cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.869j5
title: Data from: Symbiont strain is the main determinant of variation in Wolbachia-mediated protection against viruses across Drosophila species

description: Wolbachia is a common heritable bacterial symbiont in insects. Its
 evolutionary success lies in the diverse phenotypic effects it has on its
 hosts coupled to its propensity to move between host species over
 evolutionary timescales. In a survey of natural host–symbiont associations
 in a range of Drosophila species, we found that 10 of 16 Wolbachia strains
 protected their hosts against viral infection. By moving Wolbachia strains
 between host species, we found that the symbiont genome had a much greater
 influence on the level of antiviral protection than the host genome. The
 reason for this was that the level of protection depended on the density
 of the symbiont in host tissues, and Wolbachia rather than the
 host-controlled density. The finding that virus resistance and symbiont
 density are largely under the control of symbiont genes in this system has
 important implications both for the evolution of these traits and for
 public health programmes using Wolbachia to prevent mosquitoes from
 transmitting disease.
description: Survival data in
 experiment 1 (Original hosts)Column headers
 correspond to the Fly species, the Wolbachia strain (W_strain), the
 Wolbachia infection status (Status), the virus infection treatment
 (Treatment), the vial number, the total number of flies in a replicate
 vial (Sum), the number of flies lost during the experiment (Lost) and the
 number of days post-viral infection. Values in the latter columns indicate
 the cumulative number of dead flies after virus
 infection.Survival_experiment1.txtSurvival data in experiment 2 (Original hosts and STCP line)Column headers correspond to the batch of infection, the type of host, the Fly species, the Wolbachia strain (W_strain), the Wolbachia infection status (Status), the virus infection treatment (Treatment), the vial number, the total number of flies in a replicate vial (Sum), the number of flies lost during the experiment (Lost) and the number of days post-viral infection. Values in the latter columns indicate the cumulative number of dead flies after virus infection.Survival_experiment2.txtFHV titer qPCR data in experiment 1 (Original hosts)Column headers correspond to the Wolbachia infection status (Status), the Wolbachia strain (W_strain), the Ct values for FHV and the control fly gene Rpl32 (2 technical replicates for each).FHV_titer_experiment1.txtFHV titer qPCR data in experiment 2 (Original hosts and STCP line)Column headers correspond to the type of host, the fly species, the Wolbachia strain (W_strain), the Wolbachia infection status (Status), the Ct values for FHV and the control fly gene Rpl32 (2 technical replicates for each).FHV_titer_experiment2.txtWolbachia density qPCR data in experiment 2 (Original hosts and STCP line)Column headers correspond to the type of host, the fly species, the Wolbachia strain (W_strain), the Ct values for the Wolbachia gene atpD and the control fly gene Rpl32 (2 technical replicates for each).Wolbachia_density_experiment2.txt
DOI: 10.5061/dryad.2hv6c
title: Data from: What controls variation in carbon use efficiency among Amazonian tropical forests?

description: Why do some forests produce biomass more efficiently than others?
 Variations in Carbon Use Efficiency (CUE: total Net Primary Production
 (NPP)/ Gross Primary Production (GPP)) may be due to changes in wood
 residence time (Biomass/NPPwood), temperature, or soil nutrient status. We
 tested these hypotheses in 14, one ha plots across Amazonian and Andean
 forests where we measured most key components of net primary production
 (NPP: wood, fine roots, and leaves) and autotrophic respiration (Ra; wood,
 rhizosphere, and leaf respiration). We found that lower fertility sites
 were less efficient at producing biomass and had higher rhizosphere
 respiration, indicating increased carbon allocation to belowground
 components. We then compared wood respiration to wood growth and
 rhizosphere respiration to fine root growth and found that forests with
 residence times &lt;40 yrs had significantly lower maintenance
 respiration for both wood and fine roots than forests with residence times
 &gt;40 yrs. A comparison of rhizosphere respiration to fine root
 growth showed that rhizosphere growth respiration was significantly
 greater at low fertility sites. Overall, we found that Amazonian forests
 produce biomass less efficiently in stands with residence times &gt;40
 yrs and in stands with lower fertility, but changes to long-term mean
 annual temperatures do not impact CUE.
description: Biotropica_Doughty__dataMonthly carbon cycling data (total NPP and autotrophic respiration) for all plots mentioned in the paper. Mean plot characteristics such as soil chemistry, texture, temperature, and precipitation also listed.
DOI: 10.15468/dl.yt7z8b
title: Occurrence Download

description: A dataset containing 394168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Geometry POLYGON((-79.49664 8.41317,-78.34105 8.26458,-77.66727 9.08024,-77.66727 10.09923,-79.72481 10.09923,-80.27681 9.25242,-80.00021 8.23304,-79.49664 8.41317))",
 "Geometry POLYGON((-81.00863 -2.85247,-80.37584 -2.86423,-79.74013 -2.54297,-79.10572 -1.19515,-78.94505 -0.79733,-78.53968 0.19906,-79.07294 1.68696,-80.96285 1.68696,-81.00863 -2.85247))",
 "Geometry POLYGON((-79.05589 1.45794,-79.1441 -0.20232,-77.82467 1.36953,-77.23373 2.26162,-76.70516 3.653,-78.96305 3.54864,-79.05589 1.45794))",
 "Geometry POLYGON((-78.21305 3.60637,-76.78551 3.55788,-76.65218 4.14334,-76.59471 5.82576,-76.56096 6.19873,-76.65623 7.27095,-77.03181 8.44549,-77.98586 9.23932,-78.44274 8.06193,-78.21305 3.60637))"
 ]
 },
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 394168 records from 279 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000783-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1368p
title: Data from: Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada's Great Bear Lake

description: Range expansion in north-temperate fishes subsequent to the retreat of the
 Wisconsinan glaciers has resulted in the rapid colonization of previously
 unexploited, heterogeneous habitats and, in many situations, secondary
 contact among conspecific lineages that were once previously isolated.
 Such ecological opportunity coupled with reduced competition likely
 promoted morphological and genetic differentiation within and among
 post-glacial fish populations. Discrete morphological forms existing in
 sympatry, for example, have now been described in many species, yet few
 studies have directly assessed the association between morphological and
 genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are
 found in several large-lake systems including Great Bear Lake (GBL),
 Northwest Territories, Canada, where several shallow-water forms are
 known. Here, we assess microsatellite and mitochondrial DNA variation
 among four morphotypes of Lake Trout from the five distinct arms of GBL,
 and also from locations outside of this system to evaluate several
 hypotheses concerning the evolution of morphological variation in this
 species. Our data indicate that morphotypes of Lake Trout from GBL are
 genetically differentiated from one another, yet the morphotypes are still
 genetically more similar to one another compared with populations from
 outside of this system. Furthermore, our data suggest that Lake Trout
 colonized GBL following dispersal from a single glacial refugium (the
 Mississippian) and support an intra-lake model of divergence. Overall, our
 study provides insights into the origins of morphological and genetic
 variation in post-glacial populations of fishes and provides benchmarks
 important for monitoring Lake Trout biodiversity in a region thought to be
 disproportionately susceptible to impacts from climate change.
description: Genepop Data
 FileGenepop data file (3
 digit format) used for analyses - sample codes are listed in Table 1 of
 the manuscript.Genepop 3Dig - All
 Samples
DOI: 10.5061/dryad.vm11r
title: Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum

description: The life cycles and dispersal of edible fungi are still poorly known, thus
 limiting our understanding of their evolution and domestication. The
 prized Tuber melanosporum produces fruitbodies (fleshy organs where
 meiospores mature) gathered in natural, spontaneously inoculated forests
 or harvested in plantations of nursery-inoculated trees. Yet, how
 fruitbodies are formed remains unclear, thus limiting yields, and how
 current domestication attempts affect population genetic structure is
 overlooked. Fruitbodies result from mating between two haploid
 individuals: the maternal parent forms the flesh and the meiospores, while
 the paternal parent only contributes to the meiospores. We analyzed the
 genetic diversity of T. melanosporum comparatively in spontaneous forests
 versus plantations, using SSR polymorphism of 950 samples from South-East
 France. All populations displayed strong genetic isolation by distance at
 the metric scale, possibly due to animal dispersal, meiospore persistence
 in soil, and/or exclusion of unrelated individuals by vegetative
 incompatibility. High inbreeding was consistently found, suggesting that
 parents often develop from meiospores produced by the same fruitbody.
 Unlike maternal genotypes, paternal mycelia contributed to few fruitbodies
 each, did not persist over years, and were undetectable on tree
 mycorrhizae. Thus, we postulate that germlings from the soil spore bank
 act as paternal partners. Paternal genetic diversity and outbreeding were
 higher in plantations than in spontaneous truffle-grounds, perhaps because
 truffle growers disperse fruitbodies to maintain inoculation in
 plantations. However, planted and spontaneous populations were not
 genetically isolated, so that T. melanosporum illustrates an early step of
 domestication where genetic structure remains little affected.
description: Truffle genotyping
 dataOpen document files
 (.odt) of genotyping data (11 to 13 microsatellites and mating-type) at
 three different sampling scales (described in the manuscript). Each file
 contain a first slide with the description of column names and several
 slides for the data from the different samplings sites (brûlés or
 truffle-grounds).Truffle-genotyping_data.zipzygotes genotypes & scriptZygotic genotypes and R script to estimate heterozygote deficits from the zygotic genotype obtained by spore extraction from Tuber melanosporum fruitbodies sampled at brûlé scale (PB1, PB2, PB3, SB1, SB2). For each locus, the first allele corresponds to the maternal one (genotype of the gleba) and the second one to the paternal one (detected after spore extraction).
DOI: 10.5061/dryad.qt7nr84
title: Data from: Trait patterns across space and time suggest an interplay of facilitation and competition acting on Neotropical hummingbird-pollinated plant communities

description: Pollinators may influence plant community assembly through biotic
 filtering and/or plant-plant competition and facilitation. The relative
 importance of each process, however, vary according to the scale and how
 strongly plants share their pollinators, and possibly in relation to the
 pollinator groups considered. We here investigated the assembly of three
 Atlantic forest hummingbird-pollinated plant communities across space
 (among all species in the communities) and time, i.e. yearly flowering
 phenology (between pairs of co-flowering species), based on the pairwise
 distances of multiple floral traits (corolla length, anther and stigma
 height, colour and nectar). Because tropical hummingbird-pollinated plants
 are often subdivided in two pollination niches (hermits vs. non-hermits),
 we also analyzed these groups separately. We found that trait structure
 across space was clustered for some floral traits, suggesting biotic
 filtering and facilitation. All floral traits had weak phylogenetic
 signal, indicating that closely related species were not more similar than
 distantly related species. Moreover, floral traits were randomly
 structured along the phenology when analyzing all plants together. On the
 other hand, we found similar corolla length but divergent anther height in
 co-flowering pairs within the same pollination niche. Thus, plants may
 benefit from flowering together and avoid competition through fine
 adjustments in reproductive traits. Our results also suggest that clear
 signals of competition and facilitation among plants are only apparent
 when species strongly share their pollinators and depending on the traits
 that are considered. Our study illustrate a complex interplay of biotic
 filtering, facilitation and competition as processes structuring
 assemblages of plants sharing the same functional group of pollinators.
description: Effective corolla
 lengthEffective corolla length
 of the hummingbird-pollinated plant species of the Atlantic forest.
 Species abbreviations can be found on the supplementary
 material.EF.csvAnther and stigma heightAnther and stigma height of the hummingbird-pollinated plant species of the Atlantic forest. Species abbreviations can be found on the supplementary material.ASL.csvColour distancesMatrix of colour distances of the hummingbird-pollinated plant species of the Atlantic forest. Species abbreviations can be found on the supplementary material.matriz_colour.xlsxNectar traitsNectar traits of the hummingbird-pollinated plant species of the Atlantic forest. Species abbreviations can be found on the supplementary material.NE.csvPhenology dataNumber of flowers of the hummingbird-pollinated plant species of the Atlantic forest on each community. Species abbreviations can be found on the supplementary material.clump2.txt
DOI: 10.15468/dl.epds99
title: Occurrence Download

description: A dataset containing 2718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xenostegia tridentata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2718 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000795-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7g60t
title: Data from: Life-history evolution in response to changes in metapopulation structure in an arthropod herbivore

description: The persistence and dynamics of populations largely depends on the way
 they are configured and integrated into space and the ensuing
 eco-evolutionary dynamics. We manipulated spatial and temporal variation
 in patch size in replicated experimental metapopulations of the herbivore
 mite Tetranychus urticae and followed evolutionary dynamics over
 approximately 30 generations. A significant divergence in life history
 traits, physiological endpoints and gene expression was recorded in the
 spatially and spatiotemporally variable metapopulation, but also a
 remarkable convergence relative to the stable reference metapopulation in
 traits related to size and fecundity and in its transcriptional
 regulation. The observed evolutionary dynamics are tightly linked to
 demographic changes, more specifically frequent episodes of resource
 shortage that increased the reproductive performance of mites on tomato, a
 challenging host plant. This points towards a general, adaptive stress
 response in stable spatial variable and spatiotemporal variable
 metapopulations that pre-adapts a herbivore arthropod to novel
 environmental stressors.
description: Overviewdata 4
 DRYADRaw data on life history
 and physiology evolution of T. urticae in response to the 3 metapopulation
 treatments.
DOI: 10.5061/dryad.td470
title: Data from: Sexual signals reveal males’ oxidative stress defenses: testing the hypothesis in an invertebrate

description: 1.The hypothesis that sexual traits reveal the oxidative stress resistance
 of their bearers has been widely tested in vertebrates but remains
 unexplored in invertebrates. Here, Hetaerina americana was used to test
 whether oxidative stress defenses are advertised by male wing spot size
 and color (a male sexual trait). To this end we asked (1) whether
 oxidative stress reduced survival, (2) whether wing spot size revealed
 males’ antioxidant defenses, and (3) how wing spot size and color were
 affected by oxidative stress. 2.We elevated oxidative stress by injecting
 adult males with paraquat (a compound that favors the production of free
 radicals) and then examined how this affected male survival and wing spot
 size. We then related the expression of wing spot size to indicators of
 oxidative stress – H2O2 and total Antioxidant Capacity (TAC), Super Oxide
 Dismutase (SOD) and Catalase (CAT) – in adult males (whose wing spot is
 fixed) injected with Paraquat (PQ). In teneral males, whose wing-spots are
 still forming, we compared wing-spot size, color (red and yellow chroma)
 and brightness in individuals injected with paraquat, or water as a
 control. 3.Oxidative stress reduced the survival of adult and teneral
 males. While the H2O2 and TAC markers of antioxidant defenses were
 positively correlated with wing spot size, there was no correlation with
 CAT and a negative correlation with SOD. In teneral males, PQ increased
 the yellow chroma and brightness of wing spots, but did not affect spot
 size or red chroma. 4.Our results highlight the importance of measuring
 different markers as indicators of male oxidative stress defenses, and
 that the sexual signals of invertebrates may reveal the oxidative stress
 status of their bearers.
description: Oxidative stress defense
 in males of Hetaerina americanaEach objective in the
 data file corresponds with a specific objective in the
 paper.Oxidative stress in
 Hetaerina.xlsx
DOI: 10.5061/dryad.0f8n6sj
title: Data from: Haemosporidian infection and co-infection affect host survival and reproduction in wild populations of great tits

description: Theoretical studies predict that parasitic infection may impact host
 longevity and ultimately modify the trade-off between reproduction and
 survival. Indeed, a host may adjust its energy allocation in current
 reproduction to balance the negative effects of parasitism on its survival
 prospects. However, very few empirical studies tested this prediction.
 Avian haemosporidian parasites provide an excellent opportunity to assess
 the influence of parasitic infection on both host survival and
 reproduction. They are represented by three main genera (Plasmodium,
 Haemoproteus and Leucocytozoon) and are highly prevalent in many bird
 populations. Here we provide the first known long-term field study (12
 years) to explore the effects of haemosporidian parasite infection and
 co-infection on fitness in two populations of great tits (Parus major),
 using a multistate modelling framework. We found that while co-infection
 decreased survival probability, both infection and co-infection increased
 reproductive success. This study provides evidence that co-infections can
 be more virulent than single infections. It also provides support for the
 life-history theory which predicts that reproductive effort can be
 adjusted to balance one’s fitness when survival prospects are challenged.
description: Monitoring of great tits
 reproductive success, body condition and infection
 statusWe investigated the
 impact of haemosporidian parasite infections on reproduction and survival
 of two populations of great tits (Parus major) located in two study sites
 in Switzerland: Dorigny and Monod. Birds were sampled during the breeding
 season for 12 consecutive years (2005-2016). Nest boxes were regularly
 inspected from mid-March and laying date (1 April = day 1), clutch size
 and fledging success were recorded. Adults were marked with an
 individually numbered aluminium ring (Swiss Ornithological Institute,
 Switzerland), weighed with an electronic balance and the tarsus was
 measured using digital callipers (0.01 mm). Adult sex and age were
 determined using plumage characteristics or ringing records when
 available. In order to investigate avian haemosporidian infection, 30-50
 μl of blood were sampled by brachial venipuncture. Parasites were detected
 from blood samples by nested PCR. Nested PCR products were sequenced and
 identified by performing a local BLAST search in the MalAvi database.
 Because Plasmodium and Haemoproteus gene fragments were amplified with the
 same primer pair, we were not able to differentiate co-infections by
 Plasmodium and Haemoproteus lineages from mixed infections between
 Plasmodium or Haemoproteus lineages.Data_IJP_2018.xlsx
DOI: 10.5061/dryad.7f0c4
title: Data from: Cannibalism by damselflies increases with rising temperature

description: Trophic interactions are likely to change under climate warming. These
 interactions can be altered directly by changing consumption rates, or
 indirectly by altering growth rates and size asymmetries among individuals
 that in turn affect feeding. Understanding these processes is particularly
 important for intraspecific interactions, as direct and indirect changes
 may exacerbate antagonistic interactions. We examined the effect of
 temperature on activity rate, growth and intraspecific size asymmetries,
 and how these temperature dependencies affected cannibalism in Lestes
 congener, a damselfly with marked intraspecific variation in size.
 Temperature increased activity rates and exacerbated differences in body
 size by increasing growth rates. Increased activity and changes in body
 size interacted to increase cannibalism at higher temperatures. We argue
 that our results are likely to be general to species with life-history
 stages that vary in their temperature dependencies, and that the effects
 of climate change on communities may depend on the temperature
 dependencies of intraspecific interactions.
DOI: 10.5061/dryad.1f217
title: Data from: The evolution of genetic architectures underlying quantitative traits

description: In the classic view introduced by R. A. Fisher, a quantitative trait is
 encoded by many loci with small, additive effects. Recent advances in
 quantitative trait loci mapping have begun to elucidate the genetic
 architectures underlying vast numbers of phenotypes across diverse taxa,
 producing observations that sometimes contrast with Fisher's
 blueprint. Despite these considerable empirical efforts to map the genetic
 determinants of traits, it remains poorly understood how the genetic
 architecture of a trait should evolve, or how it depends on the selection
 pressures on the trait. Here, we develop a simple, population-genetic
 model for the evolution of genetic architectures. Our model predicts that
 traits under moderate selection should be encoded by many loci with highly
 variable effects, whereas traits under either weak or strong selection
 should be encoded by relatively few loci. We compare these theoretical
 predictions with qualitative trends in the genetics of human traits, and
 with systematic data on the genetics of gene expression levels in yeast.
 Our analysis provides an evolutionary explanation for broad empirical
 patterns in the genetic basis for traits, and it introduces a single
 framework that unifies the diversity of observed genetic architectures,
 ranging from Mendelian to Fisherian.
description: rajon_plotkin_prsb_2013_codeThe folders starting with "Simul_" contain C++ and R code for obtaining and analyzing simulation results. The two remaining folders contain R and Sweave code for making the figures in the manuscript. See the enclosed README.txt file for more information.