cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8ff46
title: Data from: Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis) on Newfoundland and Cape Breton Island

description: Island populations have long been important for understanding the dynamics
 and mechanisms of evolution in natural systems. While genetic drift is
 often strong on islands due to founder events and population bottlenecks,
 the strength of selection can also be strong enough to counteract the
 effects of drift. Here, we used several analyses to identify the roles of
 genetic drift and selection on genetic differentiation and diversity of
 Canada lynx (Lynx canadensis) across eastern Canada, including the islands
 of Cape Breton and Newfoundland. Specifically, we assessed whether we
 could identify a genetic component to the observed morphological
 differentiation that has been reported across insular and mainland lynx.
 We used a dinucleotide repeat within the promoter region of a functional
 gene that has been linked to mammalian body size, insulin-like growth
 factor-1 (IGF-1). We found high genetic differentiation at neutral
 molecular markers but convergence of allele frequencies at the IGF-1
 locus. Thus, we showed that while genetic drift has influenced the
 observed genetic structure of lynx at neutral molecular markers, natural
 selection has also played a role in the observed patterns of genetic
 diversity at the IGF-1 locus of insular lynx.
description: Lynx genetic
 dataThis file contains
 genetic scores at 14 neutral microsatellites and the dinucleotide repeat
 within the promoter region of the IGF-1 gene in Canada lynx sampled from
 eastern Canada (Quebec, Labrador, New Brunswick and the islands of
 Newfoundland and Cape Breton Island).Dryad_Lynx genetic
 data.xlsx
DOI: 10.5061/dryad.pj846h4f
title: Data from: Direct and indirect ecosystem effects of evolutionary adaptation in the Trinidadian guppy (Poecilia reticulata)

description: Ecological and evolutionary processes may interact on the same timescale,
 but we are just beginning to understand how. Several studies have examined
 the net effects of adaptive evolution on ecosystem properties. However, we
 do not know if the these effects are confined to direct interactions or if
 they propagate further through indirect ecological pathways. Even less
 well understood is how the combination of direct and indirect ecological
 effects of the phenotype promotes or inhibits evolutionary change. We
 coupled mesocosm experiments and ecosystem modeling to evaluate the
 ecological effects of local adaptation in Trinidadian guppies (Poecilia
 reticulata). The experiments show that guppies adapted to life with and
 without predators alter the ecosystem directly through differences in
 diet. The ecosystem model reveals that the small total indirect effect of
 the phenotype observed in the experiments is likely a combination of
 several large indirect effects which act in opposing directions. The model
 further suggests that these indirect effects can reverse the direction of
 selection that direct effects alone exert back on phenotypic variation. We
 conclude that phenotypic divergence can have major effects deep in the web
 of indirect ecological interactions and even small total indirect effects
 can radically change the dynamics of adaptation.
description: Data for
 Dryad
DOI: 10.5061/dryad.bn37p
title: Data from: Fitness consequences of occasional outcrossing in a functionally asexual plant (Oenothera biennis)

description: Many clonal organisms occasionally outcross, but the long-term
 consequences of such infrequent events are often unknown. During five
 years, representing three to five plant generations, we followed 16
 experimental field populations of the forb, Oenothera biennis, originally
 planted with the same 18 original genotypes. Oenothera biennis usually
 self-fertilizes, which due to its genetic system (Permanent Translocation
 Heterozygosity), results in seeds that are clones of the maternal plant.
 However, rare outcrossing produces genetically novel offspring (but
 without recombination or increased heterozygosity). We sought to
 understand whether novel genotypes produced through natural outcrossing
 had greater fecundity or different multigenerational dynamics compared to
 our original genotypes. We further assessed whether any differences in
 fitness or abundances through time between original and novel genotypes
 were exaggerated in the presence versus absence of insect herbivores. Over
 the course of the experiment, we genotyped &gt;12,500 plants using
 microsatellite DNA markers to identify and track the frequency of specific
 genotypes and estimated fecundity on a subset (&gt;3000) of plants.
 The effective outcrossing rate was 7.3% in the first year and ultimately
 50% of the plants were of outcrossed origin by the final year of the
 experiment. Lifetime fruit production per plant was on average 32% higher
 across all novel genotypes produced via outcrossing compared to the
 original genotypes, and this fecundity advantage was significantly
 enhanced in populations lacking herbivores. Among 43 novel genotypes that
 were abundant enough to phenotype with replication, plants produced nearly
 30% more fruits than the average of their specific two parental genotypes,
 and marginally more fruits (8%) than their most fecund parent. Mean per
 capita fecundity of novel genotypes predicted their relative frequencies
 at the end of the experiment. Novel genotypes increased more dramatically
 in herbivore-present compared to suppressed populations (45% vs. 27% of
 all plants), countering the increased competition from dandelions
 (Taraxacum officinale) that resulted from herbivore suppression. Increased
 interspecific competition likely also lead to the lower realized fitness
 of novel versus original genotypes in herbivore-suppressed populations.
 These results demonstrate that rare outcrossing and the generation of
 novel genotypes can create high-fecundity progeny, with the biotic
 environment influencing the dynamical outcome of such advantages.
description: fecundity data
 2008-2012Fecundity data for all
 Oenother biennis plants that were genotyped in each plot each year
 2008-2012.frequency of
 genotypesFrequency data for the
 original 18 genotypes and the 8 most common outcrossed genotypes by year
 and plot. Frequencies sum to 1 as rare genotypes are
 excluded.
DOI: 10.5061/dryad.1mr07
title: Data from: Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs.

description: Parallel (and convergent) phenotypic variation is most often studied in
 the wild, where it is difficult to disentangle genetic versus
 environmentally-induced effects. As a result, the potential contributions
 of phenotypic plasticity to parallelism (and non-parallelism) are rarely
 evaluated in a formal sense. Phenotypic parallelism could be enhanced by
 plasticity that causes stronger parallelism across populations in the wild
 than would be expected from genetic differences alone. Phenotypic
 parallelism could be dampened if site-specific plasticity induced
 differences between otherwise genetically-parallel populations. We used a
 common-garden study of three independent lake-stream stickleback
 population pairs to evaluate the extent to which adaptive divergence has a
 genetic or plastic basis, and to investigate the enhancing versus
 dampening effects of plasticity on phenotypic parallelism. We found that
 lake-stream differences in most traits had a genetic basis, but that
 several traits also showed contributions from plasticity. Moreover,
 plasticity was much more prevalent in one watershed than in the other two.
 In most cases, plasticity enhanced phenotypic parallelism, whereas in a
 few cases plasticity had a dampening effect. Genetic and plastic
 contributions to divergence seem to play a complimentary, likely adaptive,
 role in phenotypic parallelism of lake-stream stickleback. These findings
 highlight the value of formally comparing wild-caught and lab-reared
 individuals in the study of phenotypic parallelism.
description: Geometric morphometric
 data (males)Data from geometric
 morphometrics in the form of relative warp values for each
 fishRW data
 for dryad.xlsxUnivariate measurement
 dataData from linear
 measurements and gill raker measurements and counts, for each fish and for
 both sexes.Univar data for
 dryad.xlsx
DOI: 10.5061/dryad.b0314
title: Data from: Resource limitation and responses to rivals in males of the fruit fly Drosophila melanogaster

description: Diet has a profound direct and indirect effect on reproductive success in
 both sexes. Variation in diet quality and quantity can significantly alter
 the capacity of females to lay eggs and of males to deliver courtship.
 Here, we tested the effect of dietary resource limitation on the ability
 of male Drosophila melanogaster to respond adaptively to rivals by
 extending their mating duration. Previous work carried out under ad
 libitum diet conditions showed that males exposed to rivals prior to
 mating significantly extend mating duration, transfer more ejaculate
 proteins and achieve higher reproductive success. Such adaptive responses
 are predicted to occur because male ejaculate production may be limited.
 Hence, ejaculate resources require allocation across different
 reproductive bouts, to balance current vs. future reproductive success.
 However, when males suffer dietary limitation, and potentially have fewer
 reproductive resources to apportion, we expect adaptive allocation of
 responses to rivals to be minimized. We tested this prediction and found
 that males held on agar-only diets for 5–7 days lost the ability to extend
 mating following exposure to rivals. Interestingly, extended mating was
 retained in males held on low yeast/sugar: no sugar/yeast diet treatments,
 but was mostly lost when males were maintained on ‘imbalanced’ diets in
 which there was high yeast: no sugar and vice versa. Overall, the results
 show that males exhibit adaptive responses to rivals according to the
 degree of dietary resource limitation and to the ratio of individual diet
 components.
description: Mason et al 2016
 combined raw dataAll raw data and
 metadata for Mason et al. 2016.
DOI: 10.5061/dryad.1pp2c
title: Data from: The impact of insecticide resistance on Culex pipiens immunity

description: Because of their role as vectors of diseases, the evolution of insecticide
 resistance in mosquitoes has been intensively investigated. Insecticide
 resistance is associated to a wide range of pleiotropic effects on several
 key life history traits of mosquitoes such as longevity and behavior.
 However, despite its potential implications in pathogen transmission, the
 effects of insecticide resistance on mosquito immunity have received
 little, if any, attention. Here, we investigate the impact of insecticide
 resistance in Culex pipiens, an epidemiologically important vector of a
 wide array of pathogens. Using both isogenic laboratory strains and
 field-caught mosquitoes, we investigate the impact of two main insecticide
 resistance mechanisms (metabolic detoxification and target site
 modification) on the relative transcription of several genes involved in
 the immune response to pathogens, at both their constitutive and inducible
 levels. Our results show a discrepancy between the isogenic laboratory
 lines and field collected mosquitoes: while in the isogenic strains
 insecticide resistant mosquitoes show a drastic increase in immune gene
 expression, no such effect appears in the field. We speculate on the
 different mechanisms that may underlie this discrepancy, and discuss the
 risks of making inferences on the pleiotropic effects of insecticide
 resistant genes by using laboratory-selected insecticide resistant lines.
description: Dataset Vézilier et al.
 2012 wild mosquitoesqPCR data for the
 wild-caught mosquitoes experiment described in "The impact of
 insecticide resistance on Culex pipiens immunity"Dataset Vézilier et al
 2012 IsogenicqPCR data for the
 isogenic mosquitoes experiment described in Vézilier et al. 2012,
 "The impact of insecticide resistance on Culex pipiens
 immunity"
DOI: 10.15468/dl.mn2kcp
title: Occurrence Download

description: A dataset containing 291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stylisma pickeringii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 291 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000792-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.78nq4
title: Data from: Predation and the formation of multicellular groups in algae

description: Background: The evolution of multicellular organisms must, at some point,
 have involved the congregating of single-celled organisms. Algal species
 exist that sometimes live in groups and sometimes live as single cells.
 Understanding the conditions that lead to algal assemblage in such cases
 may cast light on the selective forces that favour multicellularity.
 Hypothesis: Forming groups could defend algae against predation if
 predators are unable to engulf large-sized entities. Organisms: Three
 algal prey (Chlorella sorokiniana, Chlorella vulgaris, and Scenedesmus
 obliquus) and three predators (Ochromonas spp., Tetrahymena thermophila,
 and Daphnia magna). Methods: We tested the tendency to aggregate in all
 nine different prey–predator combinations. Results: At least two of the
 predators, Ochromonas and Daphnia, were significant predators because
 their presence decreased algal density. In all nine combinations, adding
 the predator species led to the formation of algal groups. In three
 combinations, adding merely products of the predators in the absence of
 the predators themselves stimulated group formation.
description: Experimental
 dataThe
 Data.xlsx
DOI: 10.5061/dryad.2ph6s
title: Data from: Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying

description: Camellia seed oil has been used as high quality and healthy food for over
 two thousand years. Seed drying management effects oil quality and
 quantity. however, the molecular mechanisms of fatty acid biosynthesis and
 accumulation during the drying process remain unknown. In this study, the
 transcriptomes of Camellia meiocarpa and C. oleifera seed were
 characterized at five moisture content levels (10 - 50%) to identify the
 major processes and reveal genes affecting lipid metabolism in response to
 nature drying. We found a total of 111,156 unigenes by de novo assembled
 from RNA-Seq libraries of five moisture content levels during
 after-ripening of C. meiocarpa (74,016) and C. oleifera (76,374). Ten
 pathways were closely linked to changes in oil content and composition
 with 244 genes involved in fatty acid synthesis and accumulation. Gene
 Ontology enrichment of differentially expressed genes (DEGs) indicated
 that fatty acid synthesis and accumulation are essential in C. meiocarpa
 while fatty acid accumulation in C. oleifera during nature drying process.
 Comparative analyses of DEGs between any two consecutive moisture
 contents, identified six and three key unigenes in C. Meiocarpa and C.
 oleifera seeds, respectively, and one additional unigene responsible for
 the difference between the two species’ fatty acid synthesis and
 accumulation. Natural drying has improved the quality and quantity of the
 camellia seed oil. The study provided: a) global transcriptional profiles
 at five moisture content levels during seed nature drying, b) insights
 into highlighting transcripts putatively involved in the regulation of the
 gene expression program and in specific processes likely essential for
 lipid metabolism, and c) an opportunity to discovering genes associated
 with oil seed quantity and quality improvement for the studied two
 camellia species.
description: Sequence of unigene
 related with lipid metabolismSequence of unigenes
 related with lipid metabolismsequence of unigene related
 with lipid metabolism.xlsx
DOI: 10.5061/dryad.g10f7
title: Data from: Landscape-level crop diversity benefits biological pest control

description: 1.Landscape-level crop diversification is a promising tool for ecological
 intensification, whereby biodiversity and ecosystem services are enhanced,
 and pesticide applications reduced. Yet evidence for the effects of crop
 diversity at multiple scales and in different landscape contexts is
 lacking. Here, we investigate the potential benefits and
 context-dependencies of multiscale crop diversity on natural enemies and
 overall biological control in winter wheat. Simultaneously, we examine the
 mediating effects of bird predation on aphid regulation in this system.
 2.Eighteen conventional winter wheat fields were selected along two
 independent gradients of crop diversity and seminatural habitat cover
 (SNH). We assessed biological control using a natural enemy exclusion
 experiment (‘Open Treatment’, ‘Bird Exclosure’, ‘Full Exclosure’).
 Biological control, predator and parasitoid densities within cages were
 analysed as functions of landscape (crop diversity x SNH), bird predation
 (yes/no) and temporal change (three surveys) on six spatial scales
 (100-3000 m). 3.Crop diversity rather than SNH enhanced aphid regulation
 in our study system. Biological control in fields with high
 landscape-level crop diversity was 8 to 33% higher than in low diversity
 landscapes, with main effects observed on scales &lt;500 m. 4.Predator
 and parasitoid densities increased with crop diversity on small (100–250m)
 and large (2000-3000 m) spatial scales, respectively. Nevertheless, our
 findings suggest that natural enemies other than birds, parasitoids and
 aerial arthropods facilitated biological control. 5.Synthesis and
 applications. Our study shows that landscape-level crop diversification
 can improve biological control in agroecosystems. Therefore, increased
 crop diversity could lower dependence on insecticides while enhancing
 yield stability through ecological intensification of farming. We also
 highlight the need to assess biological control rather than natural enemy
 abundances to avoid bias due to sampling artefacts or species
 interactions. Lastly, simple measures of crop diversity (e.g. ‘effective
 number of crop types’) help in science communication and the development
 of farm management guidelines.
description: Crop diversity effects
 on biological pest controlData was collected in a
 field study. The file contains all data used in the analyses of this
 paper. Metadata provided within file.CageExp_Data_Redlich_etal_2018_JAPPL.xlsx
DOI: 10.5061/dryad.qd018
title: Data from: MHC variation reflects the bottleneck histories of New Zealand passerines

description: Most empirical evidence suggests that balancing selection does not counter
 the effects of genetic drift in shaping post-bottleneck MHC genetic
 diversity when population declines are severe or prolonged. However, few
 studies have been able to include data from historical specimens, or to
 compare populations/species with different bottleneck histories. In this
 study we examined MHC class II B and microsatellite diversity in four New
 Zealand passerine (songbird) species that experienced moderate to very
 severe declines. We compared diversity from historical samples (collected
 circa 1884-1938) to present day populations. Using a Bayesian framework,
 we found that the change in genetic diversity from historical to
 contemporary samples was affected by three main factors: 1) whether the
 data were based on MHC or microsatellite markers, 2) species (as a
 surrogate for bottleneck severity) and 3) whether the comparison between
 historical and contemporary samples was made using historical samples
 originating from the mainland or using historical samples originating from
 islands. The greatest losses in genetic diversity occurred for the most
 severely bottlenecked species, particularly between historical mainland
 and contemporary samples. Additionally, where loss of diversity occurred,
 the change was greater for MHC genes compared to microsatellite loci.
description: Microsatellite_Genotypes_SaddlebacksMicrosatellite_Genotypes_robinsMHC_Genotypes_robins_North IslandMHC_Genotypes_robins_South IslandMHC_Genotypes_saddlebacks_North IslandMHC_Genotypes_saddlebacks_South IslandRscript_univariate modelsR script with package MCMCglmm for the univariate-response Bayesian mixed-effects meta-analysis (BMM) models described in Table 2.
DOI: 10.5061/dryad.719cn
title: Data from: Non-invasive monitoring of temporal and spatial blood flow during bone graft healing using diffuse correlation spectroscopy

description: Vascular infiltration and associated alterations in microvascular blood
 flow are critical for complete bone graft healing. Therefore, real-time,
 longitudinal measurement of blood flow has the potential to successfully
 predict graft healing outcomes. Herein, we non-invasively measure
 longitudinal blood flow changes in bone autografts and allografts using
 diffuse correlation spectroscopy in a murine femoral segmental defect
 model. Blood flow was measured at several positions proximal and distal to
 the graft site before implantation and every week post-implantation for a
 total of 9 weeks (autograft n = 7 and allograft n = 10). Measurements of
 the ipsilateral leg with the graft were compared with those of the intact
 contralateral control leg. Both autografts and allografts exhibited an
 initial increase in blood flow followed by a gradual return to baseline
 levels. Blood flow elevation lasted up to 2 weeks in autografts, but this
 duration varied from 2 to 6 weeks in allografts depending on the spatial
 location of the measurement. Intact contralateral control leg blood flow
 remained at baseline levels throughout the 9 weeks in the autograft group;
 however, in the allograft group, blood flow followed a similar trend to
 the graft leg. Blood flow difference between the graft and contralateral
 legs (ΔrBF), a parameter defined to estimate graft-specific changes, was
 elevated at 1–2 weeks for the autograft group, and at 2–4 weeks for the
 allograft group at the proximal and the central locations. However, distal
 to the graft, the allograft group exhibited significantly greater ΔrBF
 than the autograft group at 3 weeks post-surgery (p &lt; 0.05). These
 spatial and temporal differences in blood flow supports established trends
 of delayed healing in allografts versus autografts.
description: BloodFlow
DOI: 10.15468/dl.s8s698
title: Occurrence Download

description: A dataset containing 366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhodiola fastigiata"
 ]
}

 The dataset includes 366 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000793-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.