cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4d0d2
title: Data from: Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds

description: Birds are the most diverse living tetrapod group and are a model of
 large-scale adaptive radiation. Neontological studies suggest a radiation
 within the avian crown group, long after the origin of flight. However,
 deep time patterns of bird evolution remain obscure because only limited
 fossil data have been considered. We analyse cladogenesis and limb
 evolution on the entire tree of Mesozoic theropods, documenting the
 dinosaur–bird transition and immediate origins of powered flight. Mesozoic
 birds inherited constraints on forelimb evolution from non-flying
 ancestors, and species diversification rates did not accelerate in the
 earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit
 both phenotypic release of the hindlimb and increased diversification
 rates, unparalleled in magnitude at any other time in the first 155 Myr of
 theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group
 birds was enabled by restructuring of the terrestrial locomotor module,
 which represents a key innovation. Our results suggest two phases of
 radiation in Avialae: with the Cretaceous diversification overwritten by
 extinctions of stem-group birds at the Cretaceous–Palaeogene boundary, and
 subsequent diversification of the crown group. Our findings illustrate the
 importance of fossil data for understanding the macroevolutionary
 processes generating modern biodiversity.
description: Benson & Choiniere
 2013 data package
DOI: 10.5061/dryad.gr1qp
title: Data from: Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage

description: Large-scale adaptive radiations might explain the runaway success of a
 minority of extant vertebrate clades. This hypothesis predicts, among
 other things, rapid rates of morphological evolution during the early
 history of major groups, as lineages invade disparate ecological niches.
 However, few studies of adaptive radiation have included deep time data,
 so the links between extant diversity and major extinct radiations are
 unclear. The intensively studied Mesozoic dinosaur record provides a model
 system for such investigation, representing an ecologically diverse group
 that dominated terrestrial ecosystems for 170 million years. Furthermore,
 with 10,000 species, extant dinosaurs (birds) are the most speciose living
 tetrapod clade. We assembled composite trees of 614–622 Mesozoic
 dinosaurs/birds, and a comprehensive body mass dataset using the scaling
 relationship of limb bone robustness. Maximum-likelihood modelling and the
 node height test reveal rapid evolutionary rates and a predominance of
 rapid shifts among size classes in early (Triassic) dinosaurs. This
 indicates an early burst niche-filling pattern and contrasts with previous
 studies that favoured gradualistic rates. Subsequently, rates declined in
 most lineages, which rarely exploited new ecological niches. However,
 feathered maniraptoran dinosaurs (including Mesozoic birds) sustained
 rapid evolution from at least the Middle Jurassic, suggesting that these
 taxa evaded the effects of niche saturation. This indicates that a long
 evolutionary history of continuing ecological innovation paved the way for
 a second great radiation of dinosaurs, in birds. We therefore demonstrate
 links between the predominantly extinct deep time adaptive radiation of
 non-avian dinosaurs and the phenomenal diversification of birds, via
 continuing rapid rates of evolution along the phylogenetic stem lineage.
 This raises the possibility that the uneven distribution of biodiversity
 results not just from large-scale extrapolation of the process of adaptive
 radiation in a few extant clades, but also from the maintenance of
 evolvability on vast time scales across the history of life, in key
 lineages.
description: Benson et al. dinosaur
 body mass
DOI: 10.5061/dryad.q9533
title: Data from: In situ measurements of animal morphological features; a non-invasive method

description: 1) Measurements of morphological features are important for ecological
 studies, especially on free-ranging wild animal species. Conventionally,
 specimens either dead or in captivity are used for morphometric studies,
 which is difficult in the case of wild species for several reasons.
 Capturing would be even futile when research questions are relating to
 issues such as prey size selection or estimation of intake rate in under
 field conditions, where in situ morphometric measurements are inevitable.
 Remotely estimating morphometric features via, avian bill and head length
 are always laden with wide variances. Hence, we developed this technique
 for in situ measurements of animal morphology through digital photographs.
 2) This non-invasive novel method for in situ estimation of individuals’
 morphometric measurements uses digital photographs' metadata. We
 extracted the metadata (field of view, focal length, subject-distance
 etc.,) in Exchangeable Image File Format (EXIF) from digital images using
 freely available software, and the unknown sizes were estimated from each
 image. Cardboard (fish) models were, at first, used to estimate the
 accuracy of measurements comparing actual and estimated values, and the
 same protocol was repeated on museum specimens (bird). Finally, we checked
 the repeatability of this method under field conditions using free ranging
 Chickens (Gallus gallus domesticus). The results under different
 conditions were subjected to rigorous statistical testing. 3) Upon
 comparing the actual with estimated values, obtained from three distinct
 types of objects (1. Cardboard model, 2. Museum specimens, and 3. Live
 birds under field conditions), variations were found non-significant
 affirming the assumption that actual value (Y) = estimated value (X) with
 inconsequential variance of the Y from X. Moreover, both the relative and
 absolute errors between the actual and estimated values were so low,
 indicating that this method yielded neither over-estimation nor
 under-estimation. 4) The advantage of this non-invasive method is that it
 could generate reasonably accurate morphometric measurements at a
 relatively low cost for routine morphometric works in field conditions. We
 envisage significant utility of this non-invasive technique in different
 fields of science such as biology, morphology, ecology, evolution,
 wildlife, conservation science, agriculture, forensics and engineering
 design.
description: Data sets Mahen In situ
 14SEP2017It includes data on (a)
 actual and estimated subject-distance for all the 29 images of cardboard
 model fish in the first worksheet. (b) EXIF information for all the 29
 images in the second worksheet.
DOI: 10.5061/dryad.80r64
title: Data from: Individual consistency of long-distance migration in a songbird: significant repeatability of autumn route, stopovers and wintering sites but not in timing of migration

description: Through new tracking techniques, data on timing and routes of migration in
 long-distance migrant birds are accumulating. However, studies of the
 consistency of migration of the same individuals between years are still
 rare in small-sized passerine birds. This type of information is important
 to understand decisions and migration abilities at the individual level,
 but also for life history theory, for understanding carry over effects
 between different annual cycle stages and for conservation. We analysed
 individual repeatability of migration between years in great reed warblers
 Acrocephalus arundinaceus; a medium-sized European songbird migrating to
 sub-Saharan Africa. In seven males, with geolocator data from 2–4 yr per
 bird, we found low to moderate (non significant) repeatability in timing
 of migration parameters (R ≤ 0.41), but high (and significant)
 repeatability for most spatial parameters, i.e. autumn route (R = 0.64)
 and stopover sites (R = 0.59–0.87) in Europe, and wintering sites (R =
 0.77–0.99) in sub-Saharan Africa. This pattern of high spatial but low
 temporal within-individual repeatability of migration between years
 contrasts other tracking studies of migrating birds that generally have
 found consistency in timing but flexibility in routes. High spatial
 consistency of migration in the great reed warbler may be due to it being
 a specialist in wetlands, an unevenly distributed habitat, favouring a
 strategy of recurrence at previously visited sites. Low temporal
 repeatability may be caused by large between-year variation in carry-over
 effects from the breeding season, high flexibility in decision rules
 during migration or high sensitivity to environmental factors (weather,
 wind) during migration.
description: IndividualConsistencyRepeatabilityFile1This file contains the information for the repeatability analyses and calculations of within-individual and between-individual means, variance, SD and distances. In the excel file, 'Sheet 1' contains data, and the 'info' sheet contains explanations for the column headings of the data sheet.IndividualConsistencyMapsDataFile2This file contains the basic information underlying the maps of migration stopovers, routes and wintering sites (spatial and temporal parameters). In the excel file, ‘Sheet 1’ contains data, and the ‘info’ sheet contains explanations for the column headings of the data sheet.IndividualConsistencyRepeatErrorKvmDataFile3This file contains information to measure the ‘on the bird’ measurement error (mean and SE) for the same logger when estimating the longitude and latitude for the same site (the breeding site Kvismaren) in two consecutive years (autumn year 1 versus spring year 2). In the excel file, ‘Sheet 1’ contains data, and the ‘info’ sheet contains explanations for the column headings of the data sheet.
DOI: 10.5061/dryad.k0n77
title: Data from: Hidden genetic variation in the germline genome of Tetrahymena thermophila

description: Genome architecture varies greatly among eukaryotes. This diversity may
 profoundly affect the origin and maintenance of genetic variation within a
 population. Ciliates are microbial eukaryotes with unusual genome
 features, such as separation of germline and somatic genomes within a
 single cell and amitotic division. These features have previously been
 proposed to increase the rate of molecular evolution in these species.
 Here, we assessed the fitness effects of genetic variation in the two
 genomes of natural isolates of the ciliate Tetrahymena thermophila. We
 find more extensive genetic variation in fitness in the
 transcriptionally-silent germline genome than in the expressed somatic
 genome. Surprisingly, this variation is not primarily deleterious, but has
 both beneficial and deleterious effects. We conclude that Tetrahymena
 genome architecture allows for the maintenance of genetic variation that
 would otherwise be eliminated by selection. We consider the effect of
 selection on the two genomes and the impacts of reproductive strategies
 and the mechanism of sex determination on the structure of this variation.
description: Dimond_Zufall_data_dryad3Raw measurements and categorical data used for all analyses in manuscript# JEB12868.
DOI: 10.5061/dryad.7kd15
title: Data from: Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

description: Genotyping errors are present in almost all genetic data and can affect
 biological conclusions of a study, particularly for studies based on
 individual identification and parentage. Many statistical approaches can
 incorporate genotyping errors, but usually need accurate estimates of
 error rates. Here, we used a new microsatellite data set developed for
 brown rockfish (Sebastes auriculatus) to estimate genotyping error using
 three approaches: (i) repeat genotyping 5% of samples, (ii) comparing
 unintentionally recaptured individuals and (iii) Mendelian inheritance
 error checking for known parent–offspring pairs. In each data set, we
 quantified genotyping error rate per allele due to allele drop-out and
 false alleles. Genotyping error rate per locus revealed an average overall
 genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007
 and 0.008 per allele error rate) from replicate genotypes, known
 parent–offspring pairs and unintentionally recaptured individuals,
 respectively. By direct-count error estimates, the recapture and known
 parent–offspring data sets revealed an error rate four times greater than
 estimated using repeat genotypes. There was no evidence of correlation
 between error rates and locus variability for all three data sets, and
 errors appeared to occur randomly over loci in the repeat genotypes, but
 not in recaptures and parent–offspring comparisons. Furthermore, there was
 no correlation in locus-specific error rates between any two of the three
 data sets. Our data suggest that repeat genotyping may underestimate true
 error rates and may not estimate locus-specific error rates accurately. We
 therefore suggest using methods for error estimation that correspond to
 the overall aim of the study (e.g. known parent–offspring comparisons in
 parentage studies).
description: Parent-offspring
 dataset_for dryadincludes microsatellite
 data for four known mother-offspring familiesRecapture dataset_for
 dryadincludes microsatellite
 data for recaptures, end of file quantifies #
 comparisonsRepeat Genotypes
 dataset_for dryadincludes microsatellite
 data for repeated samples
DOI: 10.5061/dryad.h0g89
title: Data from: Testing a post-copulatory pre-zygotic reproductive barrier in a passerine species pair

description: Sexual selection may drive speciation, but most research focuses on
 pre-copulatory sexual selection, overlooking post-copulatory processes.
 Post-copulatory sexual selection in allopatric populations could drive
 divergence in post-copulatory pre-zygotic (PCPZ) phenotypes, limiting gene
 flow upon secondary contact. Here, we performed in vitro experiments
 examining one potential PCPZ barrier between two closely related passerine
 species, house sparrows (Passer domesticus) and Spanish sparrows (Passer
 hispaniolensis). In birds, crossing in the vagina may be particularly
 challenging for sperm, so we tested the effect of female reproductive
 tract fluids on sperm swimming speed and motility. If a PCPZ barrier
 exists at this stage of the fertilization process, heterospecific female
 fluids are predicted to reduce sperm swimming speed or motility relative
 to conspecific female fluid. We found that house sparrow female fluids
 affected the two species’ sperm asymmetrically, depending on the control
 sperm velocity and male species. Overall, however, sperm performed equally
 in conspecific and heterospecific female fluids, and the species had
 similar sperm morphology and sperm swimming performance. Low divergence in
 PCPZ phenotypes between species, perhaps because post-copulatory sexual
 selection is stabilizing or only moderately strong in these taxa, may be
 insufficient to cause an overall PCPZ barrier. Reinforcement may be
 unlikely to drive PCPZ barriers for this species pair, because relatively
 effective pre-copulatory barriers exist between the species, and because
 hybrids can be quite successful. Testing the role of PCPZ barriers in
 birds with more divergent PCPZ phenotypes will improve our understanding
 of speciation in passerines.
description: Data connected to Cramer
 et al BES 2014Included in this data
 set are four .csv files containing data, one .xlsx file with information
 on the naming of columns in the data files (information for each data file
 is in a separate tab in the .xlsx file), and R code. Note that one of the
 R packages used in this publication (languageR) is no longer functional,
 and so the R code does not completely replicate tests presented in the
 manuscript. However, this R script should be sufficient to understand
 exactly how analyses were performed.Justification for analysis decisions
 is indicated in the manuscript.BESpaper.7z
DOI: 10.5061/dryad.13jv6
title: Data from: Metabolic rate covaries with fitness and the pace of the life history in the field

description: Metabolic rate reflects the ‘pace of life’ in every organism. Metabolic
 rate is related to an organism's capacity for essential maintenance,
 growth and reproduction—all of which interact to affect fitness. Although
 thousands of measurements of metabolic rate have been made, the
 microevolutionary forces that shape metabolic rate remain poorly resolved.
 The relationship between metabolic rate and components of fitness are
 often inconsistent, possibly because these fitness components incompletely
 map to actual fitness and often negatively covary with each other. Here we
 measure metabolic rate across ontogeny and monitor its effects on actual
 fitness (lifetime reproductive output) for a marine bryozoan in the field.
 We also measure key components of fitness throughout the entire life
 history including growth rate, longevity and age at the onset of
 reproduction. We found that correlational selection favours individuals
 with higher metabolic rates in one stage and lower metabolic rates in the
 other—individuals with similar metabolic rates in each developmental stage
 displayed the lowest fitness. Furthermore, individuals with the lowest
 metabolic rates lived for longer and reproduced more, but they also grew
 more slowly and took longer to reproduce initially. That metabolic rate is
 related to the pace of the life history in nature has long been suggested
 by macroevolutionary patterns but this study reveals the microevolutionary
 processes that probably generated these patterns.
description: Selection analysis and
 covariance among traits dataTotal lifetime
 reproductive output data used to determine the strength and direction of
 selection on metabolic rate. Growth, longevity and age at onset of
 reproduction data used to determine the relationship between metabolic
 rate and life-history traits.
DOI: 10.5061/dryad.fd930
title: Data from: Resolving the prevalence of somatic transposition in Drosophila

description: Somatic transposition in mammals and insects could increase cellular
 diversity and neural mobilization has been implicated in age-dependent
 decline. To understand the impact of transposition in somatic cells it is
 essential to reliably measure the frequency and map locations of new
 insertions. Here we identified thousands of putative somatic transposon
 insertions in neurons from individual Drosophila melanogaster using
 whole-genome sequencing. However, the number of de novo insertions did not
 correlate with transposon expression or fly age. Analysing our data with
 exons as "immobile genetic elements" revealed a similar
 frequency of unexpected exon translocations. A new sequencing strategy
 that recovers transposon : chromosome junction information revealed most
 putative de novo transposon and exon insertions likely result from
 unavoidable chimeric artefacts. Reanalysis of other published data
 suggests similar artefacts are often mistaken for genuine somatic
 transposition. We conclude that somatic transposition is less prevalent in
 Drosophila than previously envisaged.
description: Sample01WGS data - Sample 01Sample02WGS data - Sample 02Sample03WGS data - Sample 03Sample04WGS data - Sample 04Sample05WGS data - Sample 05Sample06WGS data - Sample 06Sample07WGS data - Sample 07Sample08WGS data - Sample 08Sample09WGS data - Sample 09Sample10WGS data - Sample 10Sample11WGS data - Sample 11Sample12WGS data - Sample 12Sample13WGS data - Sample 13Sample14WGS data - Sample 14Sample15WGS data - Sample 15Sample16WGS data - Sample 16Sample17WGS data - Sample 17Sample18WGS data - Sample 18Sample19WGS data - Sample 19Sample20WGS data - Sample 20Sample21WGS data - Sample 21Sample22WGS data - Sample 22Sample23WGS data - Sample 23Sample24WGS data - Sample 24DMSimFolder containing modified reference gene with simulated IGE deletions, the list of IGE sequences and the location of those IGEs in DMSim. DMSim is based on Drosophila melanogaster Release 5.57.TransposonsList of reference transposon sequences used for TEMP in this study.md5_checksumsmd5 checksums
DOI: 10.5061/dryad.s267j33
title: Data from: Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments

description: Reaction norms or tolerance curves have often been used to predict how
 organisms deal with fluctuating environments. A potential drawback is that
 reaction norms measured in different constant environments may not capture
 all aspects of organismal responses to fluctuating environments. We
 examined growth of the filamentous fungus Neurospora crassa in fluctuating
 temperatures and tested if growth in fluctuating temperatures can be
 explained simply by growth in different constant temperatures or if more
 complex models are needed. In addition, as previous studies on fluctuating
 environments have revealed that past temperatures that organisms have
 experienced can affect their response to current temperature, we tested
 the roles of different epigenetic mechanisms in response to fluctuating
 environments using different mutants. We found that growth of Neurospora
 can be predicted in fluctuating temperatures to some extent if acclimation
 times are taken into account in the model. Interestingly, while
 fluctuating environments have been linked with epigenetic responses we
 found only some evidence of involvement of epigenetic mechanisms on
 tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36
 methylation had slightly impaired response to temperature fluctuations, in
 addition the H3K4 methylation mutant and a mutant in the RNA interference
 pathway had altered acclimation times.
description: Kronholm_Ketola_data_scriptsThe data and R scripts required to repeat the analyses done in the manuscript. Contains a readme file with explanations for the different files and column names.
DOI: 10.15468/dl.sg4fc4
title: Occurrence Download

description: A dataset containing 1231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Manis pentadactyla"
 ]
}

 The dataset includes 1231 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001008-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.