cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j0zpc86bg
title: Data (D2H values) from: Generational shift in the migratory common noctule bat: first-year males lead the way to hibernacula at higher latitudes

description: Supplementary_Table_3_D2H values noctules_Kravchenko et al The dataset
 contains stable hydrogen values (D2H) (column "sample_value") in
 fur keratin of 413 common noctule bats (Nyctalus noctula) from Kharkiv
 (Ukraine). Samples were collected in winter colonies over 12 years
 (2004-2015). Each row is one individual. Column "sample_ID" is
 an ID of an individual. Columns "lat" and "long" are
 coordinates of Kharkiv city (sampling site). Column "sex" is sex
 of individuals. Column "age1" shows the age of individuals: ad -
 adult individuals, sad -subadult individuals (younger than one year).
 Column "Status" assign origin status of individuals to either 0
 - regional or 1 - migratory.  Column "Year3" represents
 the year of sample collection in a format of time in the past from the
 first year of the collection (-11) till the last year of the collection
 (0).  Column "Year" is the year of sample collection.
description: <b>Collection of fur samples and demographic
 parameters</b> Fur samples were
 obtained from the carcasses repository of the Bat Rehabilitation Center
 (BRC) of Feldman Ecopark (n=137) and live individuals were encountered at
 hibernacula or at BRC (n=276). Fur samples were taken with scissors from
 the interscapular region. We documented the date and place where the bat
 was encountered. Between 2007 and 2016, we conducted surveys of 10
 hibernacula and noted the sex and age (subadult, i.e. individuals younger
 than 1 year, adult) of bats.
 <b>Stable isotope analysis</b> Stable hydrogen
 isotope ratios of bat fur were analysed at the Leibniz Institute for Zoo
 and Wildlife Research (IZW) in Berlin as described before. Samples were
 dried in silver capsules over several days in a drying oven and then
 transferred to an autosampler. We report stable isotope ratios of
 non-exchangeable hydrogen in fur keratin in the delta notation (δ) as
 parts per thousand (‰) deviations from V-SMOW. The precision of
 measurements was always better than 3 ‰ (one standard deviation) for the
 internal keratin standards.
DOI: 10.5061/dryad.qrfj6q5cn
title: Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina

description: When divergent populations are connected by gene flow, the establishment
 of complete reproductive isolation usually requires the joint action of
 multiple barrier effects. One example where multiple barrier effects are
 coupled consists of a single trait that is under divergent natural
 selection and also mediates assortative mating. Such multiple-effect
 traits can strongly reduce gene flow. However, there are few cases where
 patterns of assortative mating have been described quantitatively and
 their impact on gene flow has been determined. Two ecotypes of the coastal
 marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore
 habitats dominated by either crab predation or wave action. There is
 evidence for divergent natural selection acting on size, and
 size-assortative mating has previously been documented. Here, we analyze
 the mating pattern in L. saxatilis with respect to size in
 intensively-sampled transects across boundaries between the habitats. We
 show that the mating pattern is mostly conserved between ecotypes and that
 it generates both assortment and directional sexual selection for small
 male size. Using simulations, we show that the mating pattern can
 contribute to reproductive isolation between ecotypes but the barrier to
 gene flow is likely strengthened more by sexual selection than by
 assortment.
DOI: 10.5061/dryad.0vt4b8gwf
title: SNP data: Population genetic structure in bull sharks (Carcharhinus leucas)

description: The bull shark (Carcharhinus leucas) is a large, mobile, circumglobally
 distributed high trophic level predator that inhabits a variety of remote
 islands and continental coastal habitats, including freshwater
 environments. Here, we hypothesise that the barriers to dispersal created
 by large oceanic expanses and deep-water trenches result in a
 heterogeneous distribution of the neutral genetic diversity between island
 bull shark populations compared to populations sampled in continental
 locations connected through continuous coastlines of continental shelves.
 We analysed 1,494 high-quality neutral Single Nucleotide Polymorphism
 (SNP) markers in 215 individual bull sharks from widespread locations
 across the Indian and Pacific Oceans (South Africa, Indonesia, Western
 Australia, Papua New Guinea, eastern Australia, New Caledonia and Fiji).
 Genomic analyses revealed partitioning between remote insular and
 continental populations, with the Fiji population being genetically
 different from all other locations sampled (FST 0.034-0.044, P &lt;
 0.001), and New Caledonia showing marginal isolation (FST 0.016-0.024, P
 &lt; 0.001; albeit based on a small sample size) from most sampled
 sites. Discriminant Analysis of Principal Components (DAPC) identified
 samples from Fiji as a distinct cluster with all other sites as one large
 cluster. Genetic structure analyses (Admixture, STRUCTURE &
 AssignPOP) further supported the genetic isolation of bull sharks from
 Fiji, with the analyses in agreement. The observed differentiation in bull
 sharks from Fiji makes this site of special interest, as it indicates a
 lack of migration through dispersal across deep-water trenches and large
 ocean expanses.
description: Bull shark samples (white muscle and fin clips, 1
 cm<sup>2</sup>) were obtained from fisheries independent
 surveys, observers on board commercial fleets, dive guides, and
 recreational and artisanal fishers from 2004 to 2017. Tissue
 samples were sent to Diversity Arrays Technology (DArT-Seq™) in Canberra
 Australia where genomic DNA was extracted from the tissues using standard
 robotic methods. DNA was processed for reduced representation library
 construction, sequenced and genotyped by DArT-Seq™ following previously
 developed and tested complexity reduction protocols for scalloped
 hammerhead sharks (<i>Sphyrna lewini</i>)
 (Marie, 2019).
DOI: 10.15468/dl.p2szck
title: Occurrence Download

description: A dataset containing 590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus mongholicus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 590 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002383-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4qrfj6q7h
title: Data from: A seasonal shift in offspring sex ratio of the brood parasitic Brown-headed Cowbird (Molothrus ater)

description: Avian obligate brood parasites do not provide parental care for their eggs
 and young, and may therefore serve as a strong model system to test
 predictions of evolutionary sex-allocation theories, independent of
 parental modulation of primary sex ratios. However, none of the handful of
 previous studies examining offspring sex ratio in brood parasitic birds
 have revealed a bias from parity at the level of the female parasite, the
 host species, or temporal scale(s). This is also surprising, because in at
 least one brood parasite, the Brown-headed Cowbird (Molothrus ater), adult
 sex ratios are consistently and heavily male-biased. Here we used a large
 database of embryonic and nestling cowbirds’ genetic sex ratios collected
 from nests of a single host species, the Prothonotary Warbler
 (Protonotaria citrea) to assess potential overall, temporal, and
 individual patterns of bias. Contrary to previous findings, we documented
 an increase in the calculated male sex ratios later in the breeding
 season. There was no effect of whether embryos or nestlings were sampled,
 implying a lack of host parental effect on shifting the
 primary-to-secondary sex ratios of brood parasitic offspring. Future work
 should explore the sex-specific survival and recruitment pattern of
 fledgling cowbirds raised by this and other host species to reconcile
 theoretical and empirical predictions and patterns.
description: Please see the published article.
DOI: 10.15468/dl.qd7nnb
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000154496, PDD 24446, PDD 24643, PDD 31336, PDD 34939, PDD 38247, PDD 48761, PDD 59721, PDD 59861, PDD 98099, K-M000836457, K-M000836466, K-M000897934, PDD 90473, PDD 90497, PDD 90806, PDD 126694)"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002384-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9kd51c5dn
title: Data from: Distinct cold tolerance traits independently vary across genotypes in Drosophila melanogaster

description: The ability to cope with low temperature is a critical adaptation in
 thermally variable environments. Cold hardiness is comprised of several
 traits, including minimum temperatures for growth and activity, ability to
 survive severe cold, and ability to recover normal function after cold
 subsides. Across species, these traits are correlated and share
 physiological mechanisms, suggesting they were shaped by shared
 evolutionary processes. However, the extent cold hardiness traits and
 their associated mechanisms covary within populations has not been
 assessed. We measured five cold hardiness traits – critical thermal
 minimum (CTmin), chill coma recovery (CCR), acute and chronic cold
 tolerance, and cold-induced changes in locomotor behavior – along with
 cold-induced expression of two genes with known roles in cold hardiness
 (Heat Shock Protein 70 and Frost) – across 12 lines of D. melanogaster
 derived from a single population. We observed significant genetic
 variation in all traits, but few correlated across genotypes, and these
 correlations were sex-dependent. Further, cold-induced gene expression
 varied by genotype, but there was no evidence supporting our hypothesis
 that cold-hardy lines would have either higher baseline expression or
 induction of stress genes. These results suggest cold hardiness traits
 possess unique mechanisms and may have the capacity to evolve
 independently.
DOI: 10.5061/dryad.4qrfj6q7j
title: Data from: Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance

description: The Neotropical region exhibits the greatest worldwide diversity and the
 diversification history of several clades is related to the puzzling
 geomorphologic and climatic history of this region. The freshwater Amazon
 ecoregion contains the main hydrographic basins of the Neotropical region
 that are highly dendritic and ecologically diverse. It contains a rich and
 endemic fish fauna, including one of its most iconic and economically
 important representatives, the bony-tongue Arapaima gigas (Teleostei,
 Osteoglossiformes). Here, we evaluated the projected distribution of the
 genus in different historical periods (Present, Last Glacial Maximum, Last
 Interglacial Maximum and Near Future) and interpreted these results in
 light of the genomic diversity and modeled historical demography. For
 that, we combined species distribution models, population genetic analysis
 using SNPs and deep learning model selection. We analyzed a representative
 sample of the genus from the two basins where it naturally occurs, four
 localities in the Amazon (Am) and three in the Tocantins-Araguaia (To-Ar)
 basin, as well as individuals from three fish farms. We inferred a
 potentially smaller distribution in the glacial period, with a possible
 refuge in central Am. Our genetic data agrees with this result, suggesting
 a higher level of genetic diversity in the Am basin, compared to that
 observed in To-Ar. Our deep learning model comparison indicated that the
 To-Ar basin was colonized by the population from the Am basin. Considering
 a global warming scenario in the near future, A. gigas could reach an even
 larger range, especially if anthropogenic related dispersal occurs,
 potentially invading new areas and impacting their communities.
DOI: 10.5061/dryad.2fqz612mh
title: Recurrent evolution of two competing haplotypes in an insect DNA virus

description: Hosts and viruses are constantly evolving in response to each other: as
 hosts attempt to suppress the virus, the virus attempts to evade and
 suppress the host’s immune system. This arms race results in the evolution
 of novel pathways in both the host and virus to gain the upper hand. Here
 we describe the coevolution between Drosophila species and a common and
 virulent DNA virus. We identify two distinct viral types that differ
 100-fold in viral titer in infected individuals, with similar effects
 across multiple species. Our analysis suggests that one of the viral types
 appears to have recurrently evolved at least 4 times in the past ~30,000
 years, including in another geographically distinct species, due to the
 high effective mutation rate which increases with titer. The higher titer
 viral type is associated with suppression of the host immune system and an
 increased transmission rate compared to the low viral titer type. Both
 types are maintained in all populations, likely due to an increased
 virulence in the high titer type creating a trade-off between effective
 transmission and virulence and resulting in nearly equal reproduction
 rates (R0) in both types. Together these results suggest that the
 reciprocal selective pressures caused by the co-evolution between host and
 virus has resulted in this recurrently evolving relationship.
DOI: 10.5061/dryad.w9ghx3fm8
title: Data from: The genetic architecture of plant defense tradeoffs in a common monkeyflower

description: Determining how adaptive combinations of traits arose requires
 understanding the prevalence and scope of genetic constraints. Frequently
 observed phenotypic correlations between plant growth, defenses, and/or
 reproductive timing have led researchers to suggest that pleiotropy or
 strong genetic linkage between variants affecting independent traits is
 pervasive. Alternatively, these correlations could arise via independent
 mutations in different genes for each trait and extensive correlational
 selection. Here we evaluate these alternatives by conducting a QTL mapping
 experiment involving a cross between two populations of common
 monkeyflower (Mimulus guttatus) that differ in growth rate as well as
 total concentration and arsenal composition of plant defense compounds,
 phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy
 underlies correlations between defense and growth rate. However, there is
 a strong genetic correlation between levels of total PPGs and flowering
 time that is largely attributable to a single shared QTL. While this
 result suggests a role for pleiotropy/close linkage, several other QTLs
 also contribute to variation in total PPGs. Additionally, divergent PPG
 arsenals are influenced by a number of smaller-effect QTLs that each
 underlie variation in one or two PPGs. This result indicates that chemical
 defense arsenals can be finely-adapted to biotic environments despite
 sharing a common biochemical precursor. Together, our results show
 correlations between defense and life history traits are influenced by
 pleiotropy or genetic linkage, but genetic constraints may have limited
 impact on future evolutionary responses, as a substantial proportion of
 variation in each trait is controlled by independent loci.
description: This entry provides all trait data (.csv) for the parent lines,
 F1 lines and F2 lines described in the manuscript. It also provides an the
 rQTL format input files for the F2 mapping population.  Please see the
 readme files for details on each file.
DOI: 10.5061/dryad.1jwstqjrx
title: Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography

description: Phylogeography investigates historical drivers of species’ geographic
 distribution. Special attention has been given to ecological, climatic,
 and geological processes in the diversification of the Neotropical biota.
 Several species sampled across the dry diagonal of South America (DDSA,
 comprising the Caatinga, Cerrado, and Chaco biomes) experienced range
 shifts coincident with Quaternary climatic changes. However, studies
 across different spatial, temporal, and biological scales on species from
 South America’s dry biomes are still poorly represented. Here, we combine
 phylogeographic model selection and machine learning predictive frameworks
 to investigate the influence of Pleistocene climatic changes on both plant
 and animal species from the DDSA. We assembled mitochondrial/chloroplastic
 DNA sequences in public repositories and inferred the historical
 demographic responses of 70 lineages. We then built a random forest model
 using both biotic and abiotic information to identify potential traits for
 predicting whether species underwent population expansion, contraction, or
 stasis during the Pleistocene. Finally, we estimated the temporal
 synchrony of species demographic responses using hierarchical approximate
 Bayesian computation (hABC). Biotic variables largely predicted how
 species responded to Pleistocene climatic changes, and demographic changes
 were mostly synchronous during the Middle Pleistocene. Although many DDSA
 species underwent demographic expansion, presumably associated with the
 spread of aridity during glacial Pleistocene periods, our findings suggest
 that some species exhibited the opposite response and that
 species-specific attributes might have been related to these differences.
DOI: 10.5061/dryad.bnzs7h47p
title: Data from: Heritable variation in root secondary metabolites is associated with recent climate

description: 1. Plants can adapt to changing environments by adjusting the production
 and maintenance of diverse sets of bioactive secondary metabolites. To
 date, the impact of climatic conditions relative to other factors such as
 soil abiotic factors and herbivore pressure on the evolution of plant
 secondary metabolites is poorly understood, especially for plant roots. 2.
 We explored associations between root latex secondary metabolites in 63
 Taraxacum officinale populations across Switzerland and climatic
 conditions, soil abiotic parameters, root herbivore pressure and cytotype
 distribution. To assess the contribution of environmental effects, root
 secondary metabolites were measured in F0 plants in nature and F2 plants
 under controlled greenhouse conditions. 3. Concentrations of root latex
 secondary metabolites were most strongly associated with climatic
 conditions, while current soil abiotic factors or root herbivore pressure
 did not show a clear association with root latex chemistry. Results were
 similar for natural and controlled conditions, suggesting heritable
 variation rather than environmental plasticity as underlying factor. 4.
 Synthesis. We conclude that climatic conditions likely play a major role
 in the evolution of root secondary metabolites. These results may hint at
 a novel role of root latex metabolites in tolerance of abiotic stress.
description: Raw data: Description and environmental parameters of 63 natural
 populations of dandelion; chemical analyses of plants growing in natural
 habitat (F0) and plants growing in greenhouse (F2); maximal leaf length of
 F2 plants as proxy for leaf and root biomass.
DOI: 10.5061/dryad.18931zct8
title: Data from: Does parasitoid pressure elicit defensive polyphenism in the green peach aphid?

description: Aphids are capable of adapting to parasitoid pressure in the absence of
 sexual reproduction using epigenetically controlled polyphenism. Asexual
 lineages of aphids could thus become resistant to parasitoids over time
 and with repeated exposure, hampering biocontrol efforts that rely on
 parasitoid wasps. Prior to this study, wing polyphenism and reproductive
 polyphenism had been reported as parasitoid-adaptive responses in asexual
 lineages of at least two species of aphids, but it remained unclear
 whether parasitoid exposure could induce other defensive polyphenisms.
 Using a rigorous, replicated experimental evolution design, we aimed to
 induce adaptive polyphenisms in the green peach aphid, Myzus persicae
 Sulzer, through serial exposures of single asexual lines to the parasitoid
 Aphidius colemani Viereck over four consecutive generations. We attempted
 to measure changes in parasitoid susceptibility, reproductive schedule,
 body size, and production of pink or alate offspring compared to aphid
 control lines not exposed to parasitoids. Despite this consistently strong
 selective parasitoid pressure, there was no evidence that asexual lineages
 of M. persicae adapt to parasitoid pressure using adaptive polyphenism.
 Our data indicate that pseudo-crowding stress – where aphids disturbed by
 parasitoids or predators wander within a colony, increasing aphid-to-aphid
 contact and creating the illusion of a more crowded environment – may be
 necessary for M. persicae to produce defensive polyphenisms in response to
 parasitoid attack.
description: Data collected by YU over the course of the experiment described
 in the manuscript "Parasitoid pressure does not elicit defensive
 polyphenism in the green peach aphid" Data is
 compartmentalized into multiple Excel spreadsheets.