cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3p8j3
title: Data from: The genetic architecture of defence as resistance to and tolerance of bacterial infection in Drosophila melanogaster

description: Defence against pathogenic infection can take two forms: resistance and
 tolerance. Resistance is the ability of the host to limit a pathogen
 burden, whereas tolerance is the ability to limit the negative
 consequences of infection at a given level of infection intensity.
 Evolutionarily, a tolerance strategy that is independent of resistance
 could allow the host to avoid mounting a costly immune response and,
 theoretically, to avoid a co-evolutionary arms race between pathogen
 virulence and host resistance. Biomedically, understanding the mechanisms
 of tolerance and how they relate to resistance could potentially yield
 treatment strategies that focus on health improvement instead of pathogen
 elimination. To understand the impact of tolerance on host defence and
 identify genetic variants that determine host tolerance, we defined
 genetic variation in tolerance as the residual deviation from a binomial
 regression of fitness under infection against infection intensity. We then
 performed a genomewide association study to map the genetic basis of
 variation in resistance to and tolerance of infection by the bacterium
 Providencia rettgeri. We found a positive genetic correlation between
 resistance and tolerance, and we demonstrated that the level of resistance
 is highly predictive of tolerance. We identified 30 loci that predict
 tolerance, many of which are in genes involved in the regulation of
 immunity and metabolism. We used RNAi to confirm that a subset of mapped
 genes have a role in defence, including putative wound repair genes grainy
 head and debris buster. Our results indicate that tolerance is not an
 independent strategy from resistance, but that defence arises from a
 collection of physiological processes intertwined with canonical immunity
 and resistance.
description: Mean_values_adjusted_unadjusted_20161207Adjusted and unadjusted mean values used for mapping in PLINKraw load data for GWASAll bacterial load data used for GWASalldgrploaddata3.24.14.txtraw survival data for GWASall survival data used for GWASALLsurvivaldata4.5.14.xlsextremes survSurvival data associated with Figure 2extsurvallrepswithsum_20150609.txtextremes loadLoad data associated with figure 2extloadallreps_20150608.txtAct5c survSurvival from RNAi experiment with Actin5C driverCompleteSurvivalActin5C_20150219.xlsxAct5c loadLoad data from RNAi experiment with Actin5c driverallunbaisedact_load_20150212.txtc564 survsurvival data from RNAi experiments with c564 driverallrepspinsurvc564_20150627.txtc564 loadload data from RNAi experiments with c564 driverc564pinload3reps_20150616.txt
DOI: 10.5061/dryad.c87rm
title: Data from: Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

description: Past glaciation events have played a major role in shaping the genetic
 diversity and distribution of wild sheep in North America. The advancement
 of glaciers can isolate populations in ice-free refugia, where they can
 survive until the recession of ice sheets. The major Beringian refugium is
 thought to have held thinhorn sheep (Ovis dalli) populations during times
 of glacial advance. While isolation in the major refugium can account for
 much of the genetic and morphological diversity seen in extant thinhorn
 sheep populations, mounting evidence suggests the persistence of
 populations in smaller minor refugia. We investigated the refugial origins
 of thinhorn sheep using ~10 000 SNPs obtained via a cross-species
 application of the domestic sheep ovine HD BeadChip to genotype 52
 thinhorn sheep and five bighorn sheep (O. canadensis) samples.
 Phylogenetic inference revealed a distinct lineage of thinhorn sheep
 inhabiting British Columbia, which is consistent with the survival of a
 group of thinhorn sheep in a minor refugium separate from the Beringian
 refugium. Isolation in separate glacial refugia probably mediated the
 evolution of the two thinhorn sheep subspecies, the white Dall's
 sheep (O. d. dalli), which persisted in Beringia, and the dark
 Stone's sheep (O. d. stonei), which utilized the minor refugium. We
 also found the first genetic evidence for admixture between sheep from
 different glacial refugia in south-central Yukon as a consequence of post
 glacial expansion and recolonization. These results show that glaciation
 events can have a major role in the evolution of species inhabiting
 previously glaciated habitats and the need to look beyond established
 refugia when examining the evolutionary history of such species.
description: SNP dataset in plink
 formatthsphylo_final.zip
DOI: 10.15468/dl.5q7urg
title: Occurrence Download

description: A dataset containing 298 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Living Specimen, Human Observation, Specimen)",
 "Country is Türkiye",
 "TaxonKey is Cedrus libani"
 ]
}

 The dataset includes 298 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000609-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2tk2040
title: Data from: Linking Darwin's naturalisation hypothesis and Elton's diversity‐invasibility hypothesis in experimental grassland communities

description: 1. Darwin's naturalisation hypothesis posing that phylogenetic
 distance of alien species to native residents predicts invasion success,
 and Elton's diversity‐invasibility hypothesis posing that diversity
 of native communities confers resistance to invasion, are both rooted in
 ideas of species coexistence. Because the two hypotheses are inherently
 linked, the mechanisms underlying them may interact in driving the
 invasion success. Even so, these links and interactions have not been
 explicitly disentangled in one experimental study before. 2. To
 disentangle the links between the two hypotheses, we used 36 native
 grassland herbs to create greenhouse mesocosms with 90 grassland
 communities of different diversities, and introduced each of five
 herbaceous alien species as seeds and seedlings. We used phylogeny and
 four functional traits (plant height, specific leaf area, leaf size, seed
 mass) to calculate different measures of phylogenetic and functional
 distance and diversity. Specifically, we tested how the alien‐native
 distance (phylogenetic or functional) and the native diversity
 (phylogenetic or functional) affected each other in their effects on
 germination, seedling survival, growth and reproduction of the aliens. 3.
 Overall, our results supported both hypotheses. Multivariate functional
 distance based on four traits jointly had stronger positive effects than
 phylogenetic distance and the univariate ones based on each trait
 separately. Moreover, the aliens were more successful if they were more
 competitive by being taller and having larger leaves with a lower SLA than
 the native residents. Univariate functional diversity based on each trait
 separately had stronger negative effects than phylogenetic and
 multivariate functional diversity. Most importantly, we found that the
 effects of alien‐native phylogenetic and multivariate functional distance
 became stronger as diversity increased. Our analyses with single traits
 also showed that the strength of the effects of both alien‐native
 hierarchical functional distances (indicative of competitive inequalities)
 and absolute functional distances (indicative of niche differences)
 increased at higher diversities, where competition is more severe. 4.
 SynthesisOur study explicitly demonstrates for the first time how the
 mechanisms underlying the two classical invasion hypotheses interact in
 driving invasion success in grassland communities. This may help to
 explain some of the puzzling results of studies testing either of the two
 hypotheses.
description: pfdivThis is a data file
 related to the paper entitled "Linking Darwin's naturalisation
 hypothesis and Elton’s diversity-invasibility hypothesis in experimental
 grassland communities"
DOI: 10.5061/dryad.10453
title: Data from: Strong natural selection during plant restoration favors an unexpected suite of plant traits

description: Restoration is an opportunity to study natural selection: one can measure
 the distribution of traits in source propagules used to found populations,
 compare this with the distribution of traits in successful recruits, and
 determine the strength and direction of selection on potentially adaptive
 traits. We asked if natural selection influenced seedling establishment
 during post-fire restoration in the Great Basin, an area where large-scale
 restoration occurs with a few widely available cultivars planted over a
 large range of environmental conditions. We collected seeds from
 established plants of the perennial grass Elymus elymoides ssp.
 californicus (squirreltail) at two restoration sites, and compared the
 distribution of phenotypic traits of surviving plants with the original
 pool of restoration seeds. Seeds were planted in common gardens for two
 generations. Plants grown from seeds that established in the field were a
 non-random subset of the original seeds, with directional selection
 consistently favoring a correlated suite of traits in both field sites:
 small plant and seed size, and earlier flowering phenology. These results
 demonstrate that natural selection can affect restoration establishment in
 strong and predictable ways, and that adaptive traits in these sites were
 opposite of the current criteria used for selection of restoration
 material in this system.
description: Kulpa Leger Evol Apps
 DataSee Readme
 file
DOI: 10.34740/kaggle/dsv/14631940
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.rg8d4
title: Data from: Life history differences in age-dependent expressions of multiple ornaments and behaviors in a lekking bird

description: Age is a major factor explaining variation in life-history traits among
 individuals with typical patterns of increasing trait values early in
 life, maximum trait expression, and senescence. However, age-dependent
 variation in the expressions of sexually selected traits has received less
 attention, although such variation underpins differences in male
 competitive abilities and female preference, which are central to sexual
 selection. In contrast to previous studies focusing on single traits, we
 used repeated measures of seven sexually selected morphological and
 behavioral traits in male black grouse (Tetrao tetrix) to quantify the
 effects of age and life span on their expressions and quantified this
 variation in relation to male reproductive effort. Trait expression
 increased with age, but long-lived males had a slower increase and delayed
 maxima in trait values compared with short-lived males. There was evidence
 of terminal investment (increasing trait values during the last breeding
 season) in some traits and senescence in all traits. These trait dynamics
 were largely explained by the timing of male peak lekking effort. This
 study shows that fully understanding the variation in sexually selected
 traits and fitness benefits associated with sexual selection requires
 accounting for the complex interaction among individual age, life span,
 and the timing of individuals’ investment in reproduction.
description: Kervinen_et_al_age_and_traits_dataThis package contains the data from: Life history differences in age-dependent expressions of multiple ornaments and behaviors in a lekking bird, by Kervinen, Matti, Lebigre, Christophe, Alatalo, Rauno V., Siitari, Heli, and Soulsbury, Carl D. 'Kervinen_et_al_all_data.xlsx' is the complete data set used in all but the senescence analyses, where 'Kervinen_et_al_senescence_data.xlsx' was used instead. Variable descriptions are given in the metafiles 'Kervinen_et_al_all_data_metafile.xlsx' and 'Kervinen_et_al_senescence_data.xlsx', respectively.Kervinen_et_al_data.rar
DOI: 10.5061/dryad.v3b42mv1
title: Data from: Covariation in life-history traits: differential effects of diet on condition, hormones, behavior and reproduction in genetic finch morphs

description: The relative contribution of genetic and environmental factors in
 determining variation in life-history traits is of central interest to
 evolutionary biologists, but the physiological mechanisms underlying these
 traits are still poorly understood. Here we experimentally demonstrate
 opposing effects of nutritional stress on immune function, endocrine
 physiology, parental care and reproduction between red and black
 head-color morphs of the Gouldian finch (Erythrura gouldiae). Although
 body condition of black morphs was largely unaffected by diet
 manipulation, red birds were highly sensitive to dietary changes,
 exhibiting considerable within-individual changes in condition and immune
 function. Consequently, nutritionally stressed red birds delayed breeding,
 produced smaller broods and reared fewer and lower-quality foster
 offspring than black morphs. Differences in offspring quality were largely
 due to morph-specific differences in parental effort; red morphs reduced
 parental provisioning, whereas black morphs adaptively elevated their
 provisioning effort to meet the increased nutritional demands of their
 foster brood. Nutritionally stressed genetic morphs also exhibited
 divergent glucocorticoid responses. Black morphs showed reduced
 corticosterone-binding globulin (CBG) concentrations and increased levels
 of free corticosterone, whereas red morphs exhibited reduced free
 corticosterone levels and elevated CBG concentrations. These opposing
 glucocorticoid responses highlight intrinsic differences in endocrine
 sensitivities and plasticity between genetic morphs, which may underlie
 the morph-specific differences in condition, behavior and reproduction,
 and thus ultimately contribute to the evolution and maintenance of color
 polymorphism.
description: Pryke et al. Am Nat
 52740
DOI: 10.5061/dryad.p0c02
title: Data from: The size advantage model of sex allocation in the protandrous sex-changer Crepidula fornicata: role of the mating system, sperm storage, and male mobility

description: Sequential hermaphroditism is adaptive when the reproductive value of an
 individual varies with size or age, and this relationship differs between
 males and females. In this case, theory shows that the lifetime
 reproductive output of an individual is increased by changing sex (a
 hypothesis referred to as the size-advantage model). Sex-linked
 differences in size-fitness curves can stem from differential costs of
 reproduction, the mating system, and differences in growth and mortality
 between sexes. Detailed empirical data is required to disentangle the
 relative roles of each of these factors within the theory. Quantitative
 data are also needed to explore the role of sperm storage, which has not
 yet been considered with sequential hermaphrodites. Using experimental
 rearing and paternity assignment, we report relationships between size and
 reproductive success of Crepidula fornicata, a protandrous (male-first)
 gastropod. Male reproductive success increased with size due to the
 polygamous system and stacking behavior of the species, but females
 nonetheless had greater reproductive success than males of the same size,
 in agreement with the size-advantage theory. Sperm storage appeared to be
 a critical determinant of success for both sexes, and modeling the effect
 of sperm storage showed that it could potentially accelerate sex change in
 protandrous species.
description: fecundityGenotypes_adultsGenotypes_larvaegrowthreproductive_successsire_contributions
DOI: 10.15468/dl.7dgz8y
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Portuguese Snakeflies (Raphidioptera)"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000610-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rg70p
title: Data from: Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites

description: Given their large population sizes and presumed high dispersal capacity,
 protists are expected to exhibit homogeneous population structure over
 large spatial scales. On the other hand, the fragmented and short-lived
 nature of the lentic freshwater habitats that many protists inhabit
 promotes strong population differentiation. We used microsatellites in two
 benthic freshwater diatoms, Eunotia bilunaris ‘robust’ and Sellaphora
 capitata, sampled from within a pond and connected ponds, through isolated
 ponds from the same region to western Europe to determine the spatial
 scale at which differentiation appears. Because periods of low genotypic
 diversity contribute to population differentiation, we also assessed
 genotypic diversity. While genotypic diversity was very high to maximal in
 most samples of both species, some had a markedly lower diversity, with up
 to half (Eunotia) and over 90% (Sellaphora) of the strains having the same
 multilocus genotype. Population differentiation showed an
 isolation-by-distance pattern with very low standardized FST values
 between samples from the same or connected ponds but high values between
 isolated ponds, even when situated in the same region. Partial rbcL
 sequences in Eunotia were consistent with this pattern as isolated ponds
 in the same region could differ widely in haplotype composition.
 Populations identified by Structure corresponded to the source ponds,
 confirming that ‘pond’ is the main factor structuring these populations.
 We conclude that freshwater benthic diatom populations are highly
 fragmented on a regional scale, reflecting either less dispersal than is
 often assumed or reduced establishment success of immigrants, so that
 dispersal does not translate into gene flow.
description: Alignment_complete_rbcL_EunotiaAlignment of complete rbcL sequences of the Eunotia bilunaris/flexuosa complex used for phylogeny reconstruction (Fig. S1).Alignment_cox1_Sellaphora_capitataAlignment of partial cox1 sequences of Sellaphora used for phylogeny reconstruction (Fig. S2).Alignment_partial_rbcL_EunotiaPartial rbcL sequences of Eunotia bilunaris "robust" strains used for phylogeography of the species in Western Europe (Fig. 2).BI_consensus_phylogeny_cox1_Sellaphora_capitataTree file of Sellaphora Bayesian Inference phylogeny based on partial cox1 sequences (Fig. S2).BI_consensus_phylogeny_rbcL_EunotiaTree file of full rbcL Bayesian Inference phylogeny of the Eunotia bilunaris/flexuosa species complex.Isolation_by_distanceMatrices of pairwise standardized Fst values and (log-transformed) geographic distances between sampling locations of Eunotia bilunaris "robust" and Sellaphora capitata respectively, for assessment of isolation-by-distance patterns (Fig. 3).MLG_data_Ebilunaris_robustMicrosatellite allelic composition of Eunotia bilunaris "robust" strains.MLG_data_Sellaphora_capitataMicrosatellite allelic composition of Sellaphora capitata strains.
DOI: 10.5061/dryad.k5mt1
title: Data from: Immigrant and extrinsic hybrid seed inviability contribute to reproductive isolation between forest and dune ecotypes of Epipactis helleborine (Orchidaceae)

description: Reproductive isolation caused by divergent natural selection arising from
 differences between ecological environments or ecological interactions
 represents a major mechanism contributing to speciation, but its relative
 importance is poorly known. In this study, controlled reciprocal crossings
 and seed germination experiments were combined with genetic and
 morphometric analyses to test the hypothesis that previously described
 differences in mycorrhizal communities between forest and dune ecotypes of
 Epipactis helleborine were sufficiently strong to create complete
 reproductive isolation between the two ecotypes. The results showed that
 immigrant seeds had a significantly lower probability of protocorm
 formation than native seeds, indicating strong immigrant inviability.
 Although both ecotypes were able to cross easily and to produce a large
 number of viable seeds, hybrid seeds showed significantly lower protocorm
 formation than pure seeds, further contributing to reproductive isolation.
 Molecular analyses using 770 SNP markers showed that the two ecotypes were
 genetically distinct and that populations of the dune ecotype were
 genetically impoverished compared to populations of the forest ecotype.
 Morphologically, the two ecotypes were also significantly different, with
 plants of the dune ecotype generally being smaller than plants of the
 forest ecotype. Overall, these results indicate that interfertile
 populations of a widespread orchid adapting to contrasting environments
 diverge as a consequence of concurrent selection acting against immigrants
 and hybrids and suggest that mycorrhizal fungi can play a role in the
 early stages of plant speciation.
description: Epipactis
 SNPsIndividual SNP alleles
 in Genalex format.DRYAD_Jacquemyn et al.
 2017.xlsx
DOI: 10.5061/dryad.tb4k5
title: Data from: Associations between changes in city and address specific temperature and QT interval - the VA Normative Aging Study

description: Background: The underlying mechanisms of the association between ambient
 temperature and cardiovascular morbidity and mortality are not well
 understood, particularly for daily temperature variability. We evaluated
 if daily mean temperature and standard deviation of temperature was
 associated with heart rate-corrected QT interval (QTc) duration, a marker
 of ventricular repolarization in a prospective cohort of older men.
 Methods: This longitudinal analysis included 487 older men participating
 in the VA Normative Aging Study with up to three visits between 2000–2008
 (n = 743). We analyzed associations between QTc and moving averages (1–7,
 14, 21, and 28 days) of the 24-hour mean and standard deviation of
 temperature as measured from a local weather monitor, and the 24-hour mean
 temperature estimated from a spatiotemporal prediction model, in
 time-varying linear mixed-effect regression. Effect modification by
 season, diabetes, coronary heart disease, obesity, and age was also
 evaluated. Results: Higher mean temperature as measured from the local
 monitor, and estimated from the prediction model, was associated with
 longer QTc at moving averages of 21 and 28 days. Increased 24-hr standard
 deviation of temperature was associated with longer QTc at moving averages
 from 4 and up to 28 days; a 1.9°C interquartile range increase in 4-day
 moving average standard deviation of temperature was associated with a 2.8
 msec (95%CI: 0.4, 5.2) longer QTc. Associations between 24-hr standard
 deviation of temperature and QTc were stronger in colder months, and in
 participants with diabetes and coronary heart disease.
 Conclusion/Significance: In this sample of older men, elevated mean
 temperature was associated with longer QTc, and increased variability of
 temperature was associated with longer QTc, particularly during colder
 months and among individuals with diabetes and coronary heart disease.
 These findings may offer insight of an important underlying mechanism of
 temperature-related cardiovascular morbidity and mortality in an older
 population.
description: Env_Data_PONE-D-13-50148_081514This dataset in csv format consists of all environmental data (moving average mean temperature, moving average standard deviation of temperature, 24-hr mean relative humidity, 4-hr lag black carbon) linked to each unique participant and date of examination visit used in the analysis. This dataset is sorted by participant ID and date of examination visit.