cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bc94c
title: Data from: Intralocus sexual conflict and the tragedy of the commons in seed beetles

description: The evolution of male traits that inflict direct harm on females during
 mating interactions can result in a so-called tragedy of the commons,
 where selfish male strategies depress population viability. This tragedy
 of the commons can be magnified by intralocus sexual conflict (IaSC)
 whenever alleles that reduce fecundity when expressed in females spread in
 the population because of their benefits in males. We evaluated this
 prediction by detailed phenotyping of 73 isofemale lines of the seed
 beetle Callosobruchus maculatus. We quantified genetic variation in life
 history and morphology, as well as associated covariance in male and
 female adult reproductive success. In parallel, we created replicated
 artificial populations of each line and measured their productivity.
 Genetic constraints limited independent trait expression in the sexes, and
 we identified several instances of sexually antagonistic covariance
 between traits and fitness, signifying IaSC. Population productivity was
 strongly positively correlated to female adult reproductive success but
 uncorrelated with male reproductive success. Moreover, male (female)
 phenotypic optima for several traits under sexually antagonistic selection
 were exhibited by the genotypes with the lowest (highest) population
 productivity. Our study forms a direct link between individual-level
 sex-specific selection and population demography and places life-history
 traits at the epicenter of these dynamics.
description: Dryad
 dataExcel-file containing
 data on Morphology, Life history, Development times and Population
 Productivity. For data on sex-specific lifetime reproductive success, see
 Berger et al. 2014 (Evolution).
DOI: 10.5061/dryad.6c2s3
title: Data from: Reed warbler hosts fine-tune their defenses to track three decades of cuckoo decline

description: Interactions between avian hosts and brood parasites can provide a model
 for how animals adapt to a changing world. Reed warbler (Acrocephalus
 scirpaceus) hosts employ costly defenses to combat parasitism by common
 cuckoos (Cuculus canorus). During the last three decades cuckoos have
 declined markedly across England, reducing parasitism at our study site
 (Wicken Fen) from 24% of reed warbler nests in 1985 to 1% in 2012. Here we
 show with experiments that host mobbing and egg rejection defenses have
 tracked this decline in local parasitism risk: the proportion of reed
 warbler pairs mobbing adult cuckoos (assessed by responses to cuckoo
 mounts and models) has declined from 90% to 38%, and the proportion
 rejecting non-mimetic cuckoo eggs (assessed by responses to model eggs)
 has declined from 61% to 11%. This is despite no change in response to
 other nest enemies or mimetic model eggs. Individual variation in both
 defenses is predicted by parasitism risk during the host's egg-laying
 period. Furthermore, the response of our study population to temporal
 variation in parasitism risk can also explain spatial variation in egg
 rejection behavior in other populations across Europe. We suggest that
 spatial and temporal variation in parasitism risk has led to the evolution
 of plasticity in reed warbler defenses.
description: Thorogood&Davies_datasetsData collected in field from surveys of reed warbler nests and experiments with model cuckoo eggs and model adult cuckoos. Parasitism rate calculated over three-day period from laying of the first egg. See methods in MS for more details.
DOI: 10.15468/dl.mft6hp
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bouchetia anomala",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 230 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000823-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d52q0
title: Data from: Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

description: The extraction and characterization of DNA from aquatic environmental
 samples offers an alternative, non-invasive approach for the detection of
 rare species. Environmental DNA, coupled with PCR and next-generation
 sequencing (“metabarcoding”), has proven to be very sensitive for the
 detection of rare aquatic species. Our study used a custom designed
 group-specific primer set and next-generation sequencing for the detection
 of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida;
 Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis
 photogenis), one invasive species (Round Goby, Neogobius melanostomus) and
 an additional 78 native species from two large Great Lakes tributary
 rivers in southern Ontario, Canada; the Grand River and the Sydenham
 River. Out of 82 fish species detected in both rivers using capture-based
 and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish
 species in the Grand River and the Sydenham River, respectively, which
 included our four target species. Our analyses also identified significant
 positive and negative species co-occurrence patterns between our target
 species and other identified species. Our results demonstrate that eDNA
 metabarcoding that targets the fish community as well as individual
 species of interest provides a better understanding of factors affecting
 the target species spatial distribution in an ecosystem than possible with
 only target species data. Additionally, eDNA is easily implemented as an
 initial survey tool, or alongside capture-based methods, for improved
 mapping of species distribution patterns.
description: mec170853-sup-0001-SupplementaryTablesSupplementary Tables S1, S2A, S2B, S2C, S3A, S3B, S3C, and S3D.mec170853-sup0002-commandsBLASTn script and R commands used in this study.
DOI: 10.5061/dryad.dj3v1
title: Data from: The oxidative cost of reproduction depends on early development oxidative stress and sex in a bird species

description: In the early 2000’s, a new component of the cost of reproduction was
 proposed: oxidative stress. Since then the oxidative cost of reproduction
 hypothesis has, however, received mixed support. Different arguments have
 been provided to explain this. Among them, the lack of a life history
 perspective on most experimental tests was suggested. We manipulated the
 levels of a key intracellular antioxidant (glutathione) in captive zebra
 finches (Taeniopygia guttata) during a short period of early life and
 subsequently tested the oxidative cost of reproduction. Birds were allowed
 to mate freely in an outdoor aviary during several months. We repeatedly
 enlarged or reduced their broods to increase or reduce, respectively,
 breeding effort. Birds whose glutathione levels were reduced during growth
 showed higher erythrocyte resistance to free radical-induced hemolysis
 when forced to rear enlarged broods. This supports the hypothesis
 predicting the occurrence of developing programs matching early and adult
 environmental conditions to improve fitness. Moreover, adult males rearing
 enlarged broods endured higher plasma levels of lipid oxidative damage
 than control males, whereas adult females showed the opposite trend. Since
 most previous studies reporting non-significant or opposite results used
 females only, we also discuss some sex-related particularities that may
 contribute to explain unexpected results.
description: @REPOSITORY Romero-Haro
 et al. The oxidative cost of reproduction depends on early development
 oxidative stress and sex inDatafile for the
 manuscript: The oxidative cost of reproduction depends on early
 development oxidative stress and sex in a bird species
DOI: 10.5061/dryad.158pb518
title: Data from: Adaptation with gene flow across the landscape in a dune sunflower

description: Isolation by adaptation increases divergence at neutral loci when natural
 selection against immigrants reduces the rate of gene flow between
 different habitats. This can occur early in the process of adaptive
 divergence and is a key feature of ecological speciation. Despite the
 ability of isolation by distance and other forms of landscape resistance
 to produce similar patterns of neutral divergence within species, few
 studies have used landscape genetics to control for these other forces. We
 have studied the divergence of Helianthus petiolaris ecotypes living in
 active sand dunes and adjacent non-dune habitat, using landscape genetics
 approaches, such as circuit theory and multiple regression of distance
 matrices, in addition to coalescent modelling. Divergence between habitats
 was significant, but not strong, and was shaped by isolation by distance.
 We expected that increased resistance due to patchy and unfavourable
 habitat in the dunes would contribute to divergence. Instead, we found
 that landscape resistance models with lower resistance in the dunes
 performed well as predictors of genetic distances among subpopulations.
 Nevertheless, habitat class remained a strong predictor of genetic
 distance when controlling for isolation by resistance and isolation by
 distance. We also measured environmental variables at each site and
 confirmed that specific variables, especially soil nitrogen and vegetation
 cover, explained a greater proportion of variance in genetic distance than
 did landscape or the habitat classification alone. Asymmetry in effective
 population sizes and numbers of migrants per generation was detected using
 coalescent modelling with Bayesian inference, which is consistent with
 incipient ecological speciation being driven by the dune habitat.
description: Population_datagsd_main_15l.strugsd_migrate_12l
DOI: 10.6084/m9.figshare.31152310.v1
title: data of figure1

description: Growth characteristics of <i>Trichophyton schoenleinii </i>isolates from sporadic and endemic regions at different temperatures.<br>
DOI: 10.5061/dryad.4p7n5
title: Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards

description: Dating the time of divergence and understanding speciation processes are
 central to the study of the evolutionary history of organisms but are
 notoriously difficult. The difficulty is largely rooted in variations in
 the ancestral population size or in the genealogy variation across loci.
 To depict the speciation processes and divergence histories of three
 monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear
 loci and combined with one mitochondrial locus published in GenBank. They
 were analyzed by a multispecies coalescent approach within a Bayesian
 framework. Divergence dating based on the gene tree approach showed high
 variation among loci, and the divergence was estimated at an earlier date
 than when derived by the species tree approach. To test whether variations
 in the ancestral population size accounted for the majority of this
 variation, we conducted computer inferences using isolation-with-migration
 (IM) and approximate Bayesian computation (ABC) frameworks. The results
 revealed that gene flow during the early stage of speciation was strongly
 favored over the isolation model, and the initiation of the speciation
 process was far earlier than the dates estimated by gene- and
 species-based divergence dating. Due to their limited dispersal ability,
 it is suggested that geographic isolation may have played a major role in
 the divergence of these Takydromus species. Nevertheless, the current
 study reveals a more complex situation and demonstrates that gene flow
 during the speciation process cannot be overlooked and may have a great
 impact on divergence dating. By using multilocus data and incorporating
 Bayesian coalescence approaches, we provide a more biologically realistic
 framework for delineating the divergence history of Takydromus.
description: alignmentDNA sequence alignmentsSpecies tree files in this studySpecies tree of Takydromus constructed by (A) mtDNA and 16 nuclear loci (B) mtDNA only (C) nuclear loci only using substitution rate prior. Divergence times are shown at the nodes with 95% highest posterior densities in brackets. Bayesian posterior probabilities are shown above the branchesspeciestree files.zip12S sequence alignment12S sequence alignment used in this study12S.fas
DOI: 10.5061/dryad.p5k2r
title: Data from: Passive rafting is a powerful driver of transoceanic gene flow

description: Dispersal by passive oceanic rafting is considered important for the
 assembly of biotic communities on islands. However, not much is known
 about levels of population genetic connectivity maintained by rafting over
 transoceanic distances. We assess the evolutionary impact of kelp-rafting
 by estimating population genetic differentiation in three kelp-associated
 invertebrate species across a system of islands isolated by oceanic gaps
 for over 5 million years, using mtDNA and AFLP markers. The species occur
 throughout New Zealand's subantarctic islands, but lack pelagic
 stages and any opportunity for anthropogenic transportation, and hence
 must rely on passive rafting for long-distance dispersal. They all have
 been directly observed to survive transoceanic kelp-rafting journeys in
 this region. Our analyses indicate that regular gene flow occurs among
 populations of all three species between all of the islands, especially
 those on either side of the subtropical front oceanographic boundary.
 Notwithstanding its perceived sporadic nature, long-distance kelp-rafting
 appears to enable significant gene flow among island populations separated
 by hundreds of kilometres of open ocean.
description: AFLP genotype data from
 island populations of kelp-associated marine
 invertebratesNikula et al 2012_AFLP
 DataSheets for Dryad.xlsx
DOI: 10.5061/dryad.0hj6g
title: Data from: Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in northwest Europe

description: Glacial and post-glacial processes are known to be important determinants
 of contemporary population structuring for many species. In Europe,
 refugia in the Italian, Balkan and Iberian peninsulas are believed to be
 the main sources of species colonising northern Europe after the glacial
 retreat, however, there is increasing evidence of small, cryptic refugia
 existing north of these for many cold-tolerant species. This study
 examined the glacial history of Atlantic salmon in Western Europe using
 two independent classes of molecular markers, nuclear microsatellites and
 mitochondrial DNA variation. Alongside the well-documented refuge in the
 Iberian Peninsula, evidence for a cryptic refuge in northwest France is
 also presented. Critically, methods utilised to estimate divergence times
 between the refugia indicated that salmon in these two regions had
 diverged a long time before the last glacial maximum; coalescence analysis
 (as implemented in the program IMa2) estimated divergence times at around
 60,000 years before present. Through the examination of haplotype
 frequencies, previously glaciated areas of northwest Europe, i.e. Britain
 and Ireland, appear to have been colonised from salmon expanding out of
 both refugia, with the southwest of England being the primary contact zone
 and exhibiting the highest genetic diversity.
description: MICROS_&_RFLPFINAL2new copyRaw data for microsatellite loci and RFLP-derived ND1 haplotypes. Excel spreadsheet, msats in standard 2-column format. Corresponding ND1 sequence data available in EMBL (Accn No.s HF586486 – HF586505)
DOI: 10.5061/dryad.0fm71
title: Data from: From nature to the labratory: the impact of founder effects in adaptation

description: Most founding events entail a reduction of population size, which in turn
 leads to genetic drift effects that can deplete alleles. Besides reducing
 neutral genetic variability, founder effects can in principle shift
 additive genetic variance for phenotypes that underlie fitness. This could
 then lead to different rates of adaptation among populations that have
 undergone a population size bottleneck as well as an environmental change,
 even when these populations have a common evolutionary history. Thus
 theory suggests that there should be an association between observable
 genetic variability for both neutral markers and phenotypes related to
 fitness. Here we test this scenario by monitoring the early evolutionary
 dynamics of six laboratory foundations derived from founders taken from
 the same source natural population of Drosophila subobscura. Each
 foundation was in turn three-fold replicated. During their first few
 generations, these six foundations showed an abrupt increase in their
 genetic differentiation, within and between foundations. The eighteen
 populations that were monitored also differed in their patterns of
 phenotypic adaptation according to their immediately ancestral founding
 sample. Differences in early genetic variability and in effective
 population size were found to predict differences in rate of adaptation
 during the first 21 generations of laboratory evolution. We show that
 evolution in a novel environment is strongly contingent not only on the
 initial composition of a newly-founded population but also on the
 stochastic changes which occur during the first generations of
 colonization. Such effects make laboratory populations poor guides to the
 evolutionary genetic properties of their ancestral wild populations.
description: Genotypes for the 6
 Foundations_DryadIndividual genotypes for
 9 microsatellites of the six foundations at generations zero (G0), three
 (G3) and 14/15 (G14/G15)three fold replicated for generations 3 and 14/15
 - data used for estimating genetic variability and differentiation. The
 first three digits correspond to one allele and the next three to the
 other allele at each locus.Phenotypic data for the
 6 Foundations_DryadMean values of
 life-history traits per generation and foundation that were used to trace
 evolutionary trajectories. Mean values were obtained as the difference
 between each replicate value and the control replicate with the same
 randomly defined number.
DOI: 10.5061/dryad.9hk3g
title: Data from: Strategic exploitation of fluctuating asymmetry in male Endler's guppy courtship displays is modulated by social environment

description: Lateral asymmetry in signalling traits enables males to strategically
 exploit their best side. In many animals, both body colouration and
 fluctuating asymmetry are signals of male attractiveness. We demonstrated
 experimentally that even sexually naïve male Poecilia wingei were able to
 identify their most attractive side (i.e. that with a higher proportion of
 carotenoid pigmentation) and use it preferentially during courtship.
 Notably, males retained their strategic signalling in a male-biased social
 environment, whereas they ceased to signal strategically in a
 female-biased environment. The degree of asymmetry in colouration did not
 affect overall courtship activity. Strategic lateralization in courtship
 displays was strongest and most repeatable in the male-biased social
 environment where males competed with rivals for matings. Individual
 asymmetry in colouration changed considerably over a period of 3 months.
 This suggests that colouration is a dynamic feature during adulthood and
 that males are capable of tracking and strategically exploiting their
 lateral asymmetry in accordance with their social environment.
description: Data on color and
 behavior of courting malesRaw data and basic
 indexes used for the analysis
DOI: 10.5061/dryad.8n3m4
title: Data from: Groundwater salinisation intensifies drought impacts in forests and reduces refuge capacity

description: 1. Shallow groundwater aquifers regularly support drought refuges for
 water-dependent ecosystems. However, many aquifers are impacted by
 over-extraction and pollution, potentially degrading their ability to
 support groundwater-fed drought refuges. 2. We investigated the response
 of groundwater-connected riverine forests to a drought considered
 equivalent in intensity to those predicted under severe climate change for
 2030. The drought's impact was investigated in an area where shallow
 groundwater resources are heavily exploited and polluted by salinization.
 3. We used remotely sensed vegetation productivity (enhanced vegetation
 index) data from a long-term data set (2000–2011) at 475 riverine forest
 sites in the Campaspe catchment, south-eastern Australia. Generalized
 additive mixed models and boosted regression trees were used to model the
 relationship between groundwater and other environmental covariates with
 forest change during drought. 4. Models explained up to 44% of the
 variation in forest change during drought. Forests underwent the greatest
 declines in areas of high salinity (&gt;6000 μS cm−1) associated with
 shallow groundwater depths (0–5 m). Conversely, forests in areas of lowest
 salinity (&lt;2000 μS cm−1) and groundwater depths of more than 7·5 m
 showed the least decline during drought. 5. In landscapes where
 groundwater quality is not compromised, previous studies have shown that
 shallow groundwater provides important drought refuges and refugia. Here,
 we show that when groundwater salinization has occurred, forests connected
 to shallow groundwater are more vulnerable to drought. In effect,
 salinization reduces the capacity of groundwater-connected habitats to
 function as drought refuges. 6. Synthesis and applications. Currently,
 there is an emphasis on managing environmental flows to support freshwater
 ecosystems and associated forests under water stress. However, delivery of
 environmental water is restricted to areas within a linear stream network
 and there is often limited capacity to deliver environmental flows during
 drought. Alternatively, a focus on drought refuges and refugia and
 processes important for maintaining groundwater quality (e.g. catchment
 revegetation to reduce shallow groundwater salinization) may better allow
 drought effects to be managed across a catchment, without directly
 focusing on highly contested surface water resources.
description: Groundwater_salinity_drought_data_finalEnvironmental covariates, locations, and trends for each site and time period (for both Zhang and Yue Pilon methods): Descriptions for all environmental covariates are given in Table S2. Supporting information on Zhange and Yuepilon trends is given in "(2) Trend analysis – quantifying declines in riverine forest communities in drought."data_final.csv