cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mm11q
title: Data from: Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

description: Statistical species delimitation usually relies on singular data,
 primarily genetic, for detecting putative species and individual
 assignment to putative species. Given the variety of speciation
 mechanisms, singular data may not adequately represent the genetic,
 morphological and ecological diversity relevant to species delimitation.
 We describe a methodological framework combining multivariate and
 clustering techniques that uses genetic, morphological and ecological data
 to detect and assign individuals to putative species. Our approach
 recovers a similar number of species recognized using traditional,
 qualitative taxonomic approaches that are not detected when using purely
 genetic methods. Furthermore, our approach detects groupings that
 traditional, qualitative taxonomic approaches do not. This empirical test
 suggests that our approach to detecting and assigning individuals to
 putative species could be useful in species delimitation despite varying
 levels of differentiation across genetic, phenotypic and ecological axes.
 This work highlights a critical, and often overlooked, aspect of the
 process of statistical species delimitation—species detection and
 individual assignment. Irrespective of the species delimitation approach
 used, all downstream processing relies on how individuals are initially
 assigned, and the practices and statistical issues surrounding individual
 assignment warrant careful consideration.
description: cten_16sAlignment of sequences for the 16S gene across the Ctenophorus maculatus species complex.cten_BACH1Alignment of BACH1 sequences from across the Ctenophorus maculatus species complex.cten_GAPDAlignment of GAPD sequences from across the Ctenophorus maculatus species complex.cten_nd2Alignment of ND2 sequences from across the Ctenophorus maculatus species complex.cten_NTF3Alignment of NTF3 sequences from across the Ctenophorus maculatus species complex.cten_PRLRAlignment of PRLR sequences from across the Ctenophorus maculatus species complex.females_all_meristicMeristic character data collected from female specimens across the Ctenophorus maculatus complex.females_all_morphMorphological and continuous meristic character data collected from female specimens across the Ctenophorus maculatus complex.male_all_meristicMeristic character data collected from male specimens across the Ctenophorus maculatus complex.male_all_morphMorphological and continuous meristic character data collected from male specimens across the Ctenophorus maculatus complex.envsamplesEnvironmental data sampled from specimens across the Ctenophorus maculatus complex. Data were sourced from databases as listed in the published manuscript. Email author for further information.
DOI: 10.5061/dryad.j8s0v
title: Data from: Cytonuclear incompatibility contributes to the early stages of speciation

description: Genetic incompatibility is a hallmark of speciation. Cytonuclear
 incompatibilities are proposed to be among the first genetic barriers to
 arise during speciation. Accordingly, reproductive isolation (RI) within
 species should be heavily influenced by interactions between the organelle
 and nuclear genomes. However, there are few clear examples of cytonuclear
 incompatibility within a species. Here, we show substantial postzygotic RI
 in first-generation hybrids between differentiated populations of an
 herbaceous plant (up to 92% reduction in fitness). RI was primarily due to
 germination and survival, with moderate RI for pollen viability. RI for
 survival was asymmetric and caused by cytonuclear incompatibility, with
 the strength of incompatibility linearly related to chloroplast genetic
 distance. This cytonuclear incompatibility may be the result of a rapidly
 evolving plastid genome. Substantial asymmetric RI was also found for
 germination, but was not associated with cytonuclear incompatibility,
 indicating endosperm or maternal-zygote incompatibilities. These results
 demonstrate that cytonuclear incompatibility contributes to RI within
 species, suggesting that initial rates of speciation could be influenced
 by rates of organelle evolution. However, other genetic incompatibilities
 are equally important, indicating that even at early stages, speciation
 can be a complex process involving multiple genes and incompatibilities.
description: Information for the
 populations and crosses used in this study.Information for the
 populations and crosses used in this study.IDInfo.csvData for germination and juvenile survivalData for germination and juvenile survivalGermandJuvSurv.csvData on adult survival and flower numberData on adult survival and flower numberGreenhouse.csvSeed countsSeed countsSeedCounts.csvPollen viability scoresPollen viability scoresPollen.csv
DOI: 10.5061/dryad.f88p700
title: Data from: Among-year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana

description: Incomplete information regarding both selection regimes and the genetic
 basis of fitness limits our understanding of adaptive evolution.
 Among-year variation in the genetic basis of fitness is rarely quantified,
 and estimates of selection are typically based on single components of
 fitness, thus potentially missing conflicting selection acting during
 other life-history stages. Here, we examined among-year variation in
 selection on a key life-history trait and the genetic basis of fitness
 covering the whole life cycle in the annual plant Arabidopsis thaliana. We
 planted freshly-matured seeds of &gt;200 recombinant inbred lines
 (RILs) derived from a cross between two locally-adapted populations (Italy
 and Sweden), and both parental genotypes at the native site of the Swedish
 population in three consecutive years. We quantified selection against the
 nonlocal Italian genotype, mapped quantitative trait loci (QTL) for
 fitness and its components, and quantified selection on timing of
 germination during different life stages. In all three years, the local
 Swedish genotype outperformed the non-local Italian genotype. However,
 both the contribution of early life stages to relative fitness, and the
 effects of fitness QTL varied among years. Timing of germination was under
 conflicting selection through seedling establishment vs. adult survival
 and fecundity, and both the direction and magnitude of net selection
 varied among years. Our results demonstrate that selection during early
 life stages and the genetic basis of fitness can vary markedly among
 years, emphasizing the need for multi-year studies considering the whole
 life cycle for a full understanding of natural selection and mechanisms
 maintaining local adaptation.
description: Parents_phenotypesThis file contains data on establishment success, adult survival, fecundity, fitness (number of fruits per planted viable seed), and mean germination time of seedling in plugs planted with the parental genotypes (Italian or Swedish) in the 2012, 2013 and 2014 experiments in Sweden.RIL_phenotypes_genotypes_QTLanalysisThis file contains data on genotypes and phenotypes of Recombinant Inbred Lines (RIL) in the 2012, 2013 and 2014 experiments planted in Sweden. Variable names are explained in the file README_RIL_phenotypes_genotypes_QTLanalysis.csvfileQTLanalysisScript for QTL mapping in R
DOI: 10.5061/dryad.s8820
title: Data from: Behavioural mediators of genetic life-history trade-offs: a test of the pace-of-life syndrome hypothesis in field crickets

description: The pace-of-life syndrome (POLS) hypothesis predicts associations between
 life-history and ‘risky’ behaviours. Individuals with ‘fast’ lifestyles
 should develop faster, reproduce earlier, exhibit more risk-prone
 behaviour, and die sooner than those with ‘slow’ lifestyles. While support
 for POLS has been equivocal to date, studies have relied on
 individual-level (phenotypic) patterns in which genetic trade-offs may be
 masked by environmental effects on phenotypes. We estimated genetic
 correlations between life-history (development, lifespan, size) and risky
 behaviours (exploration, aggression) in a pedigreed population of
 Mediterranean field crickets (Gryllus bimaculatus). Path analyses showed
 that behaviours mediated some genetic relationships between life-history
 traits, though not those involved in trade-offs. Thus, while specific
 predictions of POLS-theory were not supported, genetic integration of
 behaviour and life-history was present. This implies a major role for
 risky behaviours in life-history evolution.
description: dataset Santostefano et
 al. RSPB-2017-1567dataset Santostefano et
 al. RSPB-2017-1567
DOI: 10.5061/dryad.8d9t2
title: Data from: Reciprocity and the tragedies of maintaining and providing the commons

description: Social cooperation often requires collectively beneficial but individually
 costly restraint to maintain a public good, or it needs costly generosity
 to create one. Status quo effects predict that maintaining a public good
 is easier than providing a new one. Here, we show experimentally and with
 simulations that even under identical incentives, low levels of
 cooperation (the ‘tragedy of the commons’) are systematically more likely
 in maintenance than provision. Across three series of experiments, we find
 that strong and weak positive reciprocity, known to be fundamental
 tendencies underpinning human cooperation, are substantially diminished
 under maintenance compared with provision. As we show in a fourth
 experiment, the opposite holds for negative reciprocity (‘punishment’).
 Our findings suggest that incentives to avoid the ‘tragedy of the commons’
 need to contend with dilemma-specific reciprocity.
description: GaechterKoelleQuerciaDATA&CODEContains all experimental data reported in the article and the supplementary information (in both csv and STATA format). A list of variables and their labels is in the ReadMe file. Also contains the STATA codes (do-files) of the analyses reported in the article and the Supplementary Information.
DOI: 10.5061/dryad.1ch71sd
title: Data from: Reliability modelling and analysis of a multi-state element based on a dynamic Bayesian network

description: This paper presents a quantitative reliability modelling and analysis
 method for multi-state elements (MSEs) based on a combination of the
 Markov process and a dynamic Bayesian network (DBN), taking perfect
 repair, imperfect repair and condition-based maintenance (CBM) into
 consideration. The Markov models of elements without repair and under CBM
 are established, and an absorbing set is introduced to determine the
 reliability of the repairable element. According to the state-transition
 relations between the states determined by the Markov process, a DBN model
 is built. In addition, its parameters for series and parallel systems,
 namely, conditional probability tables (CPTs), can be calculated by
 referring to the conditional degradation probabilities. Finally, the power
 of a control unit in a failure model is used as an example. A dynamic
 fault tree (DFT) is translated into a Bayesian network (BN) model, and
 subsequently extended to a DBN. The results show the state probabilities
 of an element and the system without repair, with perfect and imperfect
 repair, and under CBM, with an absorbing set plotted by differential
 equations and verified. Through referring forward, the reliability value
 of the control unit is determined in different kinds of modes. Finally,
 weak nodes are noted in the control unit.
description: Raw data of manuscript
 RSOS-171438raw
 data.docxprobability values for
 E1 and the control unit
DOI: 10.5061/dryad.k2q95
title: Data from: Genetic assessment of a summer chum salmon metapopulation in recovery

description: Programs to rebuild imperiled wild fish populations often include
 hatchery-born fish derived from wild populations to supplement natural
 spawner abundance. These programs require monitoring to determine their
 demographic, biological, and genetic effects. In 1990s in Washington
 State, the Summer Chum Salmon Conservation Initiative developed a recovery
 program for the threatened Hood Canal summer chum salmon Evolutionarily
 Significant Unit (ESU) (the metapopulation) that used in-river spawners
 (wild fish) for each respective supplementation broodstock in six
 tributaries. Returning spawners (wild-born and hatchery-born) composed
 subsequent broodstocks, and tributary-specific supplementation was limited
 to three generations. We assessed impacts of the programs on neutral
 genetic diversity in this metapopulation using 16 microsatellite loci and
 a thirty-year dataset spanning before and after supplementation, roughly
 eight generations. Following supplementation, differentiation among
 subpopulations decreased (but not significantly) and isolation by distance
 patterns remained unchanged. There was no decline in genetic diversity in
 wild-born fish, but hatchery-born fish sampled in the same spawning areas
 had significantly lower genetic diversity and unequal family
 representation. Despite potential for negative effects from
 supplementation programs, few were detected in wild-born fish. We
 hypothesize that chum salmon natural history makes them less vulnerable to
 negative impacts from hatchery supplementation.
description: HoodCanalSummerChumSalmonGenotypesSummer Chum salmon microsatellite genotypes in GenePop format
DOI: 10.5061/dryad.ks67ft7
title: Data from: Environmentally induced development costs underlie fitness tradeoffs

description: Local adaptation can lead to genotype‐by‐environment interactions, which
 can create fitness tradeoffs in alternative environments, and govern the
 distribution of biodiversity across geographic landscapes. Exploring the
 ecological circumstances that promote the evolution of fitness tradeoffs
 requires identifying how natural selection operates and during which
 ontogenetic stages natural selection is strongest. When organisms disperse
 to areas outside their natural range, tradeoffs might emerge when
 organisms struggle to reach key life history stages, or alternatively, die
 shortly after reaching life history stages if there are greater risks of
 mortality associated with costs to developing in novel environments. We
 used multiple populations from four ecotypes of an Australian native
 wildflower (Senecio pinnatifolius) in reciprocal transplants to explore
 how fitness tradeoffs arise across ontogeny. We then assessed whether the
 survival probability for plants from native and foreign populations was
 contingent on reaching key developmental stages. We found that fitness
 tradeoffs emerged as ontogeny progressed when native plants were more
 successful than foreign plants at reaching seedling establishment and
 maturity. Native and foreign plants that failed to reach seedling
 establishment died at the same rate, but plants from foreign populations
 died quicker than native plants after reaching seedling establishment, and
 died quicker regardless of whether they reached sexual maturity or not.
 Development rates were similar for native and foreign populations, but
 changed depending on the environment. Together, our results suggest that
 natural selection for environment‐specific traits early in life history
 created tradeoffs between contrasting environments. Plants from foreign
 populations were either unable to develop to seedling establishment, or
 they suffered increased mortality as a consequence of reaching seedling
 establishment. The observation of tradeoffs together with environmentally
 dependent changes in development rate suggest that foreign environments
 induce organisms to develop at a rate different from their native habitat,
 incurring consequences for lifetime fitness and population divergence.
description: Field transplant
 dataContains the fitness and
 development rate data for all parental ecotypes and populations included
 in the reciprocal transplant. Please ee the readme file for description of
 column names.p2_Walter_data.csv
DOI: 10.5061/dryad.45kf5
title: Data from: DNA metabarcoding reveals diet overlap between the endangered Walia ibex and domestic goats - implications for conservation

description: Human population expansion and associated degradation of the habitat of
 many wildlife species cause loss of biodiversity and species extinctions.
 The small Simen Mountains National Park in Ethiopia is one of the last
 strongholds for the preservation of a number of afro-alpine mammals,
 plants and birds, and it is home to the rare endemic Walia ibex, Capra
 walie. The narrow distribution range of this species as well as potential
 competition for resources with livestock, especially with domestic goat,
 Capra hircus, may compromise its future survival. Based on a curated
 afro-alpine taxonomic reference library constructed for plant taxon
 identification, we investigated the diet of the Walia ibex and addressed
 the dietary overlap with domestic goat using DNA metabarcoding of faecal
 samples. Faeces of both species were collected from different localities
 in the National Park. We show that both species are browsers, with forbs,
 shrubs and trees comprising the largest proportion of their diet,
 supplemented by grasses. There was a considerable overlap in dietary
 preferences. Several of the preferred diet items of the Walia ibex
 (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were
 also among the most preferred diet items of the domestic goat. These
 results indicate that there is potential for competition between the two
 species, especially during the dry season, when resources are limited. Our
 findings, in combination with the expected increase in domestic
 herbivores, suggest that management plans should consider the potential
 threat posed by domestic goats to ensure future survival of the endangered
 Walia ibex.
description: Afro-alpine_taxonomic_ref_library_v2Sequences of the taxonomic reference library version 2.0 for the African alpine flora. Sequences cover the P6 loop of the trnL. Header lines contain the species names followed by identity numbers (O-DP numbers) that correspond to specimen numbers in the herbarium of the Natural History Museum, University of Oslo, Norway.Walia_goat_diet_afroalp.tagWalia_goat_diet_embl113.tag
DOI: 10.5061/dryad.s90t6
title: Data from: Evolution of camouflage drives rapid ecological change in an insect community

description: Evolutionary change in individual species has been hypothesized to have
 far-reaching consequences for entire ecological communities, and such
 coupling of ecological and evolutionary dynamics (“eco-evolutionary
 dynamics”) has been demonstrated for a variety systems. However, the
 relative importance of evolutionary dynamics for ecological dynamics
 remains unclear. Here, we investigate how spatial patterns of local
 adaptation in the stick insect Timema cristinae, driven by natural
 selection, gene flow and founder effects, structure metapopulations,
 communities, and multitrophic interactions. Observations of a wild T.
 cristinae metapopulation show that locally imperfect camouflage reduces
 population size, and that the effect of such maladaptation is comparable
 to the effects of more traditional ecological factors, including habitat
 patch size and host-plant species identity. Field manipulations of local
 adaptation and bird predation support the hypothesis that maladaptation
 reduces population size through an increase in bird predation.
 Furthermore, these field experiments show that maladaptation in T.
 cristinae and consequent increase in bird predation reduce the pooled
 abundance and species richness of the co-occurring arthropod community,
 and ultimately cascade to decrease herbivory on host plants. An
 eco-evolutionary model of the observational data demonstrates that the
 demographic cost of maladaptation decreases habitat patch occupancy by T.
 cristinae but enhances metapopulation-level adaptation. The results
 demonstrate a pervasive effect of ongoing evolution in a spatial context
 on population and community dynamics. The eco-evolutionary model generates
 testable predictions about the influence of the spatial structure of the
 patch network on the abundance and adaptive camouflage evolution.
description: 2011exptArthropodData2011exptBushSizes2011exptHerbivoryDatabex2012databex2012Herbivory2011obsTimemaDataReadMe
DOI: 10.5061/dryad.pj02h
title: Data from: Using adaptive traits to consider potential consequences of temporal variation in selection: male guppy colour through time and space

description: Temporal variation in selection is typically evaluated by estimating and
 comparing selection coefficients in natural populations. Meta-analyses of
 these coefficients have yielded important insights, but selection
 coefficients are limited in several respects, including low statistical
 power, imperfect fitness surrogates, and uncertainty regarding
 consequences for trait change. A complementary approach without these
 limitations is to examine temporal variation in adaptive traits
 themselves, which is mechanistically easier and more directly relevant to
 evolutionary consequences. We illustrate this approach by analyzing the
 colour patterns of male guppies, Poecilia reticulata, from each of six
 sites in Trinidad in each of 6 years. This system is particularly
 appropriate for our study because key aspects of colour variation are
 genetically-based and responsive to selection. However, although spatial
 patterns of colour variation have been extensively considered in this
 system, no study has yet formally assessed annual temporal variation in
 non-manipulated populations. Matching previous conclusions for the guppy
 system, we find that guppies from different sites manifest different
 colour patterns in association with different predation regimes. We here
 add the new finding that, although some temporal variation is present,
 spatial patterns of colour variation are generally consistent across
 years. These results suggest that, when considering adaptive traits,
 spatial variation is more important than temporal variation, although our
 study system might be exceptional in this regard. Additional studies
 examining spatiotemporal variation in adaptive traits could help to
 improve our understanding of the role that spatiotemporal variation in
 selection plays in the evolutionary process.
description: BJLS-3121_R1
 DryadCSV file with raw
 data