cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d403s
title: Data from: Patterns of range-wide genetic variation in six North American bumble bee (Apidae: Bombus) species

description: The increasing evidence for population declines in bumble bee (Bombus)
 species worldwide has accelerated research efforts to explain losses in
 these important pollinators. In North America, a number of once widespread
 Bombus species have suffered serious reductions in range and abundance,
 although other species remain healthy. To examine whether declining and
 stable species exhibit different levels of genetic diversity or population
 fragmentation, we genotyped a set of microsatellite markers from
 populations sampled across the geographic distributions of two declining
 (B. occidentalis; B. pensylvanicus) and four stable (B. bifarius; B.
 vosnesenskii; B. impatiens; B. bimaculatus) Bombus species. Populations of
 declining species generally have reduced levels of genetic diversity
 throughout their range compared to co-distributed stable species. Genetic
 diversity can be affected by overall range size and degree of isolation of
 local populations, potentially confounding comparisons among species in
 some cases. We find no evidence for consistent differences in gene flow
 among stable and declining species, with all species exhibiting weak
 genetic differentiation over large distances (e.g., &gt;1,000 km).
 Populations on islands and at high elevations experience relatively strong
 genetic drift, suggesting that some conditions lead to genetic isolation
 in otherwise weakly differentiated species. Bombus bifarius and B.
 occidentalis exhibit stronger genetic differentiation than the other
 species, indicating more complex phylogeographic histories consistent with
 their broader geographic distributions across western North America.
 Screening genetic diversity in North American Bombus may prove to be
 useful for identifying species that warrant monitoring, and developing
 management strategies that promote high levels of gene flow will be a key
 component in efforts to maintain healthy bumble bee populations.
description: Lozier_etal_BombusDataForDRYAD
DOI: 10.5061/dryad.179
title: Data from: Mining of expressed sequence tag libraries of cacao for microsatellite markes using five computational tools

description: Expressed Sequence Tags (ESTs) provide researchers with a quick and
 inexpensive route for discovering new genes, and data on gene expression
 and regulation and provide genic markers that help in constructing genome
 maps. Cacao is an important perennial crop of humid tropics. Cacao EST
 sequences as available in public domain were downloaded and made into
 contigs. A total of 769 contigs were made using contigs assembly program
 pharp. Puative information of contigs were identified using NCBI and
 ExPASy tools such as BlastX, tblastn.
description: Riju Data
 Matrixblastx.xlsCocoa all primers riju et al., 2009.xls
DOI: 10.5061/dryad.q9s30
title: Data from: Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)

description: We examined differentiation within the Colombian wood turtle Rhinoclemmys
 melanosterna, and among R. melanosterna and the closely allied species R.
 diademata, R. funerea and R. punctularia, based on 1060 base pairs of the
 mitochondrial cyt b gene. We also assessed the phylogenetic relationships
 among these species using 2050 bp of mtDNA (partial cyt b, 12S and 16S
 genes) and 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and
 ODC genes). There is considerable phylogeographic structuring within R.
 melanosterna, with seven distinct clades distributed across the species’
 range. These clades correspond to some extent with previously described
 differences in the dorsal pattern of head coloration. Individual and
 combined analyses of mitochondrial and nuclear DNA indicated contradictory
 relationships among R. melanosterna, R. diademata, R. funerea and R.
 punctularia. Mitochondrial DNA sequences revealed R. melanosterna to be
 non-monophyletic with respect to R. diademata, R. funerea and R.
 punctularia. In contrast, R. melanosterna constituted a well-supported
 monophyletic clade using nuclear DNA. This conflict between mitochondrial
 and nuclear data suggests past gene flow among the allopatrically and
 parapatrically distributed species R. melanosterna, R. diademata, R.
 funerea and R. punctularia. Compared to the other Rhinoclemmys species,
 the taxa under study are weakly differentiated. To assess their taxonomic
 status, further research is warranted using additional nuclear markers and
 additional samples of R. diademata, R. funerea and R. punctularia. For the
 time being, a continued classification of R. melanosterna, R. diademata,
 R. funerea and R. punctularia as distinct species is justified owing to
 their allopatric and parapatric distributions, and to conserve the
 established usage of names that is based on characteristic and distinct
 phenotypes associated with each species.
description: Vargas-Ramirez et al.
 2013 APPENDICESAPPENDIX I and APPENDIX
 II
DOI: 10.5061/dryad.057r9
title: Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation

description: Finding the specific nucleotides that underlie adaptive variation is a
 major goal in evolutionary biology, but polygenic traits pose a challenge
 because the complex genotype-phenotype relationship can obscure the
 effects of individual alleles. However, natural selection working in large
 wild populations can shift allele frequencies and indicate functional
 regions of the genome. Previously, we showed that the two most common
 alleles of a complex amino acid insertion-deletion polymorphism in the
 Drosophila insulin receptor show independent, parallel clines in frequency
 across the North American and Australian continents. Here, we report that
 the cline is stable over at least a five-year period and that the
 polymorphism also demonstrates temporal shifts in allele frequency
 concurrent with seasonal change. We tested the alleles for effects on
 levels of insulin signaling, fecundity, development time, body size,
 stress tolerance, and lifespan. We find that the alleles are associated
 with predictable differences in these traits, consistent with patterns of
 Drosophila life history variation across geography that likely reflect
 adaptation to the heterogeneous climatic environment. These results
 implicate insulin signaling as a major mediator of life history adaptation
 in Drosophila, and suggest that life history tradeoffs can be explained by
 extensive pleiotropy at a single locus.
description: raw data for phenotype
 assaysThis Excel file contains
 the raw data for the phenotype assays.dryad.xlsx
DOI: 10.5061/dryad.6v29b
title: Data from: Heterogeneity in individual quality in birds: overall patterns and insights from a study on common terns

description: While life-history theory predicts a trade-off between reproduction and
 survival, positive covariance, indicative of heterogeneity in individual
 quality, is often reported among individuals from natural populations. We
 review longitudinal studies of wild bird populations that test the
 relationship between annual reproductive success and lifespan and find the
 majority to report a positive correlation, while none reports a negative
 correlation. Heterogeneity in individual quality in resource acquisition,
 masking resource-based trade-offs, therefore appears to be common in
 birds. Considering that there is little evidence for heritable variation
 in fitness, heterogeneity in individual quality among adults may be due to
 life-long effects of developmental conditions. In a 20-year case study on
 common terns (Sterna hirundo), we test for life-long effects of cohort
 quality and within-cohort nest quality, but find no significant effects on
 long-term proxies of quality. Since other studies do find strong life-long
 effects of developmental conditions, we suggest that the brood reduction
 strategy adopted by common terns, causing the majority of offspring to die
 rapidly after hatching, efficiently reduces variation in offspring quality
 at independence. As such, a brood reduction strategy may contribute to
 reduced heterogeneity in adult survival in stochastic environments, both
 suggested to be more common and adaptive in long-lived species. Further
 study is required to assess heterogeneity in individual reproduction,
 especially in relation to environmental stochasticity and species’
 life-history strategies, in order to assess whether the relative strength
 of selection in early and late life may indeed affect the magnitude of
 heterogeneity in individual quality over life, and how this is mediated by
 parent-offspring conflict.
description: Vedder & Bouwhuis
 2017 OikosData used for models
 presented in: Heterogeneity in individual quality in birds: overall
 patterns and insights from a study on common terns by Vedder, O. &
 Bouwhuis, S.
DOI: 10.5061/dryad.8081
title: Data from: Mitochondrial capture by a transmissible cancer

description: Canine transmissible venereal tumor (CTVT) is an infectious cell line
 circulating in many feral dog populations. It originated once, about
 10,000 years ago. Phylogenetic analyses of mitochondrial sequences from
 dogs, wolves, and a geographically diverse collection of CTVT samples
 indicate that the cancer has periodically acquired mitochondria from its
 host. We suggest that this may be because the cancer’s own mitochondria
 have a tendency to degenerate, due to high mutation rates and relaxed
 selection, resulting in host mitochondria being more fit.
description: Rebbeck
 phylogenyNexus file for
 phylogenetic tree of mitochondrial sequence data. Data collected from
 canine transmissible venereal tumor and host dog aligned with dog, wolf
 and coyote sequences.
DOI: 10.5061/dryad.2qp1v
title: Data from: Reproductive foragers: spider males choose mates by selecting among available competitive environments

description: Mate choice frequently operates differently for males and females as a
 consequence of male competition for mates. Competitive interactions can
 alter the fitness payoffs of choice and the realisation of preferences
 under natural conditions, yet the majority of male choice studies still
 use binary trials that ignore social factors. Here we test the importance
 of contest dynamics in male choice with a large scale experiment, using a
 framework where females are considered analogous to foraging patches that
 are subject to competition. We track the mate choices and interactions of
 640 spiders (Nephila plumipes) before and after manipulation of
 competition within enclosures, modelling the expected fitness payoffs of
 each male's actual choices and comparing these with all alternative
 choices available. We find that many males choose new females once social
 conditions change, and achieve higher fitness than predicted under random
 movement. Males increase their fitness not by moving to larger females but
 by choosing favourable competitive environments that balance competition
 and female fecundity. Further, we show for the first time that prior
 residence effects have a strong influence in male reproductive contests
 and can shape male mate choice. These results highlight the importance of
 situating male choice studies in the relevant social context, as
 intrasexual interactions can have profound effects on the realisation and
 payoffs of male mate choice strategies.
description: Jordan et al Am Nat 2013
 dataCoordinate data for all
 males and females at time 1 and time 2, along with measurements of weight,
 length, and death.Jordan et al Am Nat
 2013.xls
DOI: 10.5061/dryad.mp25s15
title: Data from: Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly

description: There is now clear evidence that species across a broad range of taxa
 harbour extensive heritable variation in dispersal. While studies suggest
 that this variation can facilitate demographic outcomes such as range
 expansion and invasions, few have considered the consequences of
 intraspecific variation in dispersal for the maintenance and distribution
 of genetic variation across fragmented landscapes. Here we examine how
 landscape characteristics and individual variation in dispersal combine to
 predict genetic structure using genomic and spatial data from the
 Glanville fritillary butterfly. We used linear and latent factor mixed
 models to identify the landscape features that best predict spatial
 sorting of alleles in the dispersal-related gene phosphoglucose isomerase
 (Pgi). We next used structural equation modeling to test if variation in
 Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a
 year when the population was expanding following a large decline,
 individuals with a genotype associated with greater dispersal ability were
 found at significantly higher frequencies in populations isolated by water
 and forest, and these populations showed lower levels of genetic
 differentiation at neutral loci. These relationships disappeared in the
 next year when metapopulation density was high, suggesting that the
 effects of individual variation are context dependent. Together our
 results highlight that 1) more complex aspects of landscape structure
 beyond just the configuration of habitat can be important for maintaining
 spatial variation in dispersal traits, and 2) that individual variation in
 dispersal plays a key role in maintaining genetic variation across
 fragmented landscapes.
description: genotype and patch data
 for DiLeo et al. Evol Lett 2018This folder contains
 data from DiLeo, Husby, Saastamoinen (2018) "Landscape permeability
 and individual variation in a dispersal-linked gene jointly determine
 genetic structure in the Glanville fritillary butterfly" Contents:
 genotypes.csv - this contains raw genotypes of sampled individuals. Each
 line is an individual with a unique identifier (DNA), a Family identifier
 indicating the nest the larvae was sampled from, information about the
 Patch and Year of sampling, and genotypes at candidate and neutral loci
 (KASP_) dataPerPatch.csv - this file contains information at the patch
 level. Includes the geographic coordinates of the patch (Centroid_X,
 Centroid_Y in ETRS-TM35FIN), the BAPS assigned genetic cluster, the age of
 the patch (old or new), the frequency of the Pgi-C allele, the mean
 pairwise Fst (meanFst), and connectivity indices (si_) script.R - this is
 an R script that can be used to reconstruct mixed model and structural
 equation model analyses from the paper Prepared by: Michelle DiLeo
 (michelle.dileo@gmail.com)DRYAD.zip
DOI: 10.5061/dryad.8kv2s
title: Data from: Use of ddPCR in experimental evolution studies

description: Experimental evolution is an important research framework for evolutionary
 biologists as it allows direct testing of fundamental theories about
 adaptation and diversity, which often requires the tracking of genotypes
 or alleles over time. This however requires tools such as genetic markers,
 distinguishable morphological characters or genotyping, which can be time
 and labour intensive, and especially if high-throughput processing is
 necessary. Here, we present a novel approach of combining multiplex ddPCR
 with experimental evolution for tracking genotype frequencies in different
 experimental populations over time. We found this method to be both
 precise and accurate for detecting and quantifying targets of interest,
 especially as compared to traditional PCR methods. The use of multiplex
 ddPCR to follow frequencies can be used for a wide range of experimental
 evolution applications.
description: Fig5Fig6Fig7Fig8_and_Fig9Fig10Fig11AFig11BFig12Fig13
DOI: 10.5061/dryad.24qp1
title: Data from: Scatterhoarders drive long- and short-term population dynamics of a nut-producing tree, while pre-dispersal seed predators and herbivores have little effect

description: 1.Both seed predators and herbivores can have profound effects on
 individual plant growth, reproduction and survival, but their population
 level effects are less well understood. While most plants interact with a
 suite of seed predators and herbivores over their life cycle, few studies
 incorporate the effects of multiple interacting partners and multiple life
 stages on plant population growth. 2.We constructed a matrix model using
 six years of data from a rare, seed-producing population of American
 chestnut (Castanea dentata). We combined field demographic data with
 published experimental results on the effects of pre-dispersal seed
 predators (weevils) and post-dispersal seed predators (scatter-hoarding
 vertebrates) and incorporated the effect of vertebrate herbivores
 estimated from the field data. We explored the impact of these three
 different animal interactions for short-term (transient) and long-term
 (asymptotic) tree population growth. In addition, we used the model to
 explore the conditions under which scatter-hoarding would function as a
 mutualism. 3.Seed predators had greater effect on both short- and
 long-term population growth than herbivores. Although weevil infestation
 can greatly reduce the probability of germination, pre-dispersal seed
 predators had smaller effects on both short- or long-term population
 growth than post-dispersal predators. The elasticities of weevil-related
 parameters were also small. The effect of browsers on both the short- and
 long-term population growth rate were the smallest of the effects studied.
 Post-dispersal seed predation affected population growth the most of the
 interactions studied. The probability of seed removal was amongst the
 largest elasticities, similar in magnitude to survival of large trees.
 4.Synthesis Our results indicate that neither weevils nor the intensity of
 browse damage observed at our study site are likely to hinder tree
 regeneration or reintroduction, though both reduced population growth.
 Although researchers and forest managers often assume that seeds are
 unimportant for long-lived tree populations, our test of this assumption
 shows that scatterhoarders and other post-dispersal seed consumers can
 significantly limit natural regeneration. Forest management that alters
 scatterhoarder behaviour could have significant effects on tree population
 dynamics that are largely unexplored.
description: American chestnut
 demographic dataCADEdata.csvAmerican chestnut germination dataCADEgerminationData.csvAmerican chestnut weevil dataCADEweevilData.csv
DOI: 10.5061/dryad.67fk8
title: Data from: A complete molecular phylogeny of Claravis confirms its paraphyly within small New World ground-doves (Aves: Peristerinae) and implies multiple plumage state transitions

description: The three species in the genus Claravis (Aves: Peristerinae) are unique
 among members of the small New World ground-dove clade. All three species
 inhabit forested areas rather than open scrubby habitat, and exhibit
 obvious sexual dichromatism. However, the phylogenetic relationships
 within Claravis remain unknown. The only molecular phylogenetic study to
 include more than one species of Claravis indicated the genus is
 paraphyletic. Here we include molecular data from all three Claravis
 species, including sequences from a museum skin of the previously
 unsampled Claravis geoffroyi (purple-winged ground-dove). Using both
 mitochondrial and nuclear loci, we estimate phylogenies and divergence
 times for the small New World ground-dove clade. We also use ancestral
 state reconstruction methods to infer the evolution of male blue plumage
 (and thus sexual dimorphism) in the clade. As in the previous study we
 recover Claravis as a paraphyletic group, but with Claravis geoffroyi as
 the sister species to Claravis mondetoura (maroon-chested ground-dove).
 This result has important implications for the evolutionary history of the
 small New World ground-dove clade. In particular, we recover multiple
 independent transitions between the monomorphic and dimorphic plumage
 states, which perhaps indicates sexual dimorphism arose twice in the
 group.
description: Ground-dove MrBayes tree
 file50% majority-rule
 consensus tree from two independent MrBayes runs.Claravis_MrBayes.treGround-dove Garli tree fileMaximum likelihood tree file from two searches of 500 bootstrap replicates in GARLI.Claravis_Garli.treGround-dove BEAST tree fileMaximum clade credibility tree and divergence time estimates from BEAST.Claravis_BEAST.treGround-dove BEAST xml fileXML file used for the BEAST analysis.Claravis_BEAST.xmlGround-dove alignmentConcatenated sequence alignment for the small New World ground-dove and outgroups data. Data partitions are indicated in the SETS block.Claravis_concatenated_alignment.nex
DOI: 10.5061/dryad.p1k64
title: Data from: Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure

description: Studies monitoring changes in genetic diversity and composition through
 time allow a unique understanding of evolutionary dynamics and persistence
 of natural populations. However, such studies are often limited to species
 with short generation times that can be propagated in the laboratory or
 few exceptional cases in the wild. Species that produce dormant stages
 provide powerful models for the reconstruction of evolutionary dynamics in
 the natural environment. A remaining open question is to what extent
 dormant egg banks are an unbiased representation of populations and hence
 of the species’ evolutionary potential, especially in presence of strong
 environmental selection. We address this key question using the water flea
 Daphnia magna, which produces dormant stages that accumulate in biological
 archives over time. We assess temporal genetic stability in three
 biological archives, previously used in resurrection ecology studies
 showing adaptive evolutionary responses to rapid environmental change. We
 show that neutral genetic diversity does not decline with the age of the
 population and it is maintained in presence of strong selection. In
 addition, by comparing temporal genetic stability in hatched and unhatched
 populations from the same biological archive, we show that dormant egg
 banks can be consulted to obtain a reliable measure of genetic diversity
 over time, at least in the multi-decadal time frame studied here. The
 stability of neutral genetic diversity through time is likely mediated by
 the buffering effect of the resting egg bank.
description: Orsini_etal_OHcore_SNPsSNP genotyping results of the samples collected from the sediment core OH (Oud Heverlee, Belgium). The data in this file were obtained from D. magna resting eggs hatched and reared in the laboratory. Individual ID, location of the samples and the stress condition are shown. -9 indicates missing values.Orsini etal_LRV_Hatched_neutral_microsmicrosatellite genotyping results of the samples collected from the sediment core LRV (Lake Ring, Denmark). The data in this file were obtained from D. magna resting eggs hatched and reared in the laboratory. Individual ID, location of the samples and the stress condition are shown. -9 indicates missing values.Orsinietal_LRV_Hatched_neutral_micros.xlsOrsini etal_LRV_Unhatched_neutral_microsmicrosatellite genotyping results of the samples collected from the sediment core LRV (Lake Ring, Denmark). The data in this file were obtained from genotyping D. magna resting eggs. Individual ID, location of the samples and the stress condition in nature are shown. -9 indicates missing values.Orsinietal_LRV_Unhatched_neutral_micros.xls