cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mt2tk
title: Data from: Parasite transmission among relatives halts Red Queen dynamics

description: The theory that coevolving hosts and parasites create a fluctuating
 selective environment for one another (i.e., produce Red Queen dynamics)
 has deep roots in evolutionary biology; yet, empirical evidence for Red
 Queen dynamics remains scarce. Fluctuating coevolutionary dynamics
 underpin the Red Queen Hypothesis for the evolution of sex, as well as
 hypotheses explaining the persistence of genetic variation under sexual
 selection, local parasite adaptation, the evolution of mutation rate and
 the evolution of non-random mating. Coevolutionary models that exhibit Red
 Queen dynamics typically assume that hosts and parasites encounter one
 another randomly. However, if related individuals aggregate into family
 groups or are clustered spatially, related hosts will be more likely to
 encounter parasites transmitted by genetically similar individuals. Using
 a model that incorporates familial parasite transmission, we show that a
 slight degree of familial parasite transmission is sufficient to halt
 coevolutionary fluctuations. Our results predict that evidence for Red
 Queen dynamics, and its evolutionary consequences, are most likely to be
 found in biological systems in which hosts and parasites mix mainly at
 random, and are less likely to be found in systems with familial
 aggregation. This presents a challenge to the Red Queen Hypothesis and
 other hypotheses that depend on coevolutionary cycling.
description: Data for figures and
 simulation codeThe following are found
 in this folder: (1) code for the one locus model, (2) code for the two
 locus model, (3) data for the figures of the main text and supplement, (4)
 Mathematica file with the analytical portion. There is also a document
 with a description of the data.data +
 code.zip
DOI: 10.5061/dryad.8v58n
title: Data from: Correlational selection on personality and social plasticity: morphology and social context determine behavioural effects on mating success

description: Despite a central line of research aimed at quantifying relationships
 between mating success and sexually dimorphic traits (e.g., ornaments),
 individual variation in sexually selected traits often explains only a
 modest portion of the variation in mating success. Another line of
 research suggests that a significant portion of the variation in mating
 success observed in animal populations could be explained by correlational
 selection, where the fitness advantage of a given trait depends on other
 components of an individual's phenotype and/or its environment. We
 tested the hypothesis that interactions between multiple traits within an
 individual (phenotype dependence) or between an individual's
 phenotype and its social environment (context dependence) can select for
 individual differences in behaviour (i.e., personality) and social
 plasticity. To quantify the importance of phenotype- and context-dependent
 selection on mating success, we repeatedly measured the behaviour, social
 environment and mating success of about 300 male stream water striders,
 Aquarius remigis. Rather than explaining individual differences in
 long-term mating success, we instead quantified how the combination of a
 male's phenotype interacted with the immediate social context to
 explain variation in hour-by-hour mating decisions. We suggest that this
 analysis captures more of the mechanisms leading to differences in mating
 success. Males differed consistently in activity, aggressiveness and
 social plasticity. The mating advantage of these behavioural traits
 depended on male morphology and varied with the number of rival males in
 the pool, suggesting mechanisms selecting for consistent differences in
 behaviour and social plasticity. Accounting for phenotype and context
 dependence improved the amount of variation in male mating success we
 explained statistically by 30–274%. Our analysis of the determinants of
 male mating success provides important insights into the evolutionary
 forces that shape phenotypic variation. In particular, our results suggest
 that sexual selection is likely to favour individual differences in
 behaviour, social plasticity (i.e., individuals adjusting their
 behaviour), niche preference (i.e., individuals dispersing to particular
 social conditions) or social niche construction (i.e., individuals
 modifying the social environment). The true effect of sexual traits can
 only be understood in interaction with the individual's phenotype and
 environment.
description: metadataThis file describes all the files and variables.data.act.2011Data on male activity (see metadata.txt).data.agg.2011Data on male aggressiveness (see metadata.txt).data.start.2011Data on male mating rate (see metadata.txt).data.stop.2011Data on male mating duration (see metadata.txt).scriptsR scripts used to analyse the data.figuresR scripts used to create the figures presented in the paper.
DOI: 10.5061/dryad.4jk02
title: Data from: Widespread ecomorphological convergence in multiple fish families spanning the marine–freshwater interface

description: The theoretical definition and quantification of convergence is an
 increasingly topical focus in evolutionary research, with particular
 growing interest on study scales spanning deep phylogenetic divergences
 and broad geographical areas. While much progress has recently been made
 in understanding the role of convergence in driving terrestrial (e.g.
 anole lizards) and aquatic (e.g. cichlids) radiations, little is known
 about its macroevolutionary effects across environmental gradients. This
 study uses a suite of recently developed comparative approaches
 integrating diverse aspects of morphology, dietary data, habitat
 affiliation and phylogeny to assess convergence across several well-known
 tropical–temperate fish families in the percomorph suborder Terapontoidei,
 a clade with considerable phenotypic and ecological diversity radiating in
 both marine and freshwater environments. We demonstrate significant
 widespread convergence across many lineages occupying equivalent trophic
 niches, particularly feeding habits such as herbivory and biting of
 attached prey off hard substrates. These include several examples of
 convergent morphotypes evolving independently in marine and freshwater
 clades, separated by deep evolutionary divergences (tens of millions of
 years). The Terapontoidei present a new example of the macroevolutionary
 dynamics of morphological and ecological coevolution in relation to
 habitat and trophic preferences, at a greater phylogenetic and habitat
 scale than most well-studied adaptive radiations.
description: Terapontoidei Consensus
 Tree (Newick format)Phylogeny for 88
 Terapontoidei speciesTerapontoidei_CON_TREE.nwkTerapontoidei Trees (Nexus format)500 trees evenly sampled from the posterior BEAST distribution of 88 Terapontoidei speciesTerapontoidei_500_trees.tre
DOI: 10.5061/dryad.88j7k
title: Data from: The importance of forest structure to biodiversity-productivity relationships

description: While various relationships between productivity and biodiversity are
 found in forests, the processes underlying these relationships remain
 unclear and theory struggles to coherently explain them. In this work, we
 analyse diversity–productivity relationships through an examination of
 forest structure (described by basal area and tree height heterogeneity).
 We use a new modelling approach, called ‘forest factory’, which generates
 various forest stands and calculates their annual productivity
 (above-ground wood increment). Analysing approximately 300 000 forest
 stands, we find that mean forest productivity does not increase with
 species diversity. Instead forest structure emerges as the key variable.
 Similar patterns can be observed by analysing 5054 forest plots of the
 German National Forest Inventory. Furthermore, we group the forest stands
 into nine forest structure classes, in which we find increasing,
 decreasing, invariant and even bell-shaped relationships between
 productivity and diversity. In addition, we introduce a new index, called
 optimal species distribution, which describes the ratio of realized to the
 maximal possible productivity (by shuffling species identities). The
 optimal species distribution and forest structure indices explain the
 obtained productivity values quite well (R2 between 0.7 and 0.95), whereby
 the influence of these attributes varies within the nine forest structure
 classes.
description: Appendix D: all forest
 stands generated by the forest factory. Bohn et al. 2016,
 RSOSThis R-Workspace
 includes all analysed forest stands. "forests" contains the
 forest properties (BA,Theta, Omega, meanHeight), the productivity of each
 year (AWP2000 – AWP2004), the species richness and a column called
 mixture. The number in this column refers to the line in
 "mixtureSpecies" wherein the mixtures are described. The numbers
 in these strings refers to the rows of "species", which also
 contains the parameters of the species.Appendix_D_BohnFJ_ESM_forest_factory_data_set_analysed in_The_importance_of_forest_structure_to_biodiversity-productivity_relationships.Rdata
DOI: 10.5061/dryad.q5s4v
title: Data from: eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests

description: Understanding the geographical distribution and community composition of
 species is crucial to monitor species persistence and define effective
 conservation strategies. Environmental DNA (eDNA) has emerged as a
 powerful noninvasive tool for species detection. However, most eDNA survey
 methods have been developed and applied in temperate zones. We tested the
 feasibility of using eDNA to survey anurans in tropical streams in the
 Brazilian Atlantic forest and compared the results with short-term visual
 and audio surveys. We detected all nine species known to inhabit our focal
 streams with one single visit for eDNA sampling. We found a higher
 proportion of sequence reads and larger number of positive PCR replicates
 for more common species and for those with life cycles closely associated
 with the streams, factors that may contribute to increased release of DNA
 in the water. However, less common species were also detected in eDNA
 samples, demonstrating the detection power of this method. Filtering
 larger volumes of water resulted in a higher probability of detection. Our
 data also show it is important to sample multiple sites along streams,
 particularly for detection of target species with lower population
 densities. For the three focal species in our study, the eDNA
 metabarcoding method had a greater capacity of detection per sampling
 event than our rapid field surveys, and thus, has the potential to
 circumvent some of the challenges associated with traditional approaches.
 Our results underscore the utility of eDNA metabarcoding as an efficient
 method to survey anuran species in tropical streams of the highly
 biodiverse Brazilian Atlantic forest.
description: eDNA_Picinguaba_unfiltered
DOI: 10.5061/dryad.q1344
title: Data from: Attitudes among transplant professionals regarding shifting paradigms in eligibility criteria for live kidney donation

description: Background The transplant community increasingly accepts extended criteria
 live kidney donors, however, great (geographical) differences are present
 in policies regarding the acceptance of these donors, and guidelines do
 not offer clarity. The aim of this survey was to reveal these differences
 and to get an insight in both centre policies as well as personal beliefs
 of transplant professionals. Methods An online survey was sent to 1128
 ESOT-members. Questions were included about several extended donor
 criteria; overweight/obesity, older age, vascular multiplicity, minors as
 donors and comorbidities; hypertension, impaired fasting glucose, kidney
 stones, malignancies and renal cysts. Comparisons were made between
 transplant centres of three regions in Europe and between Europe and other
 countries worldwide. Results 331 questionnaires were completed by
 professionals from 55 countries. Significant differences exist between
 regions in Europe in acceptance of donors with several extended criteria.
 Median refusal rate for potential live donors is 15%. Furthermore,
 differences are seen regarding pre-operative work-up, both in specialists
 who perform screening as in preoperative imaging. Conclusions Remarkably,
 23.4% of transplant professionals sometimes deviate from their centre
 policy, resulting in more or less comparable personal beliefs regarding
 extended criteria. Variety is seen, proving the need for a standardized
 approach in selection, preferably evidence based.
description: All_results_motherdatabaseMotherfileresult.sav.centerSelection of respondents analyzed for the center policy analysisresult.sav.personalSelection of respondents analyzed for the personal attitudes analysisresult.sav.europe.centerSelection of European respondents for the center policy analysisresult.sav.europe.personalSelection of the European respondents for the personal attitudes analysis
DOI: 10.5061/dryad.5404r
title: Data from: Mapping resistance to Alternaria cucumerina in Cucumis melo

description: Infection with Alternaria cucumerina causes Alternaria leaf blight (ALB),
 a disease characterized by lesion formation on leaves, leading to
 substantial yield and quality losses in Cucumis melo (melon). While
 fungicides are effective against ALB, reduction in the frequency of
 application would be economically and environmentally beneficial.
 Resistant melon lines have been identified but the genetic basis of this
 resistance has not been determined. A saturated melon genetic map was
 constructed with markers developed through genotyping-by sequencing of an
 MR-1 (resistant) by Ananas Yokneum (susceptible Israeli cultivar) a
 recombinant inbred line (RIL) population (F6-F10; N=82) derived from
 single seed descent of a F2 population from a cross between the ALB
 resistant parent MR-1 and the ALB susceptible parent Ananas Yokneum. The
 population was evaluated for A. cucumerina resistance with an augmented
 block greenhouse study using inoculation with the wounded-leaf method.
 Multiple quantitative trait loci (QTL) mapping identified two QTL that
 explained 33.9% of variation in lesion area. Several candidate genes
 within range of these QTL were identified using the C. melo v3.5 genome.
 Markers linked to these QTL will be used to accelerate efforts to breed
 melon cultivars resistant to ALB.
description: TableD1Phenotypic data the Cucumis melo MR-1 × AY RIL population, including Alternaria cucumerina lesion area and lesion area BLUPs.TableD2Genotypes for the Cucumis melo MR-1 × AY RIL population at the 2,200 SNPs used for map construction and quantitative trait loci detection.TableD3Physical and genetic positions of the 2,200 SNPs used for map construction and quantitative trait loci detection in Cucumis melo.TableD4Genes located within the 1.5-LOD interval of qALB-10 or qALB-12.TableD5List of candidate genes prioritized by functional relevance.
DOI: 10.5061/dryad.b8c4r
title: Data from: Thioflavin T as an amyloid dye: fibril quantification, optimal concentration and effect on aggregation

description: Formation of amyloid fibrils underlies a wide range of human disorders,
 including Alzheimer's and prion diseases. The amyloid fibrils can be
 readily detected thanks to thioflavin T (ThT), a small molecule that gives
 strong fluorescence upon binding to amyloids. Using the amyloid fibrils of
 Aβ40 and Aβ42 involved in Alzheimer's disease, and of yeast prion
 protein Ure2, here we study three aspects of ThT binding to amyloids:
 quantification of amyloid fibrils using ThT, the optimal ThT concentration
 for monitoring amyloid formation and the effect of ThT on aggregation
 kinetics. We show that ThT fluorescence correlates linearly with amyloid
 concentration over ThT concentrations ranging from 0.2 to 500 µM. At a
 given amyloid concentration, the plot of ThT fluorescence versus ThT
 concentration exhibits a bell-shaped curve. The maximal fluorescence
 signal depends mostly on the total ThT concentration, rather than amyloid
 to ThT ratio. For the three proteins investigated, the maximal
 fluorescence is observed at ThT concentrations of 20–50 µM. Aggregation
 kinetics experiments in the presence of different ThT concentrations show
 that ThT has little effect on aggregation at concentrations of 20 µM or
 lower. ThT at concentrations of 50 µM or more could affect the shape of
 the aggregation curves, but this effect is protein-dependent and not
 universal.
description: Thioflavin T as an
 amyloid dye: fibril quantification, optimal concentration, and effect on
 aggregationXue_et_al_Data.xls
DOI: 10.5061/dryad.1f6t8
title: Data from: Genomic characterization of the evolutionary potential of the sea urchin Strongylocentrotus droebachiensis facing ocean acidification

description: Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions
 and poses a threat to marine species and communities worldwide. To better
 project the effects of acidification on organisms’ health and persistence,
 an understanding is needed of the 1) mechanisms underlying developmental
 and physiological tolerance and 2) potential populations have for rapid
 evolutionary adaptation. This is especially challenging in nonmodel
 species where targeted assays of metabolism and stress physiology may not
 be available or economical for large-scale assessments of genetic
 constraints. We used mRNA sequencing and a quantitative genetics breeding
 design to study mechanisms underlying genetic variability and tolerance to
 decreased seawater pH (-0.4 pH units) in larvae of the sea urchin
 Strongylocentrotus droebachiensis. We used a gene ontology-based approach
 to integrate expression profiles into indirect measures of cellular and
 biochemical traits underlying variation in larval performance (i.e.,
 growth rates). Molecular responses to OA were complex, involving changes
 to several functions such as growth rates, cell division, metabolism, and
 immune activities. Surprisingly, the magnitude of pH effects on molecular
 traits tended to be small relative to variation attributable to
 segregating functional genetic variation in this species. We discuss how
 the application of transcriptomics and quantitative genetics approaches
 across diverse species can enrich our understanding of the biological
 impacts of climate change.
description: All reported data and
 scriptsArchive of all scripts
 and data files necessary to reproduce analyses reported in the
 field.data_submission.zip
DOI: 10.5061/dryad.bp765
title: Data from: Genomic islands of divergence linked to ecotypic variation in sockeye salmon

description: Regions of the genome displaying elevated differentiation (genomic islands
 of divergence) are thought to play an important role in local adaptation,
 especially in populations experiencing high gene flow. However, the
 characteristics of these islands as well as the functional significance of
 genes located within them remain largely unknown. Here, we used data from
 thousands of SNPs aligned to a linkage map to investigate genomic islands
 of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka)
 from a single drainage in southwestern Alaska. We found ten islands
 displaying high differentiation among ecotypes, contrasting neutral
 structure throughout the rest of the genome which was low and not
 partitioned by ecotype. One island on linkage group 13 was particularly
 large and contained six SNPs with FST &gt; 0.14 (average FST of
 neutral SNPs = 0.01). Functional annotation revealed that the peak of this
 island contained a non-synonymous mutation in a gene involved in growth in
 other species (TULP4). The islands that we discovered were relatively
 small (80 - 402 Kb), loci found in islands did not show reduced levels of
 diversity, and loci in islands displayed slightly elevated linkage
 disequilibrium. These attributes suggest that the islands discovered here
 were likely generated by divergence hitchhiking, however, we cannot rule
 out the possibility that other mechanisms may have produced them. Our
 results suggest that islands of divergence serve an important role in
 local adaptation with gene flow and represent a significant advance
 towards understanding the genetic basis of ecotypic differentiation.
description: genepop_wood_river_sockeyeGenepop formatted file containing genotypes from the 6,254 filtered SNPs and 286 individuals with &gt;80% genotyping rate used in this study. SNP names are radtag_snp position i.e. a SNP named 12_46 would be on radtag number 12 and the SNP would be at position 46 in the tag. Population abbreviations are identical to those in Table S1 of the publication.genepop_wr_for_dryad.txt
DOI: 10.5061/dryad.5337t
title: Data from: An experimental evolution study confirms that discontinuous gas exchange does not contribute to body water conservation in locusts

description: The adaptive nature of discontinuous gas exchange (DGE) in insects is
 contentious. The classic “hygric hypothesis”, which posits that DGE serves
 to reduce respiratory water loss (RWL), is still the best supported. We
 thus focused on the hygric hypothesis in this first ever experimental
 evolution study of any of the competing adaptive hypotheses. We compared
 populations of the migratory locust (Locusta migratoria) that underwent
 ten consecutive generations of selection for desiccation-resistance with
 control populations. Selected locusts survived 36% longer under
 desiccation stress but DGE prevalence did not differ between these and
 control populations (~75%). Evolved changes in DGE properties in the
 selected locusts included longer cycle and interburst durations. However,
 in contrast to predictions of the hygric hypothesis, these changes were
 not associated with reduced RWL rates. Other responses observed in the
 selected locusts were higher body water content when hydrated and lower
 evaporative water loss rates. Hence, our data suggest that DGE cycle
 properties in selected locusts are a consequence of an evolved increased
 ability to store water, and thus an improved capacity to buffer
 accumulated CO2, rather than an adaptive response to desiccation. We
 conclude that DGE is unlikely to be an evolutionary response to
 dehydration challenge in locusts.
description: Dehydration
 testRaw data of dehydration
 test of selected and control populations of Locusta migratoria. This file
 contains locusts masses that measured by analytical scales at different
 hydration states (full hydrated, at death, and dry
 mass).Respirametry recording
 filesCO2 (channel 1) and H2O
 (channel 2) emission traces of locusts that recorded by Expedata software
 (Sable Systems International, Las Vegas, NV, USA). The additional readme
 file contains a list of respirometry recording file manes with description
 of each individual locust (recording date, ID, population and file
 name).