cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kk466
title: Data from: SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

description: Identification of genes underlying genomic signatures of natural selection
 is key to understanding adaptation to local conditions. We used targeted
 resequencing to identify SNP markers in 5,321 candidate adaptive genes
 associated with known immunological, metabolic, and growth functions in
 ovids and other ungulates. We selectively targeted 8,161 exons in
 protein-coding and nearby 5′ and 3′ untranslated regions of chosen
 candidate genes. Targeted sequences were taken from bighorn sheep (O.
 canadensis) exon capture data and directly from the domestic sheep genome
 (O. aries v. 3; oviAri3). The bighorn sheep sequences used in the
 Dall's sheep (Ovis dalli dalli) exon capture aligned to 2,350 genes
 on the oviAri3 genome with an average of 2 exons each. We developed a
 microfluidic qPCR-based SNP-chip to genotype 476 Dall's sheep from
 locations across their range and test for patterns of selection. Using
 multiple corroborating approaches (LOSITAN and BayeScan), we detected 28
 SNP loci potentially under selection. We additionally identified candidate
 loci significantly associated with latitude, longitude, precipitation, and
 temperature, suggesting local environmental adaptation. The 3 methods
 demonstrated consistent support for natural selection on 9 genes with
 immune and disease-regulating functions (e.g., Ovar-DRA, APC, BATF2,
 MAGEB18), cell regulation signaling pathways (e.g., KRIT1, PI3K, ORRC3),
 and respiratory health (CYSLTR1). Characterizing adaptive allele
 distributions from novel genetic techniques will facilitate investigation
 of the influence of environmental variation on local adaptation of a
 northern alpine ungulate throughout its range. This research demonstrated
 the utility of exon capture for gene-targeted SNP discovery and subsequent
 SNP-chip genotyping using low quality samples in a non-model species.
description: SNP
 dataSNPdata.txt
DOI: 10.5061/dryad.qn8n3
title: Data from: Epitope-specific CD8+ T cell kinetics rather than viral variability determine the timing of immune escape in Simian Immunodeficiency Virus infection

description: CD8+ T cells are important for the control of chronic HIV infection.
 However, the virus rapidly acquires “escape mutations” that reduce CD8+ T
 cell recognition and viral control. The timing of when immune escape
 occurs at a given epitope varies widely among patients and also among
 different epitopes within a patient. The strength of the CD8+ T cell
 response, as well as mutation rates, patterns of particular amino acids
 undergoing escape, and growth rates of escape mutants, may affect when
 escape occurs. In this study, we analyze the epitope-specific CD8+ T cells
 in 25 SIV-infected pigtail macaques responding to three SIV epitopes. Two
 epitopes showed a variable escape pattern and one had a highly monomorphic
 escape pattern. Despite very different patterns, immune escape occurs with
 a similar delay of on average 18 d after the epitope-specific CD8+ T cells
 reach 0.5% of total CD8+ T cells. We find that the most delayed escape
 occurs in one of the highly variable epitopes, and that this is associated
 with a delay in the epitope-specific CD8+ T cells responding to this
 epitope. When we analyzed the kinetics of immune escape, we found that
 multiple escape mutants emerge simultaneously during the escape, implying
 that a diverse population of potential escape mutants is present during
 immune selection. Our results suggest that the conservation or variability
 of an epitope does not appear to affect the timing of immune escape in
 SIV. Instead, timing of escape is largely determined by the kinetics of
 epitope-specific CD8+ T cells.
description: KP9 epitope sequencing
 dataSimian Immunodeficiency
 Virus immune escape KP9 epitope sequencing dataKP9.xlsxKVA10 epitope sequencing dataSimian Immunodeficiency Virus immune escape KVA10 epitope sequencing dataKVA10.xlsxKSA10 epitope sequencing dataSimian Immunodeficiency Virus immune escape KSA10 epitope sequencing dataKSA10.xlsxViral loadsLog10 total viral loadsTetramer staining dataTetramer staining dataTetramer responses.xlsxVariability of the KP9, KVA10, and KSA10 epitopes in Mane-A01*084 negative animalsVariability of the KP9, KVA10, and KSA10 epitopes in Mane-A01*084 negative animalsA084-KP9,KSA,KVA_44 animals.xlsx
DOI: 10.5061/dryad.j3n0g
title: Data from: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system

description: Understanding if the members of an ecological community have
 co-diversified is a central concern of evolutionary biology, as
 co-diversification suggests prolonged association and possible
 coevolution. By sampling associated species from an ecosystem, researchers
 can better understand how abiotic and biotic factors influence
 diversification in a region. In particular, studies of co-distributed
 species that interact ecologically can allow us to disentangle the effect
 of how historical processes have helped shape community level structure
 and interactions. Here we investigate the Sarracenia alata pitcher plant
 system, an ecological community where many species from disparate
 taxonomic groups live inside the fluid-filled pitcher leaves. Direct
 sequencing of the eukaryotes present in the pitcher plant fluid enables us
 to better understand how a host plant can shape and contribute to the
 genetic structure of its associated inquilines, and to ask whether genetic
 variation in the taxa are structured in a similar manner to the host
 plant. We used 454 amplicon-based metagenomics to demonstrate that the
 pattern of genetic diversity in many, but not all, of the eukaryotic
 community is similar to that of S. alata, providing evidence that
 associated eukaryotes share an evolutionary history with the host pitcher
 plant. Our work provides further evidence that a host plant can influence
 the evolution of its associated commensals.
description: Full sequence data and
 nexus files from comparative data setSequence data following
 demultiplexing and quality control steps. These sequences were used for
 collecting taxonomic information and generating OTUs within each sample
 site and across all sample sites. Aligned nexus files of the 31 OTUs in
 the comparative data set are also included.DRYAD_Satleretal.zip
DOI: 10.5061/dryad.b7s8v
title: Data from: The influence of slavemaking lifestyle, caste and sex on chemical profiles in Temnothorax ants: insights into the evolution of cuticular hydrocarbons

description: Chemical communication is central for the formation and maintenance of
 insect societies. Generally, social insects only allow nest-mates into
 their colony, which are recognized by their cuticular hydrocarbons (CHCs).
 Social parasites, which exploit insect societies, are selected to
 circumvent host recognition. Here, we studied whether chemical strategies
 to reduce recognition evolved convergently in slavemaking ants, and
 whether they extend to workers, queens and males alike. We studied CHCs of
 three social parasites and their related hosts to investigate whether the
 parasitic lifestyle selects for specific chemical traits that reduce host
 recognition. Slavemaker profiles were characterized by shorter-chained
 hydrocarbons and a shift from methyl-branched alkanes to n-alkanes,
 presumably to reduce recognition cue quantity. These shifts were
 consistent across independent origins of slavery and were found in
 isolated ants and those emerging in their mother colony. Lifestyle
 influenced profiles of workers most profoundly, with little effect on
 virgin queen profiles. We detected an across-species caste signal, with
 workers, for which nest-mate recognition is particularly important,
 carrying more and longer-chained hydrocarbons and males exhibiting a
 larger fraction of n-alkanes. This comprehensive study of CHCs across
 castes and species reveals how lifestyle-specific selection can result in
 convergent evolution of chemical phenotypes.
description: CHC data for Kleeberg et
 alThe
 table gives relative abundances for all cuticular hydrocarbons detected.
 It also contains absolute total CHC quantities (in µg) as one column. Most
 of the analyses were conducted only considering the "original
 colony" treatment. The table also includes the "isolation"
 treatment which allows to investigate effects of the social
 environment.Data_Kleebergetal.xlsx
DOI: 10.5061/dryad.f1r72
title: Data from: The early diversification history of didelphid marsupials: a window into South America’s “Splendid Isolation”

description: The geological record of South American mammals is spatially biased
 because productive fossil sites are concentrated at high latitudes. As a
 result, the history of mammalian diversification in Amazonia and other
 tropical biomes is largely unknown. Here we report diversification
 analyses based on a time-calibrated molecular phylogeny of opossums
 (Didelphidae), a species-rich clade of mostly tropical marsupials
 descended from a Late Oligocene common ancestor. Optimizations of habitat
 and geography on this phylogeny suggest that (1) basal didelphid lineages
 inhabited South American moist forests; (2) didelphids did not diversify
 in dry-forest habitats until the Late Miocene; and (3) most didelphid
 lineages did not enter North America until the Pliocene. We also summarize
 evidence for an Early- to Middle-Miocene mass extinction event, for which
 alternative causal explanations are discussed. To the best of our
 knowledge, this study provides the first published molecular-phylogenetic
 evidence for mass extinction in any animal clade, and it is the first time
 that evidence for such an event (in any plant or animal taxon) has been
 tested for statistical significance. Potentially falsifying observations
 that could help discriminate between the proposed alternative explanations
 for didelphid mass extinction may be obtainable from diversification
 analyses of other sympatric mammalian groups.
description: R-code for generating
 figure 2Code used to evaluate
 significance of diversification plateau, as shown in Figure
 2.Figure 2
 Code.zipBEAST xml
 fileThe BEAST xml file,
 including sequence data, calibration points, and parameter settings used
 to generate Figure 1.Didelphid_BEAST.xml
DOI: 10.5061/dryad.9s1gm
title: Data from: Maternal-by-environment but not genotype-by-environment interactions in a fish without parental care

description: The impact of environmental conditions on the expression of genetic
 variance and on maternal effects variance remains an important question in
 evolutionary quantitative genetics. We investigate here the effects of
 early environment on variation in seven adult life history, morphological,
 and secondary sexual traits (including sperm characteristics) in a
 viviparous poeciliid fish, the mosquitofish Gambusia holbrooki.
 Specifically, we manipulated food availability during early development
 and then assessed additive genetic and maternal effects contributions to
 the overall phenotypic variance in adults. We found higher heritability
 for female than male traits, but maternal effects variance for traits in
 both sexes. An interaction between maternal effects variance and rearing
 environment affected two adult traits: female age at maturity and male
 size at maturity. But there was no evidence of trade-offs in maternal
 effects across environments. Our results illustrate (i) the potential for
 pre-natal maternal effects to interact with offspring environment during
 development, potentially affecting traits through to adulthood and (ii)
 that genotype-by-environment interactions might be overestimated if
 maternal-by-environment interactions are not accounted for, similar to
 heritability being overestimated if maternal effects are ignored. We also
 discuss the potential for dominance genetic variance to contribute to the
 estimate of maternal effects variance.
description: Vega-Trejo et al
 HeredityThis file contains data
 for "Maternal-by-environment but not genotype-by-environment
 interactions in a fish without parental care". Data is separated for
 females and males. Labels for each data are provided in a separate excel
 sheet.Vega_trejo_etalQG_Dryad.xlsx
DOI: 10.5061/dryad.s24121t
title: Data from: The lingering impact of stress: brief acute glucocorticoid exposure has sustained, dose-dependent effects on reproduction

description: Acutely stressful experiences can have profound and persistent effects on
 phenotype. Across taxa, individuals differ remarkably in their
 susceptibility to stress. However, the mechanistic causes of enduring
 stress effects, and of individual differences in stress susceptibility,
 are poorly understood. Here we tested whether brief, acute increases in
 glucocorticoid hormones have persistent effects on phenotype, and whether
 effects differ according to the magnitude or duration of elevation. We
 used a novel method to non-invasively manipulate hormone levels on short
 time scales: the application of corticosterone gel to a model egg secured
 in the nest. Free-living female tree swallows (Tachycineta bicolor)
 exposed to several brief corticosterone increases during incubation showed
 dose-dependent differences in behaviour throughout the reproductive
 period. Birds receiving treatments that simulated higher or longer acute
 stress responses later provisioned larger broods at lower rates; the
 resulting offspring were smaller in size. Treatment did not influence
 female body condition, oxidative stress, reproductive success, or
 inter-annual survival, but exposed females maintained higher baseline
 corticosterone after treatments ceased. Overall, these results indicate
 that brief, acute elevations in glucocorticoids in adulthood can have
 long-term consequences. Furthermore, individuals that mount a greater or
 longer acute stress response may be more likely to experience lingering
 effects of stress.
description: Data and
 codeThis file contains data
 and R code associated with "The lingering impact of stress: brief
 acute glucocorticoid exposure has sustained, dose-dependent effects on
 reproduction."Archive.zip
DOI: 10.15468/dl.epymku
title: Occurrence Download

description: A dataset containing 1106767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus, Myocastor coypus)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1106767 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000581-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4mp30
title: Data from: Widespread correlations between climatic niche evolution and species diversification in birds

description: The adaptability of species’ climatic niches can influence the dynamics of
 colonisation and gene flow across climatic gradients, potentially
 increasing the likelihood of speciation, or reducing extinction in the
 face of environmental change. However, previous comparative studies have
 tested these ideas using geographically, taxonomically and ecologically
 restricted samples, yielding mixed results, and thus the processes linking
 climatic niche evolution with diversification remain poorly understood.
 Focusing on birds, the largest and most widespread class of terrestrial
 vertebrates, we test whether variation in species diversification among
 clades is correlated with rates of climatic niche evolution, and the
 extent to which these patterns are modified by underlying gradients in
 biogeography and species’ ecology. We quantified climatic niches,
 latitudinal distribution and ecological traits for 7657 (~75%) bird
 species based on geographical range polygons, and then used Bayesian
 phylogenetic analyses to test whether niche evolution was related to
 species richness and rates of diversification across genus and
 family-level clades. We found that the rate of climatic niche evolution
 has a positive linear relationship with both species richness and
 diversification rate at two different taxonomic levels (genus and family).
 Furthermore, this positive association between labile climatic niches and
 diversification was detected regardless of variation in clade latitude or
 key ecological traits. Our findings suggest either that rapid adaptation
 to unoccupied areas of climatic niche space promotes avian
 diversification, or that diversification promotes adaptation. Either way,
 we propose that climatic niche evolution is a fundamental process
 regulating the link between climate and biodiversity at global scales,
 irrespective of the geographical and ecological context of speciation and
 extinction.
description: Summarised family-level
 dataFamily-level averages
 for diversification and climatic niche variables.Cooney_etal_JAE_summarised_data_families.csvSummarised genus-level dataGenus-level averages for diversification, climatic niche and ecological variables.Cooney_etal_JAE_summarised_data_genera.csv
DOI: 10.5061/dryad.50tc7
title: Data from: Social conflict and costs of cooperation in meerkats are reflected in measures of stress hormones

description: Measures of glucocorticoid stress hormones (e.g. cortisol) have often been
 used to characterize conflict between subordinates and dominants. In
 cooperative breeders where subordinates seldom breed in their natal group
 and assist in offspring rearing, increases in subordinate glucocorticoid
 levels may be caused by conflict among subordinates as well as by the
 energetic costs of helping behavior and fluctuations in food availability
 may exacerbate these effects. During a 6-year study of Kalahari meerkats
 (Suricata suricatta), we investigated how social, environmental, and
 individual characteristics influenced subordinate plasma cortisol levels.
 Subordinate females, who are often the target of aggression from dominant
 females, had higher cortisol levels when the dominant female in their
 group was pregnant while the cortisol levels of subordinate males were
 unaffected by the reproductive state of dominant females. Subordinates of
 both sexes had higher cortisol levels if they belonged to groups 1) where
 neither of the dominant breeders in the group were their parents, 2) that
 contained a high proportion of subordinate females, or 3) that were either
 very large or very small, especially when the weather was cold and dry.
 Subordinates in groups containing young pups had higher cortisol levels.
 Finally, cortisol levels were higher in subordinates of both sexes if they
 were lighter for their age or had lost little body mass the night prior to
 sampling. Our results show that both social conflict and cooperative
 behavior can elevate glucocorticoid levels in subordinates and that both
 effects can be modified by variation in weather and food availability.
description: Meerkat Data for
 DryadData for all analyses in
 manuscript
DOI: 10.5061/dryad.8155
title: Data from: All roads lead to home: panmixia of European eel in the Sargasso Sea

description: European eels (Anguilla anguilla) spawn in the remote Sargasso Sea in
 partial sympatry with American eels (Anguilla rostrata), and juveniles are
 transported more than 5,000 kilometres back to the European and North
 African coasts. The two species have been regarded as classic textbook
 examples of panmixia, each comprising a single, randomly mating
 population. However, several recent studies based on continental samples
 have found subtle, but significant, genetic differentiation, interpreted
 as geographical or temporal heterogeneity between samples. Moreover,
 European and American eels can hybridize, but hybrids have been observed
 almost exclusively in Iceland, suggesting hybridization in a specific
 region of the Sargasso Sea and subsequent non-random dispersal of larvae.
 Here, we report the first molecular population genetics study based on
 analysis of 21 microsatellite loci in larvae of both Atlantic eel species
 sampled directly in the spawning area, supplemented by analysis of
 European glass eel samples. Despite a clear East-West gradient in the
 overlapping distribution of the two species in the Sargasso Sea, we only
 observed a single putative hybrid, providing evidence against the
 hypothesis of a wide marine hybrid zone. Analyses of genetic
 differentiation, isolation by distance, isolation by time and assignment
 tests provided strong evidence for panmixia in both the Sargasso Sea and
 across all continental samples of European eel after accounting for the
 presence of sibs among newly hatched larvae. European eel has declined
 catastrophically, and our findings call for management of the species as a
 single unit, necessitating coordinated international conservation efforts.
description: Als et al. 2011 data
 fileData file with genotype
 data for 1010 European glass eel, 271 European eel larvae from the
 Sargasso Sea and 117 American eel larvae from the Sargasso Sea. Individual
 number: Sample code for each individual Species.ID: AA = European eel, AR
 American eel Transect/region: Transect in the Sargasso Sea or geographical
 region in Europe or North Africa Station/sample: Specific station or
 locality posLat: Latitudinal position posLon: Longitudinal position Date:
 date of sampling Length..mm: Length of eel larvae Microsatellite data are
 listed with one allele per column, i.e. two columns per locus.
 Microsatellite alleles are denoted by lenghts in bp.
DOI: 10.5061/dryad.88b5b
title: Data from: Population-specific covariation between immune function and color of nesting male threespine stickleback

description: Multiple biological processes can generate sexual selection on male visual
 signals such as color. For example, females may prefer colorful males
 because those males are more readily detected (perceptual bias), or
 because male color conveys information about male quality and associated
 direct or indirect benefits to females. For example, male threespine
 stickleback often exhibit red throat coloration, which females prefer both
 because red is more visible in certain environments, and red color is
 correlated with male immune function and parasite load. However, not all
 light environments favor red nuptial coloration: more tannin-stained water
 tends to favor the evolution of a melanic male phenotype. Do such
 population differences in stickleback male color, driven by divergent
 light environments, lead to changes in the relationship between color and
 immunity? Here, we show that, within stickleback populations, multiple
 components of male color (brightness and hue of four body parts) are
 correlated with multiple immune variables (ROS production, phagocytosis
 rates, and lymphocyte:leukocyte ratios). Some of these color-immune
 associations persist across stickleback populations with very different
 male color patterns, whereas other color-immune associations are
 population-specific. Overall, lakes with red males exhibit stronger
 color-immune covariance while melanic male populations exhibit weak if any
 color-immune associations. Our finding that color-immunity relationships
 are labile implies that any evolution of male color traits (e.g., due to
 female perceptual bias in a given light environment), can alter the
 utility of color as an indicator of male quality.
description: Bolnick_et_al_PLoS_One_Dryad_SubmissionA .csv file containing all the data used for analyses and graphics in Bolnick et al 2015 PLoS One. The same data are sufficient to recreate analyses in Bolnick et al Evolution. Raw data files (.jpg photographs, spectrophotometric files, flow cytometry .fcs files) are available upon request.