile clade Pterosauria, an intensively studied group
 that achieved substantial morphological, ecological, and taxonomic
 diversity during their 145+ million year evolutionary history. We
 characterise broadscale patterns of cranial morphological disparity for
 pterosaurs for the first time using landmark-based geometric
 morphometrics, and make comparisons to calculations of pterosaur disparity
 based on alternative metrics. Landmark-based disparity calculations
 suggest that monofenestratan pterosaurs were more diverse cranially than
 basal non-monofenestratan pterosaurs (at least when the aberrant
 anurognathids are excluded), and that peak cranial disparity may have
 occurred in the Early Cretaceous, relatively late in pterosaur evolution.
 Significantly, our cranial disparity results are broadly congruent with
 those based on whole skeleton discrete character and limb proportion
 datasets, indicating that these divergent approaches document a consistent
 pattern of pterosaur morphological evolution. Therefore, pterosaurs
 provide an exemplar case demonstrating that different proxies for
 morphological form can converge on the same disparity signal, which is
 encouraging because often only one such proxy is available for extinct
 clades represented by fossils. Furthermore, mapping phylogeny into cranial
 morphospace demonstrates that pterosaur cranial morphology is
 significantly correlated with, and potentially constrained by,
 phylogenetic relationships.
description: Pterosaur_skull_MorphoJFoth_etal_Pterosaur_MorphoJ
DOI: 10.15468/dl.cu4rrr
title: Occurrence Download

description: A dataset containing 259271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation)",
 "TaxonKey is one of (Cistus clusii, Cistus creticus, Cistus ladanifer, Cistus laurifolius, Cistus monspeliensis, Cistus osbeckiifolius, Cistus salviifolius, Cistus populifolius, Cistus crispus, Cistus, Cistus purpureus, Cistus symphytifolius)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 259271 records from 538 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001645-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.