cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8q34c
title: Data from: Restricted gene flow within and between rapidly diverging neotropical plant species

description: Speciation involves the evolution of traits and genetic differences that
 contribute to reproductive isolation and the cessation of gene flow, and
 studying closely related species and divergent populations gives insight
 into how these phenomena proceed. Here, we document patterns of gene flow
 within and between two members of a rapid Neotropical species radiation,
 Costus pulverulentus and Costus scaber (Costaceae). These species co-occur
 in the tropical rainforest and share pollinators, but are reproductively
 isolated by a series of prezygotic barriers, some of which show evidence
 of reinforcement at sympatric sites. Here, we genotype microsatellite
 markers in plants from eight sites that span the geographical range of
 both species, including four sympatric sites. We also genotype putative
 hybrids found at two sympatric sites. We find high levels of genetic
 isolation among populations within each species and low but detectable
 levels of introgression between species at sympatric sites. Putative
 hybrids identified by morphology are consistent with F1 or more advanced
 hybrids. Our results highlight the effectiveness of prezygotic isolating
 mechanisms at maintaining species boundaries in young radiations and
 provide empirical data on levels of gene flow consistent with
 reinforcement.
description: Costus microsatellite
 dataGenotypes scored at 15
 microsatellite loci. Missing data are indicated by -9. Open Document
 Spreadsheet formatCostus_microsatellites.odsSTRUCTURE input fileFile including a first row of marker names, a first column of individual codes (same as in file Costus_microsatellites.ods), and second column of population of origin.Costus_structure.txtNewHybrids input file for population OSAOSA_newHybrids.txtNewHybrids input file for population PLRPLR_newHybrids.txt
DOI: 10.5061/dryad.v2211
title: Data from: Species coexistence: macroevolutionary relationships and the contingency of historical interactions

description: Evolutionary biologists since Darwin have hypothesized that closely
 related species compete more intensely and are therefore less likely to
 coexist. However, recent theory posits that species diverge in two ways:
 either through the evolution of ‘stabilizing differences’ that promote
 coexistence by causing individuals to compete more strongly with
 conspecifics than individuals of other species, or through the evolution
 of ‘fitness differences’ that cause species to differ in competitive
 ability and lead to exclusion of the weaker competitor. We tested
 macroevolutionary patterns of divergence by competing pairs of annual
 plant species that differ in their phylogenetic relationships, and in
 whether they have historically occurred in the same region or different
 regions (sympatric vs. allopatric occurrence). For sympatrically-occurring
 species pairs, stabilizing differences rapidly increased with phylogenetic
 distance. However, fitness differences also increased with phylogenetic
 distance, resulting in coexistence outcomes that were unpredictable based
 on phylogenetic relationships. For allopatric species, stabilizing
 differences showed no trend with phylogenetic distance, whereas fitness
 differences increased, causing coexistence to become less likely among
 distant relatives. Our results illustrate the role of species’ historical
 interactions in shaping how phylogenetic relationships structure
 competitive dynamics, and offer an explanation for the evolution of
 invasion potential of non-native species.
description: Raw seed production data
 for model fittingNumbers of viable seeds
 of species i-k initially planted (Nt) and produced by plants (Nt1) in the
 experiment. The id codes of competing species i-k are listed under spi,
 spj, and spk, and the full species names names that correspond to the id
 codes are in Table S3. The experiment was replicated in a wet (w) and a
 dry (d) environment, denoted under
 'moisture'.raw data for model
 fitting.csvBayesian tree in nexus
 formatPhylogenetic tree used
 to get estimates of phylogenetic distance, calibrated to millions of years
 based on the fossil recordnexus file for phylogenetic
 tree.nex
DOI: 10.5061/dryad.2v9g0
title: Data from: Phylogeny affects host's weight, immune response and parasitism in damselflies and dragonflies

description: Host–parasite interactions are an intriguing part of ecology, and
 understanding how hosts are able to withstand parasitic attacks, e.g. by
 allocating resources to immune defence, is important. Damselflies and
 dragonflies show a variety of parasitism patterns, but large-scale
 comparative immune defence studies are rare, and it is difficult to say
 what the interplay is between their immune defence and parasitism. The aim
 of this study was to find whether there are differences in immune response
 between different damselfly and dragonfly species and whether these could
 explain their levels of gregarine and water mite parasitism. Using an
 artificial pathogen, a piece of nylon filament, we measured the
 encapsulation response of 22 different damselfly and dragonfly species and
 found that (i) there are significant encapsulation differences between
 species, (ii) body mass has a strong association with encapsulation and
 parasite prevalences, (iii) body mass shows a strong phylogenetic signal,
 whereas encapsulation response and gregarine and water mite prevalences
 show weak signals, and (iv) associations between the traits are affected
 by phylogeny. We do not know what the relationship is between these four
 traits, but it seems clear that phylogeny plays a role in determining
 parasitism levels of damselflies and dragonflies.
description: Raw field
 dataThis is the raw field
 data collected in Finland. It has detailed information of each damselfly
 and dragonfly individual we collected. Data contains coordinates, species
 number (1-22), scientific species name, sex (1 for males, 2 for females),
 wing length in millimeters (right hind wing), fresh body mass in grams,
 number of ectoparasitic larval water mites found on each individual,
 number of endoparasitic gregarines found on each individual and an implant
 value indicating the encapsulation response each individual mounted
 against an artificial implant.Final Data
 24.8.2016.xlsx
DOI: 10.5061/dryad.1vh94
title: Data from: One phase of the dormancy developmental pathway is critical for the evolution of insect seasonality

description: Evolutionary change in the timing of dormancy enables animals and plants
 to adapt to changing seasonal environments and can result in ecological
 speciation. Despite its clear biological importance, the mechanisms
 underlying the evolution of dormancy timing in animals remain poorly
 understood because of a lack of anatomical landmarks to discern which
 phase of dormancy an individual is experiencing. Taking advantage of the
 nearly universal characteristic of metabolic suppression during insect
 dormancy (diapause), we use patterns of respiratory metabolism to document
 physiological landmarks of dormancy and test which of the distinct phases
 of the dormancy developmental pathway contribute to a month-long shift in
 diapause timing between a pair of incipient moth species. Here, we show
 that divergence in life cycle between the earlier-emerging E-strain and
 the later-emerging Z-strain of European corn borer (ECB) is clearly
 explained by a delay in the timing of the developmental transition from
 the diapause maintenance phase to the termination phase. Along with recent
 findings indicating that life-cycle differences between ECB strains stem
 from allelic variation at a single sex-linked locus, our results
 demonstrate how dramatic shifts in animal seasonality can result from
 simple developmental and genetic changes. Although characterizing the
 multiple phases of the diapause developmental programme in other locally
 adapted populations and species will undoubtedly yield surprises about the
 nature of animal dormancy, results in the ECB moth suggest that focusing
 on genetic variation in the timing of the dormancy termination phase may
 help explain how (or whether) organisms rapidly respond to global climate
 change, expand their ranges after accidental or managed introductions,
 undergo seasonal adaptation, or evolve into distinct species through
 allochronic isolation.
description: Diapause
 terminationRespirometry Measures
 for diapause termination time point14399699_File000006_284969572-1.csvDiapauseRespirometry measures for diapause14399699_File000007_284969574.csv
DOI: 10.5061/dryad.qv42j11b
title: Data from: A new perspective on Punctelia subrudecta (Parmeliaceae) in North America: previously rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem

description: In North America the names Punctelia subrudecta and P. perreticulata have
 variously been applied to corticolous sorediate Punctelia specimens with
 lecanoric acid and a pale lower surface. ITS1, 5.8S, and ITS2 sequence
 data were generated from a geographically and morphologically broad
 sampling from within these specimens, and a molecular phylogeny was
 inferred. A combined approach using morphology, geography, and phylogeny
 was used to circumscribe three distinct species in North America, one of
 which is described as new to science (P. caseana), one of which is finally
 confirmed for the continent (P. jeckeri), and one whose original
 circumscription is validated (P. perreticulata). The phylogeny inferred
 from ITS sequence data supports the taxonomic value of the following
 morphological characters for distinguishing species in this group:
 presence/absence of pruina; conidium type and length (although see
 discussion of P. jeckeri), and presence/absence of scrobiculae on the
 upper surface. A key to the North American species of Punctelia is
 provided.
description: Lendemer_and_Hodkinson_Punctelia_ITSNexus file of aligned DNA sequences used for molecular phylogenetic analyses carried out for the study.
DOI: 10.5061/dryad.75g00
title: Data from: Yellowstone bison—should we preserve artificial population substructure or rely on ecological processes?

description: Halbert et al. (2012) analyzed microsatellite genotypes collected from 661
 Yellowstone bison sampled during winters from 1999 through 2003 and
 identified 2 genetically distinct subpopulations (central, northern) based
 on genotypic diversity and allelic distributions. Based on these findings,
 they raised concerns about the management and long-term conservation of
 Yellowstone bison due to disproportionate culling of the 2 subpopulations
 in some winters. The data and findings of Halbert et al. (2012) are
 significant and useful for managers charged with conserving these iconic
 wildlife. However, their article provides information regarding the
 behavior and management of Yellowstone bison that does not accurately
 portray historic or current conditions. This response clarifies those
 conditions and challenges some of their apparent deductions and
 recommendations.
description: NPSResponseToHalbert_etal_TableS1_JHered_Apr2012Breeding season ranges used by radio-collared, female bison in Yellowstone National Park during 2002-2011NPSResponseToHalbert_etal_TableS2_JHered_Apr2012Estimates of F-statistics and the number of migrants between central and northern breeding herds based on DNA extracted from fecal samples collected from male and female Yellowstone bison in both herds during the breeding seasons of 2006 and 2008 (Gardipee 2007).
DOI: 10.5061/dryad.6sb403hc
title: Data from: Extra-pair paternity and the variance in male fitness in song sparrows (Melospiza melodia)

description: The variance in fitness across population members can influence major
 evolutionary processes. In socially monogamous but genetically
 polygynandrous species, extra-pair paternity (EPP) is widely hypothesized
 to increase the variance in male fitness compared to that arising given
 the socially monogamous mating system. This hypothesis has not been
 definitively tested because comprehensive data describing males’ apparent
 (social) and realized (genetic) fitness have been lacking. We used 16
 years of comprehensive social and genetic paternity data for an entire
 free-living song sparrow (Melospiza melodia) population to quantify and
 compare variances in male apparent and realized fitness, and to quantify
 the contribution of the variances in within-pair and extra-pair
 reproductive success and their covariance to the variance in realized
 fitness. Overall, EPP increased the variance in male fitness by only 0-27%
 across different fitness and variance measures. This relatively small
 effect reflected the presence of socially unpaired males with zero
 apparent and low realized fitness, small covariance between within- and
 extra-pair reproductive success and large variance in within-pair
 reproductive success that was relatively unaffected by EPP. Therefore,
 although EPP altered individual males’ contributions to future
 generations, its impact on population-level parameters such as the
 opportunity for selection and effective population size was limited.
description: summary data
 ARSData describing
 variation in male annual reproductive successsummary data
 LRSData describing
 variation in male lifetime reproductive success and
 fitness
DOI: 10.5061/dryad.qb87r
title: Data from: Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations

description: Small and isolated populations often exhibit low genetic diversity due to
 drift and inbreeding, but may simultaneously harbour adaptive variation.
 We investigate spatial distributions of immunogenetic variation in
 American badger subspecies (Taxidea taxus), as a proxy for evaluating
 their evolutionary potential across the northern extent of the species’
 range. We compared genetic structure of 20 microsatellites and the Major
 histocompatibility complex (MHC) to evaluate if small isolated populations
 show low adaptive polymorphism relative to large and well-connected
 populations. Our results suggest that gene flow plays a prominent role in
 shaping MHC polymorphism across large spatial scales, while the interplay
 between gene flow and selection was stronger towards the northern
 peripheries. The similarity of MHC alleles within subspecies relative to
 their neutral genetic differentiation suggests that adaptive divergence
 among subspecies can be maintained despite ongoing gene flow along
 subspecies boundaries. Neutral genetic diversity were low in small
 relative to large populations, but MHC diversity within individuals was
 high in small populations. Despite reduced neutral genetic variation,
 small isolated populations harbour functional variation that likely
 contribute to the species evolutionary potential at the northern range.
 Our findings suggest that conservation approaches should focus on managing
 adaptive variation across the species range rather than protecting
 subspecies per se.
description: Taxidea taxus
 microsatellite genotypesMicrosatellite genotypes
 at 20 loci for 236 samples from eight regions of the American badger.
 Storage data format: genepop. See publication for details of sampled
 regions.Taxidea_taxus_Microsatellite_data_Rico etal 2016Taxidea_taxus_MHC_binaryGenotypes_Rico et al. 2016MHC DRB-exon 2 binary-encoded genotypes of 236 samples from eight regions of the American badger. See publication for details of the sampled regions.
DOI: 10.5061/dryad.2sb6r8p
title: Data from: Species boundaries in the Vriesea incurvata (Bromeliaceae) complex after a broad morphometric and taxonomic study

description: The genus Vriesea encompasses many species of difficult delimitation,
 including Vriesea incurvata, which shows wide morphological variation
 throughout its distribution in the Brazilian Atlantic Forest. Six other
 taxa are morphologically similar to V. incurvata: V. atrococcinea, V.
 joyae (with two varieties), V. sucrei, andV. taritubensis (with two
 varieties), which comprise the species complex. Our aims were to evaluate
 morphological variation through a morphometric study of natural
 populations to establish the limits and validity of those taxa, and to
 produce a taxonomic treatment. A total of 23 morphometric variables were
 measured among 241 individuals from 15 natural populations. The
 morphological evidence led to the recognition of five taxa: V. incurvata,
 V. sucrei, V. taritubensis var. taritubensis, V. taritubensis var.
 brevisepala, and V. taritubensis var. patens (a new variety). Three
 synonyms are proposed: V. atrococcinea (under V. sucrei), V. joyae var.
 joyae, and V. joyae var. parvula (under V. taritubensis var.
 taritubensis). The resulting taxa were re-circumscribed and data on their
 geographic distributions is updated.
description: Neves_et_al_2018_Morphometrics Vriesea_incurvata_complex_S1SUPPLEMENTAL APPENDIX 1. Minimum and maximum values, and the median of each variable in the 15 populations studied. The letters show the populations that differ significantly with H test (p&lt;0.05).Neves_et_al_2018_Morphometrics_Vriesea_incurvata_complex_DataRaw data used for analyses.
DOI: 10.15468/dl.eg4dkm
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Przewalskia tangutica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 167 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000982-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g6m34mf
title: Data from: Adaptive maternal behavioral plasticity and developmental programming mitigate the transgenerational effects of temperature in dung beetles

description: Phenotypic plasticity allows organisms to cope with rapid environmental
 change. Yet exactly when during ontogeny plastic responses are elicited,
 whether plastic responses produced in one generation influence phenotypic
 variation and fitness in subsequent generations, and the role of
 plasticity in shaping population divergences, remains overall poorly
 understood. Here, we use the dung beetle Onthophagus taurus to assess
 plastic responses to temperature at several life stages bridging three
 generations and compare these responses across three recently diverged
 populations. We find that beetles reared at hotter temperatures grow less
 than those reared at mild temperatures, and that this attenuated growth
 has transgenerational consequences by reducing offspring size and survival
 in subsequent generations. However, we also find evidence that plasticity
 may mitigate these consequences in two ways: (i) mothers modify the
 temperature of their offspring’s developmental environment via behavioral
 plasticity and (ii) in one population, offspring exhibit accelerated
 growth when exposed to hot temperatures during very early development
 (“developmental programming”). Lastly, our study reveals that offspring
 responses to temperature diverged among populations in fewer than 100
 generations, possibly in response to range-specific changes in climatic or
 social conditions.
description: All_BB_LayersThis data table organizes how many broodballs were laid in each replicate container by layer. It is used for the statistics of Phase 1 maternal behavior and the corresponding Figure 2.Phase 1 Offspring ResponsesThis data table includes details regarding the offspring values measured in Phase 1. It is used for the statistics of Phase 1 offspring responses and the corresponding Figure 3.Phase 2 Maternal and Offpsring ResponsesThis data table includes details regarding the offspring values measured in Phase 2. It is used for the statistics of Phase 2 maternal behaviors and offspring responses and the corresponding Figure 4.
DOI: 10.5061/dryad.rf0bh
title: Data from: Genetics of decayed sexual traits in a parasitoid wasp with endosymbiont-induced asexuality

description: Trait decay may occur when selective pressures shift, owing to changes in
 environment or life style, rendering formerly adaptive traits
 non-functional or even maladaptive. It remains largely unknown if such
 decay would stem from multiple mutations with small effects or rather
 involve few loci with major phenotypic effects. Here, we investigate the
 decay of female sexual traits, and the genetic causes thereof, in a
 transition from haplodiploid sexual reproduction to endosymbiont-induced
 asexual reproduction in the parasitoid wasp Asobara japonica. We take
 advantage of the fact that asexual females cured of their endosymbionts
 produce sons instead of daughters, and that these sons can be crossed with
 sexual females. By combining behavioral experiments with crosses designed
 to introgress alleles from the asexual into the sexual genome, we found
 that sexual attractiveness, mating, egg fertilization and plastic
 adjustment of offspring sex ratio (in response to variation in local mate
 competition) are decayed in asexual A. japonica females. Furthermore,
 introgression experiments revealed that the propensity for cured asexual
 females to produce only sons (because of decayed sexual attractiveness,
 mating behavior and/or egg fertilization) is likely caused by recessive
 genetic effects at a single locus. Recessive effects were also found to
 cause decay of plastic sex-ratio adjustment under variable levels of local
 mate competition. Our results suggest that few recessive mutations drive
 decay of female sexual traits, at least in asexual species deriving from
 haplodiploid sexual ancestors.
description: Ma et
 al._female_copulationpropensitycross_F_M: cross between
 females and males. SS_S: sexual females (SS) cross with sexual males (S).
 A_SS: pure sexual females (SS), here A is used to rank the groups in an
 alphabet order. mating1: successful mating (with daughter produced) is
 scored as 1. mating 0.5: unsuccessful mating (no daughter produced) is
 scored as 0.5female_copulationpropensity.xlsxMa et al._broodsize_comparisonSS_S: cross between sexual females and sexual males. SA_S: cross between F1 hybrid females and sexual males. total: brood size per familySS_SA.xlsxMa et al._offspringsexratioASS_S: sexual female "SS" cross with sexual male "S", A is the alphabet to indicate the order, does not have special meaning. total: brood size. sex ratio: proportions of male offspring per familysexratio.xlsxMa et al._localmatecompetitionSS_S: cross between sexual females "SS" and sexual males "S". total: brood size per family. sex ratio: the proportions of male offspring per family. foundress: the number of parental females per patchLMC.xlsx