cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7248c
title: Data from: Haploid selection within a single ejaculate increases offspring fitness

description: An inescapable consequence of sex in eukaryotes is the evolution of a
 biphasic life cycle with alternating diploid and haploid phases. The
 occurrence of selection during the haploid phase can have far-reaching
 consequences for fundamental evolutionary processes including the rate of
 adaptation, the extent of inbreeding depression, and the load of
 deleterious mutations, as well as for applied research into fertilization
 technology. Although haploid selection is well established in plants,
 current dogma assumes that in animals, intact fertile sperm within a
 single ejaculate are equivalent at siring viable offspring. Using the
 zebrafish Danio rerio, we show that selection on phenotypic variation
 among intact fertile sperm within an ejaculate affects offspring fitness.
 Longer-lived sperm sired embryos with increased survival and a reduced
 number of apoptotic cells, and adult male offspring exhibited higher
 fitness. The effect on embryo viability was carried over into the second
 generation without further selection and was equally strong in both sexes.
 Sperm pools selected by motile phenotypes differed genetically at numerous
 sites throughout the genome. Our findings clearly link within-ejaculate
 variation in sperm phenotype to offspring fitness and sperm genotype in a
 vertebrate and have major implications for adaptive evolution.
description: F1_abnormal.embryosNumber of abnormal embryos measured in Experiment 1B.F1_fert success_Exp1AFertilisation success in Experiment 1A.F1_sperm velocity_unfiltered_Exp1ASperm velocity data from F1 males in Experiment 1A with no applied filters, i.e. raw data. For analyses, data with VCL&gt;45 were excluded as well as any measurements beyond 40s post-fertilisation.F1_sperm velocity_unfiltered_Exp1BSperm velocity data from F1 males in Experiment 1B with no applied filters, i.e. raw data. For analyses, data with VCL&gt;45 were excluded as well as any measurements beyond 40s post-fertilisation.F1_survival_fertilisation_Exp1BData on fertilisation success and embryo survival in Experiment 1B.F1_survival_fertilsation_Exp1AData on fertilisation success and embryo survival in Experiment 1A.F2_reprod.succData on fertilisation success, number of eggs and number of abnormal embryos in F2.post-ejac_ageingData on embryo survival in the post-ejaculation ageing experiment.pre-ejac_ageinData on embryo survival in the pre-ejaculation ageing experiment.Trade-off_sperm longevity_velocityData on velocity, swimming distance and longevity for individual sperm within an ejaculate of several males.
DOI: 10.5061/dryad.5vk6219
title: Data from: Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms

description: Comparative studies can provide powerful insights into processes that
 affect population divergence and thereby help to elucidate the mechanisms
 by which contemporary populations may respond to environmental change.
 Furthermore, approaches such as genotyping by sequencing (GBS) provide
 unprecedented power for resolving genetic differences among species and
 populations. We therefore used GBS to provide a genome-wide perspective on
 the comparative population structure of two palm genera, Washingtonia and
 Brahea, on the Baja California peninsula, a region of high landscape and
 ecological complexity. First, we used phylogenetic analysis to address
 taxonomic uncertainties among five currently recognised species. We
 resolved three main clades, the first corresponding to W. robusta and W.
 filifera, the second to B. brandegeei and B. armata, and the third to B.
 edulis from Guadalupe Island. Focusing on the first two clades, we then
 delved deeper by investigating the underlying population structure.
 Striking differences were found, with GBS uncovering four distinct
 Washingtonia populations and identifying a suite of loci associated with
 temperature, consistent with ecologically mediated divergence. By
 contrast, individual mountain ranges could be resolved in Brahea and few
 loci were associated with environmental variables, implying a more
 prominent role of neutral divergence. Finally, evidence was found for
 long-distance dispersal events in Washingtonia but not Brahea, in line
 with knowledge of the dispersal mechanisms of these palms including the
 possibility of human-mediated dispersal. Overall, our study demonstrates
 the power of GBS together with a comparative approach to elucidate
 markedly different patterns of genome-wide divergence mediated by multiple
 effectors.
description: Filtered
 SNPVCF file with two palm
 genera (Brahe and Washingtonia) merged. Only preliminary filtering was
 applied.all.taxamerged.filtered.recode.vcf
DOI: 10.5061/dryad.07934k0
title: Data from: Morphology of the petrosal and stapes of Borealestes (Mammaliaformes, Docodonta) from the Middle Jurassic of Skye, Scotland

description: \We describe, in unprecedented detail, the petrosals and stapes of the
 docodont Borealestes from the Middle Jurassic of Scotland, using high
 resolution μCT and phase‐contrast synchrotron imaging. We describe the
 inner ear endocast and the vascularized interior structure of the
 petrosal, and provide the first endocranial view of a docodontan petrosal.
 Our study confirms some similarities in petrosal and stapedial morphology
 with the better known Haldanodon of the Late Jurassic of Portugal,
 including: (1) the degree of curvature of the cochlea; (2) multiple
 features related to the highly pneumatized paroccipital region; (3) the
 shape of lateral trough, the fossa of the M. tensor tympani, and the ridge
 on the promontorium; (4) the round shape of the fenestra vestibuli; and
 (5) overall morphology of the stapes. But Borealestes differs from
 Haldanodon in having a bony ridge that separates the tympanic opening of
 the prootic canal, the secondary facial foramen and the hiatus Fallopii,
 from the fenestra vestibuli. We identify two new vascular structures: the
 anterior and posterior trans‐cochlear sinuses, which traverse the pars
 cochlearis around the cochlear nerve (VIII). These trans‐cochlear sinuses
 have not been observed in previous docodont specimens, and could be an
 autapomorphy of Borealestes, or apomorphic for this clade. We also
 establish the anatomical relationship of the circum‐promontorium plexus to
 the inner endocast. The high quality of our scans has made these
 structures visible for the first time.
description: NMS G.1992.47.121.1 R.
 petrosal reconstruction with StapesThe right petrosal of
 Borealestes, NMS G.1992.47.121.1 with broken fragments of promontorium
 reconstructed, and stapes placed in life position. Digital reconstruction
 based on synchrotron scan data. Part of more complete skeleton NMS
 G.1992.47.121.1.NMS
 G.1992.47.121.1_R.petrosal.recon.wStapes.stlNMS G.1992.47.121.1 R. petrosal of BorealestesThe right petrosal of Borealestes, NMS G.1992.47.121.1, as preserved. Digital reconstruction based on synchrotron scan data. Part of more complete skeleton NMS G.1992.47.121.1.NMS G.1992.47.121.1_R.petrosal.stlNMS G.1992.47.121.1 R.stapes of BorealestesThe right stapes of Borealestes, NMS G.1992.47.121.1. Digital reconstruction based on synchrotron scan data. Part of more complete skeleton NMS G.1992.47.121.1.NMS G.1992.47.121.1_R.stapes.stlNMS G.1992.47.121.2 L. petrosal reconstruction with StapesThe left petrosal of Borealestes, NMS G.1992.47.121.2, with fragments reconstructed into life position, and stapes in position. Digital reconstruction from microCT scan data. Part of more complete skeleton NMS G.1992.47.121.1.Left_petrosal_alltogether.stlNMS G.1992.47.121.2 L. petrosal of BorealestesThe left petrosal of Borealestes, NMS G.1992.47.121.2. Digital reconstruction from microCT scan data. Part of more complete skeleton NMS G.1992.47.121.1.Left_petrosal.stl
DOI: 10.5061/dryad.6tv5ct1
title: Data from: Diversification rates of the “Old Endemic” murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity

description: Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits
 increasing interspecific competition as it ecologically diversifies.
 Repeated colonization of a region by closely related taxa may cause
 similar effects as species within each lineage compete with one another.
 This may be particularly relevant for secondary colonists, which could
 experience limited diversification due to competition with earlier,
 incumbent colonists over evolutionary time. We tested the hypothesis that
 an incumbent lineage may diminish the diversification of secondary
 colonists in two speciose clades of Philippine “Old Endemic” murine
 rodents—Phloeomyini and Chrotomyini—on the relatively old oceanic island
 of Luzon. Although phylogenetic analyses confirm the independent,
 non-contemporaneous colonization of Luzon by the ancestors of these two
 clades, we found no support for arrested diversification in either.
 Rather, it appears that diversification of both clades resulted from
 constant-rate processes that were either uniform or favored the secondary
 colonists (Chrotomyini), depending on the method used. Our results suggest
 that ecological incumbency has not played an important role in determining
 lineage diversification among Luzon murines, despite sympatric occurrence
 by constituent species within each lineage, and a substantial head start
 for the primary colonists.
description: Rowsey et al. 2018 Data
 FilesArchive containing
 necessary files to conduct diversification analyses described in the
 study.
DOI: 10.5061/dryad.d8b93
title: Data from: Population genomic evidence for adaptive differentiation in the Baltic Sea herring

description: Detecting and estimating the degree of genetic differentiation among
 populations of highly mobile marine fish having pelagic larval stages is
 challenging because their effective population sizes can be large, and
 thus, little genetic drift and differentiation is expected in neutral
 genomic sites. However, genomic sites subject to directional selection
 stemming from variation in local environmental conditions can still show
 substantial genetic differentiation, yet these signatures can be hard to
 detect with low-throughput approaches. Using a pooled RAD-seq approach, we
 investigated genomewide patterns of genetic variability and
 differentiation within and among 20 populations of Atlantic herring in the
 Baltic Sea (and adjacent Atlantic sites), where previous low-throughput
 studies and/or studies based on few populations have found limited
 evidence for genetic differentiation. Stringent quality control was
 applied in the filtering of 1 791 254 SNPs, resulting in a final data set
 of 68 182 polymorphic loci. Clear differentiation was identified between
 Atlantic and Baltic populations in many genomic sites, while
 differentiation within the Baltic Sea area was weaker and geographically
 less structured. However, outlier analyses – whether including all
 populations or only those within the Baltic Sea – uncovered hundreds of
 directionally selected loci in which variability was associated with
 either salinity, temperature or both. Hence, our results support the view
 that although the degree of genetic differentiation among Baltic Sea
 herring populations is low, there are many genomic regions showing
 elevated divergence, apparently as a response to temperature- and
 salinity-related natural selection. As such, the results add to the
 increasing evidence of local adaptation in highly mobile marine organisms,
 and those in the young Baltic Sea in particular.
description: Nucleotide diversity in
 each of the 20 herring populationsNucleotide diversity in
 each populations was obtained using popoolation, and parameters used could
 be found in the readme.txt.PiDTheta.tar.gzFst distribution across the herring genomeFst distribution across the herring genome was obtained with popoolation2m, and parameters used could be found in readme.txt.Fst.tar.gzoutlier detectionOutlier detection with both empirical and BayeScan tests in both all of the 20 and just 17 Baltic Sea herring populations.outlier.tar.gzGenetic differentiation associated with environmental parametersDetecting association between Genetic differentiation and environmental parameters with Bayenv.Bayenv_results.tar.gzEnvironmental filesEnvironmental files used in Bayenv analysis.PCs.env.tar.gzGenetic distance metrices used for PCoAPCoA_genetic_distance_metrices.txtGenetic and geographic distance metrices used for IBDIBD.tar.gzreference sequences and SNP annotationref_seq_and_SNP_annotation.tar.gz
DOI: 10.5061/dryad.112s6pp
title: Data from: Reanalyzing the Palaeoptera problem - the origin of insect flight remains obscure

description: The phylogenetic relationships of the winged insect lineages – mayflies
 (Ephemeroptera), damselflies and dragonflies (Odonata), and all other
 winged insects (Neoptera) – are still controversial with three hypotheses
 supported by different datasets: Palaeoptera, Metapterygota and
 Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus
 on detecting confounding and alternative signal. In this context, we
 provide a framework to quantitatively evaluate and assess incongruent
 molecular phylogenetic signal inherent in phylogenomic datasets. Despite
 overall support for the Palaeoptera hypothesis, we also found considerable
 signal for Chiastomyaria, which is not easily detectable by standardized
 tree inference approaches. Analyses of the accumulation of signal across
 gene partitions showed that signal accumulates gradually. However, even in
 case signal only slightly supported one over the other hypothesis,
 topologies inferred from large datasets switch from statistically strongly
 supported Palaeoptera to strongly supported Chiastomyaria. From a
 morphological point of view, Palaeoptera currently appears to be the
 best-supported hypothesis; however, recent analyses were restricted to
 head characters. Phylogenetic approaches covering all organ systems
 including analyses of potential functional or developmental convergence
 are still pending so that the Palaeoptera problem has to be considered an
 open question in insect systematics.
description: Supplementary files of
 Simon et al. 2018 (ASD, Special Issue "Insect
 Flight")Supplementary files of
 Simon et al. 2018 (ASD, Special Issue "Insect
 Flight")Simon_et_al_2018_supplementary_files.tar.gz
DOI: 10.5061/dryad.8g470
title: Data from: Finding the right coverage: The impact of coverage and sequence quality on SNP genotyping error rates

description: Restriction-enzyme-based sequencing methods enable the genotyping of
 thousands of single nucleotide polymorphism (SNP) loci in non-model
 organisms. However, in contrast to traditional genetic markers, genotyping
 error rates in SNPs derived from restriction-enzyme-based methods remain
 largely unknown. Here, we estimated genotyping error rates in SNPs
 genotyped with double digest RAD sequencing from Mendelian
 incompatibilities in known mother-offspring dyads of Hoffman's
 two-toed sloth (Choloepus hoffmanni) across a range of coverage and
 sequence quality criteria, for both reference-aligned and de
 novo-assembled datasets. Genotyping error rates were more sensitive to
 coverage than sequence quality and low coverage yielded high error rates,
 particularly in de novo-assembled datasets. For example, coverage ≥5
 yielded median genotyping error rates of ≥0.03 and ≥0.11 in
 reference-aligned- and de novo-assembled datasets, respectively.
 Genotyping error rates declined to ≤0.01 in reference-aligned datasets
 with a coverage &gt;30, but remained &gt;0.04 in the de
 novo-assembled datasets. We observed approximately 10- and 13-fold
 declines in the number of loci sampled in the reference-aligned and de
 novo-assembled datasets when coverage was increased from &gt;5 to
 &gt;30 at quality score ≥30, respectively. Finally, we assessed the
 effects of genotyping coverage on a common population genetic application,
 parentage assignments, and showed that the proportion of incorrectly
 assigned maternities was relatively high at low coverage. Overall, our
 results suggest that the tradeoff between sample size and genotyping error
 rates be considered prior to building sequencing libraries, reporting
 genotyping error rates become standard practice, and that effects of
 genotyping errors on inference be evaluated in restriction-enzyme-based
 SNP studies.
description: SAS Source Code for
 estimating genotyping error ratesContains SAS script for
 estimating genotyping error rates using Mendelian
 incompatibilities.SNP_datasetsContains the SNP datasets used for analysis of genotyping error rates from reference alignment, reference alignment rxstacks, de novo assembly and de novo assembly rxstacks.
DOI: 10.5061/dryad.qv331
title: Data from: Jammed frictional tetrahedra are hyperstatic

description: We prepare packings of frictional tetrahedra with volume fractions ϕ
 ranging from 0.469 to 0.622 using three different experimental protocols
 under isobaric conditions. Analysis via x-ray microtomography reveals that
 the contact number Z grows with ϕ, but does depend on the preparation
 protocol. While there exist four different types of contacts in tetrahedra
 packings, our analysis shows that the edge-to-face contacts contribute
 about 50% of the total increase in Z. The number of constraints per
 particle C increases also with ϕ and even the loosest packings are
 strongly hyperstatic, i.e., mechanically overdetermined with C
 approximately twice the degrees of freedom each particle possesses.
description: Packings of tetrahedra
 particles at different packing fractions and preparation
 historyRaw data of tetrahedra
 packings is obtained by X-Ray-microtomography at 100mu/voxel. A
 specifically developed particle detection algorithm finds centers and
 orientations of the tetrahedra (assuming ideal tetrahedra). For more
 details on the particle detection, refer to the supplement of the
 publication.Tetrahedra_Packings_Neudecker_PRL_2013_Coordinates.tgz
DOI: 10.5061/dryad.v16ns
title: Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

description: The paleontological record chronicles numerous episodes of mass extinction
 that severely culled the Tree of Life. Biologists have long sought to
 assess the extent to which these events may have impacted particular
 groups. We present a novel method for detecting the impact of
 mass-extinction events on molecular phylogenies, even in the presence of
 tree-wide diversification-rate variation and in the absence of additional
 information from the fossil record. Our approach is based on an episodic
 stochastic-branching process model in which rates of speciation and
 extinction are constant between events. We model three types of events:
 (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous
 tree-wide shifts in extinction rate and (iii) instantaneous tree-wide
 mass-extinction events. Each type of event is modelled as an independent
 compound Poisson process (CPP), where the waiting times between events are
 exponentially distributed with event-specific rate parameters. The
 magnitude of each event is drawn from an event-specific prior
 distribution. Parameters of the model are then estimated in a Bayesian
 statistical framework using a reversible-jump Markov chain Monte Carlo
 algorithm. This Bayesian approach enables us to distinguish between
 tree-wide diversification-rate variation and mass-extinction events by
 specifying a biologically informed prior on the magnitude of
 mass-extinction events and empirical hyperpriors on the
 diversification-rate parameters. We demonstrate via simulation that this
 method has substantial power to detect the number of mass-extinction
 events and provides unbiased estimates of the timing of mass-extinction
 events, while exhibiting an appropriate (i.e. &lt;5%) false-discovery
 rate, even when background diversification rates vary. Finally, we provide
 an empirical demonstration of this approach, which reveals that conifers
 experienced a major episode of mass extinction ≈23 Ma. This new approach –
 the CPP on Mass-Extinction Times (CoMET) model – provides an effective
 tool for detecting the impact of mass-extinction events on molecular
 phylogenies, even when the history of those groups includes temporal
 variation in diversification rates and when the fossil history of those
 groups is poorly known.
description: CoMET data
 archiveThis data archive
 contains the scripts used to generate and analyze all the data in the
 accompanying manuscript (May et al., MEE), as well as the simulated data
 that were analyzed for that work. The archive is broken into five
 subdirectores, each corresponding to one set of simulations/analyses
 performed in the manuscript. The descriptions of each subdirectory are
 provided in the README.txt file.dryad_package.zip
DOI: 10.5061/dryad.g2066
title: Data from: The relative efficiency of modular and non-modular networks of different size

description: Most biological networks are modular but previous work with small model
 networks has indicated that modularity does not necessarily lead to
 increased functional efficiency. Most biological networks are large,
 however, and here we examine the relative functional efficiency of modular
 and non-modular neural networks at a range of sizes. We conduct a detailed
 analysis of efficiency in networks of two size classes: ‘small’ and
 ‘large’, and a less detailed analysis across a range of network sizes. The
 former analysis reveals that while the modular network is less efficient
 than one of the two non-modular networks considered when networks are
 small, it is usually equally or more efficient than both non-modular
 networks when networks are large. The latter analysis shows that in
 networks of small to intermediate size, modular networks are much more
 efficient that non-modular networks of the same (low) connective density.
 If connective density must be kept low to reduce energy needs for example,
 this could promote modularity. We have shown how relative
 functionality/performance scales with network size, but the precise nature
 of evolutionary relationship between network size and prevalence of
 modularity will depend on the costs of connectivity.
description: Data from Figures 1-5 of
 the main textData from Figures 1-5 of
 the main text, fitness across all 10000 generations of
 training.Figure1_5data.xlsxData from figure 7 of the main textData from figure 7 of the main textFigure7data.xlsxModel code used to produce data in Figs 1 and 2 of the main textModel code (Matlab) used to produce data in Figs 1 and 2 of the main text. The 20 subfolders correspond to the 20 reps in each figure. Simulations start at the 'run all' file. Folders also contain files unrelated to the simulation and used for other analyses.codefig1fig2.zip