cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g416t
title: Data from: Evolutionary history of almond tree domestication in the Mediterranean basin

description: Genetic diversity of contemporary domesticated species is shaped by both
 natural and human-driven processes. However, until now, little is known
 about how domestication has imprinted the variation of fruit tree species.
 In this study, we reconstruct the recent evolutionary history of the
 domesticated almond tree, Prunus dulcis, around the Mediterranean Basin,
 using a combination of nuclear and chloroplast microsatellites (i.e. SSRs)
 to investigate patterns of genetic diversity. Whereas conservative
 chloroplast SSRs show a widespread haplotype and rare locally distributed
 variants, nuclear SSRs show a pattern of isolation by distance with clines
 of diversity from the East to the West of the Mediterranean basin, while
 Bayesian genetic clustering reveals a substantial longitudinal genetic
 structure. Both kinds of markers thus support a single domestication
 event, in the eastern side of Mediterranean basin. In addition,
 model-based estimation of the timing of genetic divergence among those
 clusters is estimated sometime during the late Holocene, a result that is
 compatible with human-mediated dispersal of almonds out of its center of
 origin. Still, the detection of region-specific alleles suggests that gene
 flow from relictual wild pre-glacial populations (in North Africa) or from
 wild counterparts (in the Near-East) could account for a fraction of the
 diversity observed.
description: 1124_dataindividual genotyping data (1124 specimen) for twelve nuclear microsatellites1124_infoDetails is given for each specimen (Country, species,geographical coordinates, name of the sampling site, origin of the specimen : field sampling or collection)chloro_dataindividual genotyping data for five chloroplast SSRs
DOI: 10.5061/dryad.3813d
title: Data from: Genetic mixture of multiple source populations accelerates invasive range expansion

description: A wealth of population genetic studies have documented that many
 successful biological invasions stem from multiple introductions from
 genetically distinct source populations. Yet, mechanistic understanding of
 whether and how genetic mixture promotes invasiveness has lagged behind
 documentation that such mixture commonly occurs. We conducted a laboratory
 experiment to test the influence of genetic mixture on the velocity of
 invasive range expansion. The mechanistic basis for effects of genetic
 mixture could include evolutionary responses (mixed invasions may harbour
 greater genetic diversity and thus elevated evolutionary potential) and/or
 fitness advantages of between-population mating (heterosis). If driven by
 evolution, positive effects of source population mixture should increase
 through time, as selection sculpts genetic variation. If driven by
 heterosis, effects of mixture should peak following first reproductive
 contact and then dissipate. Using a laboratory model system (beetles
 spreading through artificial landscapes), we quantified the velocity of
 range expansion for invasions initiated with one, two, four or six genetic
 sources over six generations. Our experiment was designed to test
 predictions corresponding to the evolutionary and heterosis mechanisms,
 asking whether any effects of genetic mixture occurred in early or later
 generations of range expansion. We also quantified demography and
 dispersal for each experimental treatment, since any effects of mixture
 should be manifest in one or both of these traits. Over six generations,
 invasions with any amount of genetic mixture (two, four and six sources)
 spread farther than single-source invasions. Our data suggest that
 heterosis provided a ‘catapult effect’, leaving a lasting signature on
 range expansion even though the benefits of outcrossing were transient.
 Individual-level trait data indicated that genetic mixture had positive
 effects on local demography (reduced extinction risk and enhanced
 population growth) during the initial stages of invasion but no consistent
 effects on dispersal ability. Our work is the first to demonstrate that
 genetic mixture can alter the course of spatial expansion, the stage of
 invasion typically associated with the greatest ecological and economic
 impacts. We suggest that similar effects of genetic mixture may be a
 common feature of biological invasions in nature, but that these effects
 can easily go undetected.
description: Wagner et
 al_patch_adjustmentsThis file contains data
 on the number of patches by which each replicate was "adjusted"
 in each generation. See the treadmill metaphor of the main
 text.Wagner et al_raw
 dataRaw data on beetle
 densities in each patch for each replicate in each
 generation.Wagner et
 al_treatment_assignmentsSource population
 composition of each replicate.
DOI: 10.5061/dryad.b59g7
title: Data from: Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew

description: An understanding of the evolution of pathogen quantitative traits in
 response to host selective pressures is essential for the development of
 durable management strategies for resistant crops. However, we still lack
 experimental data on the effects of partial host resistance on multiple
 phenotypic traits (aggressiveness) and evolutionary strategies in
 pathogens. We performed a cross-inoculation experiment with four grapevine
 hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola)
 sampled from susceptible and partially resistant grapevine varieties. We
 analysed the neutral and adaptive genetic differentiation of five
 quantitative traits relating to pathogen transmission. Isolates from
 resistant hosts were more aggressive than isolates from susceptible hosts,
 as they had a shorter latency period and higher levels of spore
 production. This pattern of adaptation contrasted with the lack of neutral
 genetic differentiation, providing evidence for directional selection. No
 specificity for a particular host variety was detected. Adapted isolates
 had traits that were advantageous on all resistant varieties. There was no
 fitness cost associated with this genetic adaptation, but several
 trade-offs between pathogen traits were observed. These results should
 improve the accuracy of prediction of fitness trajectories for this
 biotrophic pathogen, an essential element for the modelling of durable
 deployment strategies for resistant varieties.
description: PV_quanti_traits_partial_resistQuantitative traits of pathogenicity of Plasmopara viticola (oomycete) from two origins (susceptible and resistant grapevine hosts) when inoculated on different hosts (susceptible and resistant)
DOI: 10.5061/dryad.rt61j
title: Data from: Basal metabolic rate can evolve independently of morphological and behavioural traits

description: Quantitative genetic analyses of basal metabolic rate (BMR) can inform us
 about the evolvability of the trait by providing estimates of heritability
 but also of genetic correlations with other traits that may constrain the
 ability of BMR to respond to selection. Here we studied a captive
 population of zebra finches (Taeniopygia guttata) in which selection lines
 for male courtship rate have been established. We measure BMR in these
 lines to see whether selection on male sexual activity would change BMR as
 a potentially correlated trait. We find that the genetic correlation
 between courtship rate and BMR is practically zero, indicating that the
 two traits can evolve independently of each other. Interestingly, we find
 that the heritability of BMR in our population (h^2=0.45) is markedly
 higher than was previously reported for a captive zebra finch population
 from Norway. A comparison of the two studies shows that additive genetic
 variance in BMR has been largely depleted in the Norwegian population,
 especially the genetic variance in BMR that is independent of body mass.
 In our population the slope of BMR increase with body mass differs not
 only between the sexes but also between the six selection lines, which we
 tentatively attribute to genetic drift and/or founder effects being strong
 in small populations. Our study therefore highlights two things. Firstly,
 the evolvability of BMR may be less constrained by genetic correlations
 and lack of independent genetic variation than previously described.
 Secondly, genetic drift in small populations can rapidly lead to different
 evolvabilities across populations.
description: data_descriptiondatafiles.zip
DOI: 10.5061/dryad.8433
title: Data from: Gene flow among Modoc sucker and Sacramento sucker populations in the upper Pit River

description: The Modoc sucker (Catostomus microps) is a species that received legal
 protection in the United States based partially on concerns that
 anthropogenic environmental changes had restricted migration among
 populations and catalyzed hybridization with a congener, the Sacramento
 sucker (C. occidentalis). We applied eight microsatellite markers to
 samples of both species collected from throughout the range of Modoc
 suckers: two tributaries in the Pit River sub-basin and one tributary in
 the Goose Lake sub-basin. Modoc sucker populations in these three
 tributaries appeared to be largely isolated from one another: migration
 among Pit River tributaries appeared no greater than migration among
 sub-basins. Sacramento sucker populations appeared relatively more
 connected with one another, especially within the sub-basins.
 Interspecific hybrids were detected in all three tributaries. Tributaries
 in the Pit River sub-basin, which have retained typical habitats for both
 species, yielded relatively low proportions of hybrids (1.6% - 2.3%). The
 tributary in the Goose Lake sub-basin, which has undergone multiple cycles
 of hydrological change over the past two centuries, yielded a higher
 proportion of hybrids (10.9%). We conclude that hybridization between
 Modoc suckers and Sacramento suckers is not an active threat, but may be
 of conservation concern in situations where the habitat of one or both of
 these species has been eliminated or modified.
description: genotype data in CONVERT
 formatAppendix
 1
DOI: 10.5061/dryad.6mt70
title: Data from: Genotypic distribution and hepatic fibrosis among HIV/HCV co-infected individuals in Southern China: a retrospective cross-sectional study

description: Background: End-stage liver disease and hepatocellular carcinoma due to
 hepatitis C virus (HCV) co-infection are increasingly common causes of
 death among HIV-infected individuals. However, there are few clinical
 investigations of HIV/HCV co-infected individuals from low and
 middle-income nations. Here, we compare the epidemiology of HCV-infected
 and HIV/HCV co-infected individuals in Southern China and examine hepatic
 fibrosis scores in co-infected individuals. Methods: We conducted a
 retrospective cross-sectional study of treatment-naïve HIV/HCV co-infected
 and HCV mono-infected subjects. Bivariate and multivariate models were
 used to examine the association between demographics and HCV genotype.
 Among co-infected individuals, we also studied the relationship between
 fibrosis scores derived from non-invasive studies and HCV genotype.
 Results: Data were collected from 175 HCV-infected individuals, including
 89 (51 %) HIV/HCV co-infected individuals. HIV/HCV co-infection was
 correlated with intravenous drug use (AOR 46.25, p &lt; 0.001) and not
 completing high school (AOR 17.39, p &lt; 0.001) in a multivariate
 model. HIV/HCV co-infected individuals were more likely to be infected
 with HCV genotype 6a (p &lt; 0.0001) or 3a (p &lt; 0.023), whereas
 increased fibrosis (FIB-4 score) was associated with HCV genotype 3a
 infection (β 2.18, p &lt; 0.001). Discussion: Our results suggest that
 intravenous drug use is driving HIV/HCV co-infection in Southern China.
 While additional studies are needed, HCV genotype 6a is more common and
 genotype 3a appears to be associated with more severe hepatic fibrosis in
 co-infected individuals. Conclusions: Future HIV/HCV co-infection research
 in China should focus on at risk populations, HCV testing uptake, and
 genotype-specific treatment.
description: Phylogenetic
 treePhylogenetic tree
 analysis of HCV core protein gene sequences (n = 175). Shown are HCV
 mono-infected (blue circles) and HCV/HIV co-infected samples (red
 triangles)tree--combined-2013-Mar11.JPG
DOI: 10.5061/dryad.t938n
title: Data from: Senescence in duckweed: age-related declines in survival, reproduction, and offspring quality

description: 1. As they grow old, most organisms experience progressive physiological
 deterioration resulting in declining rates of survival and reproduction –
 a seemingly maladaptive phenomenon known as senescence. 2. Although
 senescence is usually defined with respect only to survival and
 reproduction, a third component of fitness, offspring quality, may also
 decline with age. Few studies, however, have assessed age-related changes
 in offspring quality using measures that truly reflect fitness. 3. In a
 controlled environment, we tested for age-related declines in three
 demographic components of fitness (survival, reproduction, and offspring
 quality) in Lemna minor, a small aquatic plant in the subfamily Lemnoideae
 (the duckweeds) with a short lifespan and rapid rate of asexual
 reproduction. Our primary measure of offspring quality, the intrinsic rate
 of increase, more closely approximates fitness than measures used in
 previous studies such as size, lifespan, and total reproductive output. 4.
 We observed strong age-related declines in all three components of
 fitness: old plants had lower rates of survival and reproduction, and
 produced lower-quality offspring than younger plants. 5. Theoretical and
 empirical research on the evolutionary biology of senescence should devote
 more attention to offspring quality. This often unrecognized component of
 fitness may change with age – as we have shown in L. minor – and may be
 shaped by, and feed back into, the same evolutionary forces that give rise
 to senescence.
description: Survival and
 Reproduction vs. Age (Phase 1)Lifespans and
 reproduction schedules for the 214 fronds of Lemna minor from Phase 1 of
 our study.BarksAndLaird_RawData_Phase1.csvOffspring Quality vs. Parental Age (Phase 2)Reproduction schedules and fitness measures for all of the offspring (n = 542) detached from 41 parental fronds of Lemna minor in Phase 2 of our study.BarksAndLaird_RawData_Phase2.csvR Code for Phase 1R code for Phase 1 to analyze changes in rates of survival and reproduction with age.BarksAndLaird_RScripts_Phase1.txtR Code for Phase 2R code for Phase 2 to analyze changes in offspring quality as a function of parental age.BarksAndLaird_RScripts_Phase2.txtR Code for GraphicsR code used to produce the figures in our paper.BarksAndLaird_RScripts_Plots.txt
DOI: 10.5061/dryad.4nv41
title: Data from: Reproductive strategies and isolation-by-demography in a marine clonal plant along an eutrophication gradient

description: Genetic diversity in clonal organisms includes two distinct components, 1)
 the diversity of genotypes or clones (i.e., genotypic richness) in a
 population, and 2) that of the alleles (i.e., allelic and gene diversity
 within populations, and differentiation between populations). We
 investigated how population differentiation and genotypic components are
 associated across a gradient of eutrophication in a clonal marine plant.
 To that end we combined direct measurements of sexual allocation (i.e.,
 flower and seed counts) and genotypic analyses, which are used as an
 estimator of effective sexual reproduction across multiple generations.
 Genetic differentiation across sites was also modeled according to an
 hypothesis here defined as isolation-by-demography, in which we use
 population-specific factors, genotypic richness and eutrophication, that
 are hypothesized to affect the source-sink dynamics and thus influence the
 genetic differentiation between a pair of populations. Eutrophic
 populations exhibited lower genotypic richness, in agreement with lower
 direct measurements of sexual allocation and contemporaneous gene flow.
 Genetic differentiation, while not explained by distance, was best
 predicted by genotypic richness and habitat quality. A multiple regression
 model using these two predictors was considered the best model (R2 =
 0.43). In this study, the relationship between environment and effective
 sexual-asexual balance is not simply (linearly) predicted by direct
 measurements of sexual allocation. Our results indicate that
 population-specific factors and the isolation-by-demography model should
 be used more often to understand genetic differentiation.
description: Oliva_et_al_data_MEIn the “Oliva_et_al_data_ME” file you will find: in the first sheet the coordinates of the sampled sites, in the second sheet the direct measurements of sexual allocation (flower and seed sets), in the third sheet the population dynamics measured descriptors (recruitment and mortality rates, demographic balance), and in the fourth sheet the multilocus genotypes (MLGs) for all the samples analysed across all the loci studied (i.e., 13 microsatellite loci) for the paper entitled “Reproductive strategies and isolation-by-demography in a marine clonal plant along an eutrophication gradient”.
DOI: 10.5061/dryad.q77rs
title: Data from: Environmental heterogeneity does not affect levels of phenotypic plasticity in natural populations of three Drosophila species

description: Adaptation of natural populations to variable environmental conditions may
 occur by changes in trait means and/or in the levels of plasticity. Theory
 predicts that environmental heterogeneity favors plasticity of adaptive
 traits. Here we investigated the performance in several traits of three
 sympatric Drosophila species freshly collected in two environments that
 differ in the heterogeneity of environmental conditions. Differences in
 trait means within species were found in several traits, indicating that
 populations differed in their evolutionary response to the environmental
 conditions of their origin. Different species showed distinct adaptation
 with a very different role of plasticity across species for coping with
 environmental changes. However, geographically distinct populations of the
 same species generally displayed the same levels of plasticity as induced
 by fluctuating thermal regimes. This indicates a weak and trait-specific
 effect of environmental heterogeneity on plasticity. Furthermore, similar
 levels of plasticity were found in a laboratory-adapted population of
 Drosophila melanogaster with a common geographic origin but adapted to the
 laboratory conditions for more than 100 generations. Thus, this study does
 not confirm theoretical predictions on the degree of adaptive plasticity
 among populations in relation to environmental heterogeneity but shows a
 very distinct role of species-specific plasticity.
description: alltraitcorPhenotypic data of several life history and stress resistance traits in 3 drosophila species from two environmentally markedly different locations
DOI: 10.5061/dryad.6m4c1
title: Data from: Flooding and soil composition determine beta-diversity of lowland forests in Northern South America

description: Beta diversity may be determined by dispersal limitation, environment and
 phylogeographic history. Our objective was to advance the understanding of
 plant species turnover in rainforests in Northern South America and
 determine which factors are affecting species beta-diversity. We evaluated
 the relative effect of environmental variables (i.e. soil, climate,
 fragmentation and flooding frequency) and dispersal limitation (i.e.
 geographical distance and resistance distance due mountain barriers) on
 tree beta diversity in 32 1-ha lowland forest plots. We found that tree
 species turnover was better explained by environmental distance than by
 geographic distance. Although, soil conditions and flooding regime were
 good predictors of tree species composition, almost half of the variance
 remained unexplained. In our study system, the Eastern Andean ridge had no
 significant effect on plant beta diversity, probably because of its young
 age in relation to the phylogeny. Our results provide support for the
 importance of environmental factors and suggests a more restricted role of
 dispersal limitation. Therefore, we advise that conservation strategies of
 lowland trees should consider specific forest types (e.g. seasonally
 flooded vs. terra firme, as well as piedmont vs. central Amazonian
 forests).
description: Stevenson et al. 2018
 Flooding_BiotropicaMatrix of species and
 plots used in the analyses. Numbers in the matrix represent the number of
 individual (DBH&gt; 10 cm.).
DOI: 10.5061/dryad.g35nt67k
title: Data from: A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales

description: This study uses a set of PCR-based methods to examine the putative
 microbiota associated with lichen thalli. In initial experiments,
 generalized oligonucleotide-primers for the 16S rRNA gene resulted in
 amplicon pools populated almost exclusively with fragments derived from
 lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This
 effectively masked the presence of other lichen-associated prokaryotes. In
 order to facilitate the study of the lichen microbiota, 16S ribosomal
 oligonucleotide-primers were developed to target Bacteria, but exclude
 sequences derived from chloroplasts and Cyanobacteria. A preliminary
 microbiotic survey of lichen thalli using these new primers has revealed
 the identity of several bacterial associates, including representatives of
 the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae
 and Brucellaceae, strains belonging to the genus Methylobacterium, and
 members of an undescribed lineage in the Rhizobiales. This new lineage was
 investigated and characterized through molecular cloning, and was found to
 be present in all examined lichens that are associated with green algae.
 There is evidence to suggest that members of this lineage may both account
 for a large proportion of the lichen-associated bacterial community and
 assist in providing the lichen thallus with crucial nutrients such as
 fixed nitrogen.
description: Hodkinson_and_Lutzoni_2009_16SThis is a NEXUS file containing all of the elements for the phylogenetic analyses run as part of the associated study. For additional details, see the "Materials and Methods: Phylogenetic Analyses" section of the associated manuscript.
DOI: 10.5061/dryad.56hk7t5
title: Data from: incR: a new R package to analyse incubation behaviour

description: Incubation represents a life stage of crucial importance for the optimal
 development of avian embryos. For most birds, incubation poses a trade-off
 between investing in self-maintenance and offspring care. Furthermore,
 incubation is affected by environmental temperatures and, therefore, will
 be likely impacted by climate change. Despite its relevance and readily
 available temperature logging methods, avian incubation research is
 hindered by recognised limitations in available software. In this paper, a
 new quantitative approach to analyse incubation behaviour is presented.
 This new approach is embedded in a free R package, incR. The flexibility
 of the R environment eases the analysis, validation and visualisation of
 incubation temperature data. The core algorithm in incR is validated here
 and it is shown that the method extracts accurate metrics of incubation
 behaviour (e.g. number and duration of incubation bouts). This paper also
 presents a suggested workflow along with detailed R code to aid the
 practical implementation of incR.
description: 10.1111jav.01710_nest_Data10.1111jav.01710_Environmental_Data