cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n7f6q
title: Data from: Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna

description: Adaptation to different environments can promote population divergence via
 natural selection even in the presence of gene flow–a phenomenon that
 typically occurs during ecological speciation. To elucidate how natural
 selection promotes and maintains population divergence during speciation,
 we investigated the population genetic structure, degree of gene flow and
 heterogeneous genomic divergence in three closely related Japanese
 phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and
 H. yasutomii. These species act as a generalist, a wild thistle (Cirsium
 spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist,
 respectively, and their ranges differ accordingly. The two specialist
 species widely co-occur but are reproductively isolated solely due to
 their high specialisation to a particular host plant. Genome-wide
 amplified fragment-length polymorphism (AFLP) markers and mitochondrial
 cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious
 genome-wide divergence associated with both geographic distance and
 ecological divergence. However, a hybridisation assessment for both AFLP
 loci and the mitochondrial sequences revealed a certain degree of
 unidirectional gene flow between the two sympatric specialist species.
 Principal coordinates analysis (PCoA) based on all of the variable AFLP
 loci demonstrated that there are genetic similarities between populations
 from adjacent localities irrespective of the species (i.e. host range).
 However, a further comparative genome scan identified a few fractions of
 loci representing approximately 1% of all loci as different-host
 associated outliers. These results suggest that these three species had a
 complex origin, which could be obscured by current gene flow, and that
 ecological divergence can be maintained with only a small fraction of the
 genome is related to different host use even when there is a certain
 degree of gene flow between sympatric species pairs.
description: Matsubayashietal_2017_JEB_AFLP_alldataAFLP genotype data for all individuals used in the paper.
DOI: 10.5061/dryad.90525
title: Data from: The molecular signal for the adaptation to cold temperature during early life on Earth

description: Several lines of evidence such as the basal location of thermophilic
 lineages in large-scale phylogenetic trees and the ancestral sequence
 reconstruction of single enzymes or large protein concatenations support
 the conclusion that the ancestors of the bacterial and archaeal domains
 were thermophilic organisms which were adapted to hot environments during
 the early stages of the Earth. A parsimonious reasoning would therefore
 suggest that the last universal common ancestor (LUCA) was also
 thermophilic. Various authors have used branch-wise non-homogeneous
 evolutionary models that better capture the variation of molecular
 compositions among lineages to accurately reconstruct the ancestral G + C
 contents of ribosomal RNAs and the ancestral amino acid composition of
 highly conserved proteins. They confirmed the thermophilic nature of the
 ancestors of Bacteria and Archaea but concluded that LUCA, their last
 common ancestor, was a mesophilic organism having a moderate optimal
 growth temperature. In this letter, we investigate the unknown nature of
 the phylogenetic signal that informs ancestral sequence reconstruction to
 support this non-parsimonious scenario. We find that rate variation across
 sites of molecular sequences provides information at different time scales
 by recording the oldest adaptation to temperature in slow-evolving regions
 and subsequent adaptations in fast-evolving ones.
description: RNA stem alignment (125
 sequences)This alignment is a
 concatenation of rRNA stem sites from small and large rRNA subunits. It
 contains 125 sequences and is in Fasta format.rRNA_125seqs_stemSites.fasUniversal protein alignment (38 sequences)This universal protein alignment is a concatenation of 56 proteins from 38 species.proteinConcat38species.fas
DOI: 10.5061/dryad.6544v
title: Data from: Sharing of clinical trial data among trialists: a cross sectional survey

description: Objective: To investigate clinical trialists’ opinions and experiences of
 sharing of clinical trial data with investigators who are not directly
 collaborating with the research team. Design and setting: Cross sectional,
 web based survey. Participants: Clinical trialists who were corresponding
 authors of clinical trials published in 2010 or 2011 in one of six general
 medical journals with the highest impact factor in 2011. Main outcome
 measures: Support for and prevalence of data sharing through data
 repositories and in response to individual requests, concerns with data
 sharing through repositories, and reasons for granting or denying
 requests. Results: Of 683 potential respondents, 317 completed the survey
 (response rate 46%). In principle, 236 (74%) thought that sharing
 de-identified data through data repositories should be required, and 229
 (72%) thought that investigators should be required to share de-identified
 data in response to individual requests. In practice, only 56 (18%)
 indicated that they were required by the trial funder to deposit the trial
 data in a repository; of these 32 (57%) had done so. In all, 149
 respondents (47%) had received an individual request to share their
 clinical trial data; of these, 115 (77%) had granted and 56 (38%) had
 denied at least one request. Respondents’ most common concerns about data
 sharing were related to appropriate data use, investigator or funder
 interests, and protection of research subjects. Conclusions: We found
 strong support for sharing clinical trial data among corresponding authors
 of recently published trials in high impact general medical journals who
 responded to our survey, including a willingness to share data, although
 several practical concerns were identified.
description: Yale Clinical Trial Data
 Sharing Survey DataCSV
 file.Yale Clinical Trial Data
 Sharing Survey Data DictionaryData
 dictionary.
DOI: 10.5061/dryad.739h56c
title: Data from: Mate-copying for a costly variant in Drosophila melanogaster females

description: Mate-copying is a form of social learning in which witnessing sexual
 interactions between conspecifics biases an observer individuals’ future
 mate-choice. Mate-copying exists in many vertebrates, as well as in
 Drosophila melanogaster. Here, we show that female fruit flies can copy
 the choice for mutant males [curly wings (Cy) mutants versus wild types
 (WT)] despite the fact that mating with Cy males induce a significant
 fitness cost for the observer female. When facing WT and Cy males, naive
 observer females of both phenotypes naturally prefer WT males. In a
 mate-copying experiment, naive observer Cy or WT females saw a
 demonstrator female copulating with either a Cy or a WT male aside a
 lonely male of the opposite phenotype. In the subsequent mate-choice test,
 Cy and WT observer female did not change their already high natural
 preference for WT males after witnessing a WT male copulating during the
 demonstration. Contrastingly, Cy and WT female increased their preference
 for the naturally non-preferred Cy males after witnessing a Cy male
 copulating, showing that mate-copying also exists for costly variants in
 invertebrates. Furthermore, mate-copying efficiency did not differ when
 using neutral artificial variants (colouring, Dagaeff et al. 2016, Animal
 Behaviour) versus phenotypic variants (this study), suggesting that these
 two types of experiments are equivalently suitable to study mate-copying.
 We finally discuss how mate-copying can participate to the maintenance of
 costly traits in a population.
description: Data-set Mate-copying of
 a costly variantThe file contains the
 data of the experiments presented in the paper. We tested wild type and
 Curly females for their innate preference for wild type and Curly males
 and then whether females of both phenotypes copy the choice of their
 conspecifics for a wild type or Curly male.
DOI: 10.5061/dryad.7hh20
title: Data from: Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory

description: Populations evolving in constant environments exhibit declining
 adaptability. Understanding the basis of this pattern could reveal
 underlying processes determining the repeatability of evolutionary
 outcomes. In principle, declining adaptability can be due to a decrease in
 the effect size of beneficial mutations, a decrease in the rate at which
 they occur, or some combination of both. By evolving Escherichia coli
 populations started from different steps along a single evolutionary
 trajectory, we show that declining adaptability is best explained by a
 decrease in the size of available beneficial mutations. This pattern
 reflected the dominant influence of negative genetic interactions that
 caused new beneficial mutations to confer smaller benefits in fitter
 genotypes. Genome sequencing revealed that starting genotypes that were
 more similar to one another did not exhibit greater similarity in terms of
 new beneficial mutations, supporting the view that epistasis acts
 globally, having a greater influence on the effect than on the identity of
 available mutations along an adaptive trajectory. Our findings provide
 support for a general mechanism that leads to predictable phenotypic
 evolutionary trajectories.
description: mutation_dataSummary of mutates genes identified in evolved clones isolated from replay populationsfig3R script to generate figure 3fig3_anc-evInput data required to generate figure 3fig1.b R scriptR script to generate figure 1bfitness change_vs_initial fitnes.Rfig1.b input dataInput data necessary to generate figure 1bfitnesschange.tabfig4_replay_clone_mutationsInput to fig4 R script. Summary of mutated genes in clones isolated from replay populations.Fig4_replay_clone_mutations.txtfig4_mutations_in_founder_also_in_replayInput file for fig. 4 R script. Summarizes mutations present in founders that also occurred in some replay clones. These mutations are omitted from calculation of the convergence metric.Fig4_mutations_progenitor_also_in_replay.txtfig4_PI_CI matrixR script to generate figure 4.Fig4_PI_CI matrix.R
DOI: 10.5061/dryad.vj5pn
title: Data from: Morph-specific patterns of reproductive senescence: connections to discrete reproductive strategies

description: How reproductive strategies contribute to patterns of senescence in
 natural populations remains contentious. We studied reproductive
 senescence in the dimorphic white-throated sparrow, an excellent species
 for exploring this issue. Within both sexes the morphs use distinct
 reproductive strategies, and disassortative pairing by morph results in
 pair types with distinct parental systems. White morph birds are more
 colorful and aggressive than tan counterparts, and white males compete for
 extra-pair matings whereas tan males are more parental. Tan males and
 white females share parental care equally, whereas white males provide
 little parental support to tan females. We found morph-specific patterns
 of reproductive senescence in both sexes. White males exhibited greater
 reproductive senescence than tan males. This result likely reflects the
 difficulty of sustaining a highly competitive reproductive strategy as
 aging progresses, rather than high physiological costs of competitiveness,
 since white males were also long-lived. Moreover, morph was not
 consistently related to reproductive senescence across the sexes, arguing
 against especially high costs of the traits associated with white morph
 identity. Rather, tan females exhibited earlier reproductive senescence
 than white females, and were short-lived, perhaps reflecting the
 challenges of unsupported motherhood. Results underscore the importance of
 social dynamics in determining patterns of reproductive senescence.
description: White-throated sparrow
 reproductive senescence dataThis data file contains
 information regarding annual reproductive success across the lifespan of
 individual white-throated sparrows (Zonotrichia albicollis). Lifetime
 reproductive success is also tabulated, as is longevity. In addition,
 information about the number of extrapair offspring is
 provided.Reproductive Senescence
 Data_AMNAT.xlsxLifetime clutch sizes
 and hatching ratesThis data file contains
 information about clutch sizes and hatching success across the lifespan of
 individual white-throated sparrows (Zonotrichia albicollis). Longevity of
 individuals is also provided.Eggs and Hatch to 2015,
 Reproductive Senescence .xlsx
DOI: 10.5061/dryad.8458257
title: Data from: No evidence for sibling or parent-offspring coadaptation in a wild population of blue tits, despite high power.

description: Parent and offspring behaviours are expected to act as both the agents and
 targets of selection. This may generate parent-offspring coadaptation in
 which parent and offspring behaviours become genetically correlated in a
 way that increases inclusive fitness. Cross-fostering has been used to
 study parent-offspring coadaptation, with the prediction that offspring
 raised by non-relatives, or parents raising non-relatives, should suffer
 fitness costs. Using long-term data from more than 400 partially crossed
 broods of blue tits (Cyanistes caeruleus) we show there is no difference
 in mass or survival between crossed and non-crossed chicks. However,
 previous studies for which the evidence for parent-offspring coadaptation
 is strongest compare chicks from fully crossed broods with those from
 non-crossed broods. When parent-offspring coadaptation acts at the level
 of the brood then partial cross-fostering experiments are not expected to
 show evidence of coadaptation. To test this, we performed an additional
 cross-fostering experiment (163 broods) in which clutches were either
 fully crossed, non-crossed, or partiallycrossed. In agreement with the
 long-term data, there was no evidence for parent-offspring coadaptationon
 offspring fitness depsite high power. In addition there was no evidence of
 effects on parental fitness, nor evidnce of sibling coadaptation, although
 the power of these tests was more modest.
description: Chick
 dataChick data (both weights
 and survival).chicks.RDataAdult dataAdult data (both fecundity and survival).adults.RDataPedigree dataPedigree dataped.RDataR codeAnalysis scriptsDryadRcode.R
DOI: 10.5061/dryad.fd407
title: Data from: Bigger testes increase paternity in a simultaneous hermaphrodite, independently of the sperm competition level

description: Hermaphroditic animals face the fundamental evolutionary optimization
 problem of allocating their resources to their male versus female
 reproductive function (e.g., testes and sperm versus ovaries and eggs) and
 this optimal sex allocation can be affected by both pre- and
 postcopulatory sexual selection. For example, local sperm competition
 (LSC)—the competition between related sperm for the fertilization of a
 partner’s ova—occurs in small mating groups and can favor a female-biased
 sex allocation, because, under LSC, investment into sperm production is
 predicted to show diminishing fitness returns. Here we test whether higher
 testis investment increases an individual's paternity success under
 sperm competition, and whether the strength of this effect diminishes when
 LSC is stronger, as predicted by sex allocation theory. We created two
 subsets of individuals of the simultaneously hermaphroditic flatworm
 Macrostomum lignano—by sampling worms from either the highest or lowest
 quartile of the testis investment distribution—and estimated their
 paternity success in group sizes of either three (strong LSC) or eight
 individuals (weak LSC). Specifically, using transgenic focal individuals
 expressing a dominant green fluorescent protein marker, we showed that
 worms with high testis investment sired 22% more offspring relative to
 those with low investment, corroborating previous findings in M. lignano
 and other species. However, the strength of this effect was not
 significantly modulated by the experienced group size, contrasting
 theoretical expectations of more strongly diminishing fitness returns
 under strong LSC. We discuss the possible implications for the
 evolutionary maintenance of hermaphroditism in M. lignano.
description: Vellnow et al. 2017 -
 DataReproductive morphology
 and offspring data
DOI: 10.25934/pr00012543.0
title: Available datapackage for study 'Scaling Up SARS-COV-2 Testing to Serve Latinx Communities'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.g62pv
title: Data from: Pre-dispersal seed predation and pollen limitation constrain population growth across the geographic distribution of Astragalus utahensis

description: 1. A central focus of ecology is to understand the conditions under which
 biotic interactions affect species’ abundance and distribution. Classic
 and recent studies have shown that biotic interactions can strongly impact
 local or regional patterns of species abundance, but two fundamental
 questions remain largely unaddressed for non-competitive biotic
 interactions. First, do the effects of these interactions on population
 performance change predictably with environmental context? Second, to what
 extent do population-scale effects contribute to limiting species’
 geographic distributions? 2. To address these questions, we experimentally
 assessed the extent to which pollen limitation and insect seed predators
 affected the fecundity and projected population growth rate (λ) of the
 native forb Astragalus utahensis. We studied populations at the center and
 northern edge of the latitudinal range of A. utahensis that occur across a
 gradient in abiotic harshness characterized primarily by declining mean
 annual precipitation. 3. Supplementing pollen and suppressing
 pre-dispersal seed predators increased seed production similarly within A.
 utahensis populations at the center and northern edge of the range.
 Integral projection population models revealed that relaxing these checks
 on seed production tended to increase λ in most populations, regardless of
 their location within the range. 4. Synthesis. Our results suggest that
 pollen limitation and insect herbivores limit population growth in A.
 utahensis similarly across the center-to-north portion of its latitudinal
 distribution. However, because A. utahensis population growth barely
 reaches the level of replacement at the northern range edge, the reduction
 in λ resulting from these interactions may contribute to limiting
 expansion at the northern edge of A. utahensis’ latitudinal range.
description: Data & R Scripts
 from: Pre-dispersal seed predation and pollen limitation constrain
 population growth across the geographic distribution of Astragalus
 utahensisThese data and R scripts
 accompany Baer & Maron (2018): Pre-dispersal seed predation and pollen
 limitation constrain population growth across the geographic distribution
 of Astragalus utahensis. Please refer to the README file for more
 information about the contents of each data file and R
 Script.Baer_&_Maron_2018_Data_&_R.Scripts.zip
DOI: 10.5061/dryad.15mk5
title: Data from: Assortative mating among animals of captive and wild origin following experimental conservation releases

description: Captive breeding is a high profile management tool used for conserving
 threatened species. However, the inevitable consequence of generations in
 captivity is broad scale and often-rapid phenotypic divergence between
 captive and wild individuals, through environmental differences and
 genetic processes. Although poorly understood, mate choice preference is
 one of the changes that may occur in captivity that could have important
 implications for the reintroduction success of captive-bred animals. We
 bred wild-caught house mice for three generations to examine mating
 patterns and reproductive outcomes when these animals were simultaneously
 released into multiple outdoor enclosures with wild conspecifics. At
 release, there were significant differences in phenotypic (e.g. body mass)
 and genetic measures (e.g. Gst and F) between captive-bred and wild adult
 mice. Furthermore, 83% of offspring produced post-release were of same
 source parentage, inferring pronounced assortative mating. Our findings
 suggest that captive breeding may affect mating preferences, with
 potentially adverse implications for the success of threatened species
 reintroduction programmes.
description: Mouse data -
 reproductive synchorny
DOI: 10.5061/dryad.6qj05
title: Data from: Keeping your options open: maintenance of thermal plasticity during adaptation to a stable environment

description: Phenotypic plasticity may allow species to cope with environmental
 variation. The study of thermal plasticity and its evolution helps
 understanding how populations respond to variation in temperature. In the
 context of climate change, it is essential to realize the impact of
 historical differences in the ability of populations to exhibit a plastic
 response to thermal variation and how it evolves during colonization of
 new environments. We have analyzed the real-time evolution of thermal
 reaction norms of adult and juvenile traits in Drosophila subobscura
 populations from three locations of Europe in the laboratory. These
 populations were kept at a constant temperature of 18ºC, and were
 periodically assayed at three experimental temperatures (13ºC, 18ºC and
 23ºC). We found initial differentiation between populations in thermal
 plasticity as well as evolutionary convergence in the shape of reaction
 norms for some adult traits, but not for any of the juvenile traits.
 Contrary to theoretical expectations, an overall better performance of
 high latitude populations across temperatures in early generations was
 observed. Our study shows that the evolution of thermal plasticity is
 trait specific, and that a new stable environment did not limit the
 ability of populations to cope with environmental challenges.
description: Raw data for adult life
 history traitsRaw data for adult life
 history traits for each population, generation and temperature assayed. MV
 indicates missing values.Adult Life History
 Trait.xlsxRaw data for juvenile
 life history traitsRaw data for juvenile
 traits for each population, generation and temperature assayed. MV refers
 to missing value.Juvenile Life History
 Trait.xlsx