cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3d23687
title: Data from: Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record

description: Simultaneously analysing morphological, molecular and stratigraphic data
 suggests a potential resolution to a major remaining inconsistency in
 crocodylian evolution. The ancient, long-snouted thoracosaurs have always
 been placed near the Indian gharial Gavialis, but their antiquity (ca 72
 Ma) is highly incongruous with genomic evidence for the young age of the
 Gavialis lineage (ca 40 Ma). We reconcile this contradiction with an
 updated morphological dataset and novel analysis, and demonstrate that
 thoracosaurs are an ancient iteration of long-snouted stem crocodylians
 unrelated to modern gharials. The extensive similarities between
 thoracosaurs and Gavialis are shown to be an almost ‘perfect storm’ of
 homoplasy, combining convergent adaptions to fish-eating, as well
 resemblances between genuinely primitive traits (thoracosaurs) and
 atavisms (Gavialis). Phylogenetic methods that ignore stratigraphy
 (parsimony and undated Bayesian methods) are unable to tease apart these
 similarities and invariably unite thoracosaurs and Gavialis. However,
 tip-dated Bayesian approaches additionally consider the large temporal gap
 separating ancient (thoracosaurs) and modern (Gavialis) iterations of
 similar long-snouted crocodyliforms. These analyses robustly favour a
 phylogeny which places thoracosaurs basal to crocodylians, far removed
 from modern gharials, which accordingly are a very young radiation. This
 phylogenetic uncoupling of ancient and modern gharial-like crocs is more
 consistent with molecular clock divergence estimates, and also the bulk of
 the crocodylian fossil record (e.g. all unequivocal gharial fossils are
 very young). Provided that the priors and models attribute appropriate
 relative weights to the morphological and stratigraphic signals—an issue
 that requires investigation—tip-dating approaches are potentially better
 able to detect homoplasy and improve inferences about phylogenetic
 relationships, character evolution and divergence dates.
description: DataAndResultFilesThis is a zipped file containing (1) The stratigraphic dates and sources in folder TableS1-StratAges (2) the executable PAUP, MrBayes and BEAST files for the following analyses: Morphology Only Morphology and DNA Morphology and DNA (additional sensitivity analyses) Parsimony bootstrap partition frequencies (for all partitions, not just those found in the bootstrap consensus). The BEAST files were written for BEAST 1.8.2 and will need slight edits to run on BEAST 1.8.3 onwards. We have left the files “as is” as these represent the exact files and BEAST version used.Appendix1_includingTableS2Appendix 1 CONSTRUCTION OF THE MORPHOLOGICAL MATRIXAppendix2APPENDIX 2: PHYLOGENETIC ANALYSES AND RESULTSFigsS1-9_andCaptionsFigures S1 to S9 with captions
DOI: 10.5061/dryad.m17c8
title: Data from: Biostratigraphy and geometric morphometrics of conchostracans (Crustacea, Branchiopoda) from the Late Triassic fissure deposits of Cromhall Quarry, UK

description: The enigmatic fissure deposits of south-eastern England and southern Wales
 are famous for their unique assemblage of Late Triassic vertebrates,
 although their age is contentious. While recent studies of palynomorphs
 have dated some as Rhaetian, their conchostracan (Crustacea, Branchiopoda)
 assemblages have not been described in detail nor used in biostratigraphy.
 We find that species determination of British Late Triassic conchostracans
 requires detailed observations of size, shape and ornamentation. We
 provide evidence that although Euestheria brodieana is invariably smaller
 than E. minuta, with some slight differences in carapace ornamentation,
 the traditional view that they are very similar is upheld. The use of
 conchostracans as a biostratigraphical tool is here tested by application
 to the British Triassic fissures at Cromhall quarry where the usual
 stratigraphical evidence provided by superposition is absent. We find no
 distinction between conchostracans from bedded Rhaetian deposits of the UK
 and specimens collected from the fissure deposits of Cromhall Quarry,
 Gloucestershire, supporting a late Rhaetian age for these deposits.
description: Data files 1-3,
 5-8Specimen and data
 listsData_files_1-3_5-8.xlsxData file 4Supplementary figures
DOI: 10.5061/dryad.48r5h
title: Data from: Trophic specialisation drives morphological evolution in sea snakes

description: Viviparous sea snakes are the most rapidly speciating reptiles known, yet
 the ecological factors underlying this radiation are poorly understood.
 Here, we reconstructed dated trees for 75% of sea snake species and
 quantified body shape (forebody relative to hindbody girth), maximum body
 length and trophic diversity to examine how dietary specialisation has
 influenced morphological diversification in this rapid radiation. We show
 that sea snake body shape and size are strongly correlated with the
 proportion of burrowing prey in the diet. Specialist predators of
 burrowing eels have convergently evolved a ‘microcephalic’ morphotype with
 dramatically reduced forebody relative to hindbody girth and intermediate
 body length. By comparison, snakes that predominantly feed on gobies are
 generally short-bodied and small headed, but there is no evidence of
 convergent evolution. The eel specialists also exhibit faster rates of
 size and shape evolution compared to all other sea snakes, including those
 that feed on burrowing gobies. Our results suggest that trophic
 specialisation to particular burrowing prey (eels) has invoked strong
 selective pressures that manifest as predictable and rapid morphological
 changes. Further studies are needed to examine the genetic and
 developmental mechanisms underlying these dramatic morphological changes
 and assess their role in sea snake speciation.
description: Analysis R
 scriptR script for the
 analyses performed in the paper.sea snake
 analyses.R47 Species phylogeny
 x500Nexus file containing
 500 sample trees of 47 speciessea snake 500
 trees.nex47 Species phylogeny
 maximum clade credibility.tre file containing
 maximum credibility tree for 47 speciessea snake MCC
 treeTrait
 dataMorphological and
 dietary data for 47 speciestrait
 data.csvSea snake diet
 dataComprehensive summary of
 dietary data for 42 species of sea snakessea snake diet
 data.xls
DOI: 10.5061/dryad.821c3j3
title: Data from: New remains of the aquatic turtle Hydromedusa casamayorensis (Pleurodira, Chelidae) from the middle Eocene of Patagonia: taxonomic validation and phylogenetic relationships

description: Twenty- seven new specimens recovered from lower levels of the Sarmiento
 Formation (Casamayoran SALMA, middle Eocene) in the ¨Cañadón Hondo¨ area,
 Chubut (Argentina), bring new information on the Palaeogene long-necked
 chelid Hydromedusa casamayorensis.The discovery of cranial and postcranial
 remains allows a complete description of the only known extinct species of
 the genus Hydromedusa recognizing diagnostic characters that revalidate
 the taxonomic status of this species. Hydromedusa casamayorensis is
 incorporated into a cladistic framework of chelid turtles. The
 unconstrained and constrained phylogenetic analyses recovered H.
 casamayorensis as a sister taxon of Hydromedusa maximiliani plus H.
 tectifera. A Danian age is proposed at least for the origin of the
 Hydromedusa clade, while a Late Cretaceous is suggested for the age of the
 split from the Yaminuechelys clade. Great differences in size are
 documented for H. casamayorensis based on the various specimens recovered
 from this study. The osteohistological study in H. casamayorensis and H.
 tectifera shows similarities in the internal cortex and cancellous bone of
 both taxa, but some differences are observed in the external cortex of H.
 casamayorensis (e.g. a parallel fibered bone on the more external surface
 of this cortex).
description: Appendix
 S1Appendix
 S2Appendix
 S1.pdfAppendix S3
 (2)Appendix
 S4Appendix
 S5Appendix
 S6
DOI: 10.5061/dryad.gb90p1c
title: Data from: The pyriform egg of the Common Murre (Uria aalge) is more stable on sloping surfaces

description: The adaptive significance of avian egg shape is a long-standing problem in
 biology. For many years, it was widely believed that the pyriform shape of
 the Common Murre (Uria aalge) egg allowed it to either “spin like a top”
 or “roll in an arc,” thereby reducing its risk of rolling off the breeding
 ledge. There is no evidence in support of either mechanism. Two recent
 alternative hypotheses suggest that a pyriform egg confers mechanical
 strength and minimizes the risk of dirt contamination of the blunt end. We
 present a new hypothesis: that the Common Murre egg's pyriform shape
 confers stability on the breeding ledge, thus reducing the chance that it
 will begin to roll. We tested this hypothesis by measuring the stability
 of Common Murre and Razorbill (Alca torda) eggs of different shapes on
 slopes of 20°, 30°, and 40° above the horizontal. Common Murre eggs were
 more stable, and easier to stabilize, than the more elliptical Razorbill
 eggs. Within Common Murre eggs, more pyriform eggs were more stable. From
 a fitness perspective, the stability of the Common Murre egg on a slope
 seems likely to confer an advantage and thus may be a strong force of
 natural selection favoring the pyriform shape.
description: READMEstabilityRcodeR notebook used to generate the Statistical SupplementStatistical SupplementThis is the Rcode and output from that code for the statistical analyses reported in this paper.StatisticalSupplement.pdfComparing stability on different slopesThis is the dataset from slope trials done by Jamie Thompson (JET) alone, to assess his ability to stabilize Razorbill and Common Murre eggs of different shapes on flat, sandpaper covered slopes of 20°, 30° and 40° above the horizontal.stability.csvStatic slopes experiment comparing participantsThis is a dataset to compare the ability of 12 naive subjects with a potentially biased subject (Jamie E Thompson; JET) in their ability to balance Razorbill and Commmon Murre eggs on surfaces with different slopes.studentdata.csvData from moving slopes experimentThis is the dataset from experiments where each egg was placed on a surface then the slope gradually increased until the egg began to roll.dynamictrials.csv
DOI: 10.5061/dryad.tb25q
title: Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease

description: Genome-wide association studies are widely used to identify "disease
 genes" conferring resistance/susceptibility to infectious diseases.
 Using a combination of mathematical models and simulations we demonstrate
 that genetic interactions between hosts and parasites (GxG interactions)
 can drastically affect the results of these association scans and hamper
 our ability to detect genetic variation in susceptibility. When hosts and
 parasites coevolve, these GxG interactions often make Genome-wide
 association studies unrepeatable over time or across host populations.
 Reanalyzing previously published data on Daphnia magna susceptibility to
 infection by Pastueria ramosa, we identify genomic regions consistent with
 GxG interactions. We conclude by outlining possible avenues for designing
 more powerful and more repeatable association studies.
description: CoGWAS_SupplementMathematica notebook deriving analytical models, numerical simulations, and for producing figures 1-4 and S1.CoGWAS_SupplementCDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1.CoGWAS_SupplementPDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1.Fig. S1 - Matching-alleles modelRow 1: Estimated allelic effects as a function of pathogen allele frequency (black: \beta_0, solid red: \beta_{Hi}, dashed red: \beta_{H1,H2}, blue \beta_{Pi}, blue dashed: \beta_{P1,P2}, purple dashed: \beta_{Hi,Pj}). Row 2: Variation explained by host additive effects only (solid red), host additive and epistatic effects (dashed red), host and pathogen additive and epistatic effects (dashed blue, overlaps with dashed red), and a full host pathogen model (dashed purple).FigS1.gifFig. S2 - GWAS of *Daphnia magna* susceptibilityGenetic associations of each SNP with C1 (red circles), C19 (blue, squares), and "mixed'' susceptibility (green, triangles). Here, the mixed case was obtained by taking each host clone and randomly choosing the data upon exposure to C1 or C19 (not both, as incorporated in the overall analysis in figure 5). Hence each SNP is represented three times, once for each genome wide scan. Note that closely linked SNPs often overlap with one another and are not all individually visible. Significant SNPs are shown in colour while those below the log-likelihood of 2 threshold or that are not clustered within a 10cM region of three other significant SNPs are shown in grey. The 10 linkage groups are delineated by vertical dashed lines.FigS2.gif
DOI: 10.5061/dryad.gv144d5
title: Data from: Automated morphological feature assessment for zebrafish embryo developmental toxicity screens

description: Detection of developmental phenotypes in zebrafish embryos typically
 involves a visual assessment and scoring of morphological features by an
 individual researcher. Subjective scoring could impact results and be of
 particular concern when phenotypic effect patterns are also used as a
 diagnostic tool to classify compounds. Here we introduce a quantitative
 morphometric approach based on image analysis of zebrafish embryos. A
 software called FishInspector was developed to detect morphological
 features from images collected using an automated system to position
 zebrafish embryos. The analysis was verified and compared with visual
 assessments of three participating laboratories using three known
 developmental toxicants (methotrexate, dexamethasone and topiramate) and
 two negative compounds (loratadine and glibenclamide). The quantitative
 approach exhibited higher sensitivity and made it possible to compare
 patterns of effects with the potential to establish a grouping and
 classification of developmental toxicants. Our approach improves the
 robustness of phenotype scoring and reliability of assay performance and,
 hence, is anticipated to improve the predictivity of developmental
 toxicity screening using the zebrafish embryo.
description: KNIME workflow to
 evaluate morphological features using the FishInspector
 softwareThis workflow allows to
 measure morphological features of zebrafish larvae (48hpf or 96 hpf) using
 the output file (json format) from the FishInspector software. The file
 should be imported to the KNIME open source analytical
 platform.FishInspector
 VAST_ToxSci.zip.knwfHeart rate analysis
 zebrafishThis workflow allows to
 measure the heart frequence of zebrafih larvae from videos obtained with
 the VAST BioImager system. The workflow should be imported to the KNIME
 open analytical platform.Heart rate
 analysis_KNIME.zip.knwfKnime workflow to rotate
 and crop zebrafish imagesThis workflow
 automatically rotates, crop the images and draws a virtual capillary based
 on a ImageJ macro.The workflow can easily be adapted to accommodate
 different image properties depending on the source of the image (e.g.
 intensity, contrast).Rotate and crop
 image.knwfOutput raw
 dataContains the output data
 (morphometric parameters, mean traveled distance -LMR- and heart rate)
 obtained from image analysis from embryos exposed to the chemicals as
 described in the article.Raw_data_allchemicals.xlsx
DOI: 10.5061/dryad.72594
title: Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds

description: The nearly neutral theory, which proposes that most mutations are
 deleterious or close to neutral, predicts that the ratio of nonsynonymous
 over synonymous substitution rates (dN/dS), and potentially also the ratio
 of radical over conservative amino acid replacement rates (Kr/Kc), are
 negatively correlated with effective population size. Previous empirical
 tests, using life-history traits (LHT) such as body-size or
 generation-time as proxies for population size, have been consistent with
 these predictions. This suggests that large-scale phylogenetic
 reconstructions of dN/dS or Kr/Kc might reveal interesting
 macroevolutionary patterns in the variation in effective population size
 among lineages. In this work, we further develop an integrative
 probabilistic framework for phylogenetic covariance analysis introduced
 previously, so as to estimate the correlation patterns between dN/dS,
 Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc
 displays stronger and more stable correlations with LHT than does dN/dS,
 which we interpret as a greater robustness of Kr/Kc, compared with dN/dS,
 the latter being confounded by the high saturation of the synonymous
 substitution rate in mitochondrial genomes. The correlation of Kr/Kc with
 LHT was robust when controlling for the potentially confounding effects of
 nucleotide compositional variation between taxa. The positive correlation
 of the mitochondrial Kr/Kc with LHT is compatible with previous reports,
 and with a nearly neutral interpretation, although alternative
 explanations are also possible. The Kr/Kc model was finally used for
 reconstructing life-history evolution in birds and mammals. This analysis
 suggests a fairly large-bodied ancestor in both groups. In birds,
 life-history evolution seems to have occurred mainly through size
 reduction in Neoavian birds, whereas in placental mammals, body mass
 evolution shows disparate trends across subclades. Altogether, our work
 represents a further step toward a more comprehensive phylogenetic
 reconstruction of the evolution of life-history and of the
 population-genetics environment.
description: Dataset from Nabholz,
 Uwimana and Lartillot 2013Dataset_Nabholz_Uwimana_Lartillot_2013.tar.gz
DOI: 10.5061/dryad.v2t5n
title: Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels

description: Tropical forests of Central and South America represent hotspots of
 biological diversity. Tree squirrels of the tribe Sciurini are an
 excellent model system for the study of tropical biodiversity as these
 squirrels disperse exceptional distances, and after colonizing the tropics
 of the Central and South America, they have diversified rapidly. Here, we
 compare signals from DNA sequences with morphological signals using
 pictures of skulls and computational simulations. Phylogenetic analyses
 reveal step-wise geographic divergence across the Northern Hemisphere. In
 Central and South America, tree squirrels form two separate clades, which
 split from a common ancestor. Simulations of ancestral distributions show
 western Amazonia as the epicenter of speciation in South America. This
 finding suggests that wet tropical forests on the foothills of Andes
 possibly served as refugia of squirrel diversification during Pleistocene
 climatic oscillations. Comparison of phylogeny and morphology reveals one
 major discrepancy: Microsciurus species are a single clade morphologically
 but are polyphyletic genetically. Modeling of morphology–diet
 relationships shows that the only group of species with a direct link
 between skull shape and diet are the bark-gleaning insectivorous species
 of Microsciurus. This finding suggests that the current designation of
 Microsciurus as a genus is based on convergent ecologically driven changes
 in morphology.
description: SI_figures_Pecnerova_etalSI_tables_Pecnerova_etalSI_legends_Pecnerova_2015_SystBiol
DOI: 10.5061/dryad.650c5
title: Data from: Body size as a driver of scavenging in theropod dinosaurs

description: Theropod dinosaurs dominated Earth's terrestrial ecosystem as a
 diverse group of predators for over 160 million years, yet little is known
 about their foraging ecology. Ranging from the chicken-sized Microraptor
 up to the whale-sized Giganotosaurus, maintaining a balanced energy budget
 presented a major challenge in the face of intense competition and the
 demands of ontogenetic growth. Facultative scavenging, a behaviour present
 in almost all modern predators, may have been an important behaviour used
 to supplement energetically expensive lifestyles. By using agent-based
 models based on the allometric relationship between size and foraging
 behaviours, we show that theropods between 27 kg and 1044 kg would have
 gained a significant energetic advantage over individuals at both the
 small and large extremes of theropod body mass through their scavenging
 efficiency. These results were robust to rate of competition, primary
 productivity, and detection distance. Our models demonstrate the potential
 importance of facultative scavenging in theropods and the role of body
 size in defining its prevalence in Mesozoic terrestrial systems.
description: IBM_Energy_inputsEnergy input from scavenging as determined from Individual based model run in net logoTheropod Scavenger ModelNet logo model of theropod scavenging for main model.Scavenger Model.nlogo
DOI: 10.5061/dryad.h5r18
title: Data from: On the comparison of the strength of morphological integration across morphometric datasets

description: Evolutionary morphologists frequently wish to understand the extent to
 which organisms are integrated, and whether the strength of morphological
 integration among subsets of phenotypic variables differ among taxa or
 other groups. However, comparisons of the strength of integration across
 datasets are difficult, in part because the summary measures that
 characterize these patterns (RV and rPLS) are dependent both on sample
 size and on the number of variables. As a solution to this issue we
 propose a standardized test statistic (a z-score) for measuring the degree
 of morphological integration between sets of variables. The approach is
 based on a partial least squares analysis of trait covariation, and its
 permutation-based sampling distribution. Under the null hypothesis of a
 random association of variables, the method displays a constant expected
 value and confidence intervals for datasets of differing sample sizes and
 variable number, thereby providing a consistent measure of integration
 suitable for comparisons across datasets. A two-sample test is also
 proposed to statistically determine whether levels of integration differ
 between datasets, and an empirical example examining cranial shape
 integration in Mediterranean wall lizards illustrates its use. Some
 extensions of the procedure are also discussed.
description: Error Rate Simulation
 CodeR
 script used to evaluate the statistical error rates of the z-score
 methodevolution.2016.adams.collyer.error.rates.rSimulation ResultsRaw Data from simulation used to evaluate method's statistical error ratesrun.results.RdataR-PLS behaviorR script used to examine the behavior of R-PLS and other statistical measures as a function of sample size and number of variablesevolution.2016.adams.collyer.r.pls.trends.r