cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rr7v5
title: Data from: Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish

description: Adaptive radiation is the evolution of ecological and phenotypical
 diversity. It arises via ecological opportunity that promotes the
 exploration of underutilized or novel niches mediating specialization and
 reproductive isolation. The assumed precondition for rapid local
 adaptation is diversifying natural selection, but random genetic drift
 could also be a major driver of this process. We used 27 populations of
 European whitefish (Coregonus lavaretus) from nine lakes distributed in
 three neighbouring subarctic watercourses in northern Fennoscandia as a
 model to test the importance of random drift versus diversifying natural
 selection for parallel evolution of adaptive phenotypic traits. We
 contrasted variation for two key adaptive phenotypic traits correlated
 with resource utilization of polymorphic fish; the number of gill rakers
 and the total length of fish, with the posterior distribution of neutral
 genetic differentiation from 13 microsatellite loci, to test if the
 observed phenotypic divergence could be achieved by random genetic drift
 alone. Our results show that both traits have been under diversifying
 selection and that the evolution of these morphs has been driven by
 isolation through habitat adaptations. We conclude that diversifying
 selection acting on gill raker number and body size has played a
 significant role in the ongoing adaptive radiation of European whitefish
 morphs in this region.
description: pheno_geno_data
DOI: 10.5061/dryad.68711
title: Data from: Early hatching enhances survival despite beneficial phenotypic effects of late-season developmental environments

description: Seasonal shifts in environmental conditions provide predictable cues to
 which organisms can respond in adaptive ways. For example, seasonal
 changes in temperature can induce phenotypes at different times of the
 year that have season-specific fitness benefits. Here, we tested the
 hypothesis that embryo responses to seasonal changes in thermal
 environments are adaptively matched to the timing of reproduction
 (environmental-matching hypothesis). We collected eggs of the brown anole
 lizard (Anolis sagrei) from early and late seasons and exposed them to
 early and late thermal regimes that mimic nest temperatures. After
 measuring offspring morphology and performance, we quantified their
 survival in the field. Females had higher fecundity, but produced smaller
 eggs, early in the season compared to late in the season. Late-season eggs
 exposed to late thermal regimes had relatively high survival, but
 early-season eggs exposed to early thermal regimes had similar survival
 rates to those exposed to mismatched conditions. Late-season nest
 temperatures and late-season eggs produced offspring that were relatively
 large and fast runners. However, despite phenotypic benefits of
 late-season conditions, early-season hatchlings had greater survival in
 the field. Our results do not fully support the environmental-matching
 hypothesis but suggest that selection favors seasonal shifts in
 reproductive investment of mothers (high early-season fecundity) over
 plastic responses of embryos to seasonal environmental changes.
description: Raw Data of Seasonal
 Plasticity in LizardsThis file contains all
 data for the analyses from the manuscriptPearson and Warner Seasonal
 Plasticity Raw Data.xlsx
DOI: 10.5061/dryad.m1n38
title: Data from: Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents and footprints of postglacial recolonisation routes

description: Understanding the factors that contribute to population genetic divergence
 across a species' range is a long-standing goal in evolutionary
 biology and ecological genetics. We examined the relative importance of
 historical and ecological features in shaping the present-day spatial
 patterns of genetic structure in two related plant species, Beta vulgaris
 subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial
 markers, we surveyed 93 populations from Brittany (France) to Morocco –
 the southern limit of their species' range distribution. Whereas B.
 macrocarpa showed a genotypic structure and a high level of genetic
 differentiation indicative of selfing, the population genetic structure of
 B. vulgaris subsp. maritima was consistent with an outcrossing mating
 system. We further showed (1) a strong geographic clustering in coastal B.
 vulgaris subsp. maritima populations that highlighted the influence of
 marine currents in shaping different lineages and (2) a peculiar genetic
 structure of inland B. vulgaris subsp. maritima populations that could
 indicate the admixture of distinct evolutionary lineages and recent
 expansions associated with anthropogenic disturbances. Spatial patterns of
 nuclear diversity and differentiation also supported a stepwise
 recolonization of Europe from Atlantic-Mediterranean refugia after the
 last glacial period, with leading-edge expansions. However, cytoplasmic
 diversity was not impacted by postglacial recolonization: stochastic
 long-distance seed dispersal mediated by major oceanic currents may
 mitigate the common patterns of reduced cytoplasmic diversity observed for
 edge populations. Overall, the patterns we documented here challenge the
 general view of reduced genetic diversity at the edge of a species'
 range distribution and provide clues for understanding how life-history
 and major geographic features interact to shape the distribution of
 genetic diversity.
description: Coordinates of sample
 locations, cytoplasmic and nuclear genotypesCoordinates of sample
 locations, cytoplasmic (4 minisatellites) and nuclear (8 microsatellites)
 genetic data from Beta vulgaris subsp. maritima and Beta macrocarpa
 populations sampled in western Europe and Morocco.Minisat_Microsat_Data-Leys et
 al.xlsx
DOI: 10.5061/dryad.hm06n7c0
title: Data from: Quantitative genetics of immunity and life history under different photoperiods

description: Insects with complex life-cycles should optimize age and size at maturity
 during larval development. When inhabiting seasonal environments,
 organisms have limited reproductive periods and face fundamental
 decisions: individuals that reach maturity late in season have to either
 reproduce at a small size or increase their growth rates. Increasing
 growth rates is costly in insects due to higher juvenile mortality,
 decreased adult survival, or increased susceptibility to parasitism by
 bacteria and viruses via compromised immune function. Environmental
 changes such as seasonality can also alter the quantitative genetic
 architecture. Here we explore the quantitative genetics of life history
 and immunity traits under two experimentally induced seasonal environments
 in the cricket Gryllus bimaculatus. Seasonality affected the life history
 but not the immune phenotypes. Individuals under decreasing day length
 developed slower and grew to a bigger size. We found ample additive
 genetic variance and heritability for components of immunity (haemocyte
 densities, proPhenoloxidase activity, resistance against Serratia
 marcescens), and for the life history traits, age and size at maturity.
 Despite genetic covariance among traits, the structure of G was
 inconsistent with genetically based trade-off between life history and
 immune traits (e.g., a strong positive genetic correlation between growth
 rate and haemocyte density was estimated). However, conditional
 evolvabilities support the idea that genetic covariance structure limits
 the capacity of individual traits to evolve independently. We found no
 evidence for GxE interactions arising from the experimentally induced
 seasonality.
description: G. bimaculatus: Immunity
 and life history dataTCuploadDryad.xls
DOI: 10.5061/dryad.b1g138g
title: Data from: Predictors of new remote cerebral microbleeds after intravenous thrombolysis for ischemic stroke

description: Objective: To assess the frequency, associated factors, and underlying
 vasculopathy of new remote cerebral microbleeds (CMB), as well as the risk
 of concomitant hemorrhagic complications related to new CMBs, after
 intravenous thrombolysis (IVT) in acute stroke patients. Methods: We
 conducted an observational study using data from our local thrombolysis
 registry. We included consecutive stroke patients with MRI (3-Tesla)-based
 IVT and a follow-up MRI the next day between 2008–2017 (n=396). Only CMBs
 located outside of the ischemic lesion(s) were considered. We also
 performed a meta-analysis on new CMBs after IVT that included two
 additional studies. Results: In our cohort, new remote CMBs occurred in
 16/396 patients (4.0%) after IVT and the distribution was strictly lobar
 in 13/16 patients (81%). Patients with pre-existing CMBs with a strictly
 lobar distribution were significantly more likely to have new CMBs after
 IVT (p=0.014). In the random-effects meta-analysis (n=741), the pooled
 cumulative frequency of new CMBs after IVT was 4.4%. A higher pre-existing
 CMB burden (&gt;2) was associated with a higher likelihood of new CMBs
 (odds ratio [OR] 3.6, 95% confidence interval [CI] 1.3–10.3) and new CMBs
 were associated with the occurrence of remote parenchymal hemorrhage (OR
 28.8, 95%CI 8.6–96.4). Conclusions: New remote CMBs after IVT occurred in
 4% of stroke patients, mainly had a strictly lobar distribution, and were
 associated with IVT-related hemorrhagic complications. Pre-existing CMBs
 with a strictly lobar distribution and a higher CMB burden were associated
 with new CMBs after IVT, which may indicate an underlying cerebral amyloid
 angiopathy.
description: PRISMA flow
 diagramPRISMA 2009 flow
 diagram.pdf
DOI: 10.5061/dryad.77rn2
title: Data from: Influence of the honeybee and trait similarity on the effect of a non-native plant on pollination and network rewiring

description: Introduced entomophilous non-native plants usually become well integrated
 into the diet of generalist pollinators. This integration can affect the
 entire recipient plant–pollinator network. Effects vary from facilitative
 to competitive, and understanding the factors that govern such variability
 is one of the fundamental goals in invasion ecology. Species traits
 determine the linking patterns between plant and pollinator species.
 Therefore, trait similarity among plants or among pollinators might
 modulate how they affect each other. We conducted a flower removal
 experiment to investigate the effects of the non-native entomophilous
 legume Hedysarum coronarium on the pollination patterns of a Mediterranean
 shrubland plant–pollinator network. Specifically, we explored whether
 effects were influenced by similarity with the resident plant species in
 flower morphology (papilionate vs. non-papilionate), and whether effects
 on the pollinator community were influenced by similarity in functional
 group with its main visitor species (bees vs. non-bees). In addition, we
 explored whether Hedysarum had an effect on the identity of interactions.
 For this purpose, we calculated the interaction rewiring, that is the
 number of plant–pollinator interactions that were gained or lost after
 invasion. Hedysarum was well integrated into the diet of 15 generalist
 pollinators having the honeybee as its main visitor species. Such
 integration did not affect visitation rates, normalized degree (i.e.
 proportion of pollinators they are visited by) nor niche overlap (i.e.
 proportion of plant species they share pollinators with) of plants,
 irrespective of their flower morphology. Only the proportion of honeybee
 visits to resident plants decreased with invasion. On the other hand,
 Hedysarum reduced visitation rates and niche overlap of pollinators,
 mainly those of bee species. Finally, we observed that changes in the
 foraging behaviour of the honeybee were positively associated with the
 interaction rewiring involving the rest (92 taxa) of pollinators. In
 conclusion, pollinators show a plastic use of floral resources, responding
 to the presence of non-native plants. When the non-native attracts highly
 competitive pollinators such as the honeybee, plasticity is especially
 significant in pollinators that are functionally close to that competitive
 pollinator. The result is an interaction rewiring, probably due to
 pollinators avoiding competition with the honeybee. Though this plasticity
 might not quantitatively affect the pollination of plants, consequences on
 their reproduction and the functioning of the network can derive from the
 interaction rewiring.
description: dataset_MonteroCastaño&Vila_FunctionalEcology_2016
DOI: 10.5061/dryad.1cv15
title: Data from: Background colour matching increases with risk of predation in a colour-changing grasshopper

description: Cryptic colouration can be adjusted to the local environment by
 physiological (rapid) change, and/or by morphological (slow) change. The
 threat-sensitivity hypothesis predicts that the degree of crypsis should
 respond to the risk of predation (assuming some cost to crypsis). This has
 not been studied for morphological colour changers, so we manipulated the
 colour of the rearing substrate (black versus white) and the perceived
 risk of predation (higher versus lower) for the grasshopper Sphingonotus
 azurescens. Over a period of several weeks, both nymphs and adults greatly
 adjusted the brightness of their body towards that of the substrate.
 Moreover, when individuals were exposed to a greater simulated predation
 risk (disturbance by hand), they became even more similar in brightness to
 their substrates, apparently augmenting their degree of crypsis. This
 study on a morphological colour changer shows that the degree of cryptic
 colouration (body brightness) is under individual control and appears to
 change adaptively in response to increased predation risk. In addition,
 based on analyses of systematic differences in colour in lab-reared
 offspring, we found indications that even in colour changers there is
 genetic variation in colouration among individuals, and that populations
 have diverged adaptively. Such integration of factors determining the
 cryptic phenotype improves our understanding of the natural selection and
 constraints imposed on crypsis, which influence both its optimization and
 evolution.
description: data adults
 grasshoppersdata_adults_.txtdata grasshopper nymphsdata_nymphs_.txtR code for statistical analysisanalysis_code newest Pim.R
DOI: 10.5061/dryad.03s86
title: Data from: Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

description: Modern analytical methods for population genetics and phylogenetics are
 expected to provide more accurate results when data from multiple
 genome-wide loci are analyzed. We present the results of an initial
 application of parallel tagged sequencing (PTS) on a next generation
 platform to sequence thousands of barcoded PCR amplicons generated from 95
 nuclear loci and 93 individuals sampled across the range of the tiger
 salamander (Ambystoma tigrinum) species complex. To manage the
 bioinformatic processing of this large data set (344,330 reads), we
 developed a pipeline that sorts PTS data by barcode and locus, identifies
 high-quality variable nucleotides, and yields phased haplotype sequences
 for each individual at each locus. Our sequencing and bioinformatic
 strategy resulted in a genome-wide data set with relatively low levels of
 missing data and a wide range of nucleotide variation. STRUCTURE analyses
 of these data in a genotypic format resulted in strongly supported
 assignments for the majority of individuals into nine geographically
 defined genetic clusters. Species tree analyses of the most variable loci
 using a multi-species coalescent model resulted in strong support for most
 branches in the species tree; however, analyses including more than 50
 loci produced parameter sampling trends that indicated a lack of
 convergence on the posterior distribution. Overall, these results
 demonstrate the potential for amplicon-based PTS to rapidly generate
 large-scale data for population genetic and phylogenetic-based research.
description: AlignmentsSecondary alignments for all samples/loci in nexus format. Individual Locus and Sample information is available in Supplemental Tables.Structure Files454_SBEASTBeast Files including: Nexus files, XML files, MCC Trees, and species trees.dummy 454_SBEAST.txtSFF FilesAll SFF files generated from 454 sequencing.SFFfiles.zipNext Allele FilesScripts, barcodes, and reference sequences used for bioinformatics.
DOI: 10.5061/dryad.24c24
title: Data from: Founder events, isolation, and inbreeding: Intercontinental genetic structure of the domestic ferret

description: Domestication and breeding for human-desired morphological traits can
 reduce population genetic diversity via founder events and artificial
 selection, resulting in inbreeding depression and genetic disorders. The
 ferret (Mustela putorius furo) was domesticated from European polecats (M.
 putorius), transported to multiple continents, and has been artificially
 selected for several traits. The ferret is now a common pet, a laboratory
 model organism, and feral ferrets can impact native biodiversity. We
 hypothesized global ferret trade resulted in distinct international
 genetic clusters and that ferrets transported to other continents would
 have lower genetic diversity than ferrets from Europe because of extreme
 founder events and no hybridization with wild polecats or
 genetically-diverse ferrets. To assess these hypotheses, we genotyped 765
 ferrets at 31 microsatellites from 11 countries among the continents of
 North America, Europe, and Australia and estimated population structure
 and genetic diversity. Fifteen M. putorius were genotyped for comparison.
 Our study indicated ferrets exhibit geographically-distinct clusters and
 highlights the low genetic variation in certain countries. Australian and
 North American clusters have the lowest genetic diversities and highest
 inbreeding metrics whereas the United Kingdom (UK) cluster exhibited
 intermediate genetic diversity. Non-UK European ferrets had high genetic
 diversity, possibly a result of introgression with wild polecats. Notably,
 Hungarian ferrets had the highest genetic diversity and Hungary is the
 only country sampled with two wild polecat species. Our research has broad
 social, economic, and biomedical importance. Ferret owners and
 veterinarians should be made aware of potential inbreeding depression.
 Breeders in North America and Australia would benefit by incorporating
 genetically-diverse ferrets from mainland Europe. Laboratories using
 ferrets as biomedical organisms should consider diversifying their genetic
 stock and incorporating genetic information into bioassays. These results
 also have forensic applications for conserving the genetics of wild
 polecat species and for identifying and managing sources of feral ferrets
 causing ecosystem damage.
description: Ferret_Microsatellite_Location_DataFerret data used in the analysis.
DOI: 10.5061/dryad.17b18
title: Data from: Host tissues as microhabitats for Wolbachia and quantitative insights into the bacterial community in terrestrial isopods

description: Animal–bacterial symbioses are highly dynamic in terms of multipartite
 interactions, both between the host and its symbionts as well as between
 the different bacteria constituting the symbiotic community. These
 interactions will be reflected by the titres of the individual bacterial
 taxa, for example via host regulation of bacterial loads or competition
 for resources between symbionts. Moreover, different host tissues
 represent heterogeneous microhabitats for bacteria, meaning that
 host-associated bacteria might establish tissue-specific bacterial
 communities. Wolbachia are widespread endosymbiotic bacteria, infecting a
 large number of arthropods and filarial nematodes. However, relatively
 little is known regarding direct interactions between Wolbachia and other
 bacteria. This study represents the first quantitative investigation of
 tissue-specific Wolbachia–microbiota interactions in the terrestrial
 isopod Armadillidium vulgare. To this end, we obtained a more complete
 picture of the Wolbachia distribution patterns across all major host
 tissues, integrating all three feminizing Wolbachia strains (wVulM, wVulC,
 wVulP) identified to date in this host. Interestingly, the different
 Wolbachia strains exhibited strain-specific tissue distribution patterns,
 with wVulM reaching lower titres in most tissues. These patterns were
 consistent across different host genetic backgrounds and might reflect
 different co-evolutionary histories between the Wolbachia strains and A.
 vulgare. Moreover, Wolbachia-infected females carried higher total
 bacterial loads in several, but not all, tissues, irrespective of the
 Wolbachia strain. Taken together, this quantitative approach indicates
 that Wolbachia is part of a potentially more diverse bacterial community,
 as exemplified by the presence of highly abundant bacterial taxa in the
 midgut caeca of several A. vulgare populations.
description: GenotypesGenotyping data at 8 loci for each individualFSTPairwise Fst values between the different laboratory lineages and field populationsTiters_Wolbachia_BacteriaQuantitative PCR data for all tissue samples