cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.362s5
title: Data from: Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data

description: Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the
 numerically dominant high order predators on pristine coral reefs, yet
 their numbers have declined even in the highly regulated Australian Great
 Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine
 scale genetic connectivity of grey reef sharks is essential for their
 effective management, but no genetic data are yet available. We
 investigated grey reef shark genetic structure in the GBR across a 1200 km
 latitudinal gradient, comparing empirical data with models simulating
 different levels of migration. The empirical data did not reveal any
 genetic structuring along the entire latitudinal gradient sampled,
 suggesting regular widespread dispersal and gene flow of the species
 throughout most of the GBR. Our simulated datasets indicate that even with
 substantial migrations (up to 25% of individuals migrating between
 neighboring reefs) both large scale genetic structure and genotypic
 spatial autocorrelation at the reef scale were maintained. We suggest that
 present migration rates therefore exceed this level. These findings have
 important implications regarding the effectiveness of networks of
 spatially discontinuous Marine Protected Areas to protect reef sharks.
description: Momigliano et al 2015
 Microsatellite DatasetDataset containing: 1)
 sampling location and sex of every individual 2) microsatellite genotypes
 of all individuals and GenBank accession numbers for ND4
 sequences
DOI: 10.5061/dryad.4c7kq
title: Data from: Back and forth Wolbachia transfers reveal efficient strains to control spotted wing drosophila populations

description: 1.Since its recent invasion of the European and American continents, the
 spotted wing Drosophila Drosophila suzukii has become a burden of the
 fruit industry. Armed with a highly sclerotized ovipositor, females can
 lay eggs in a wider variety of ripening and healthy fruits than other
 Drosophila species. Economic losses due to Drosophila suzukii reach
 millions of dollars annually and methods to control natural populations in
 the field mainly rely on the use of chemical pesticides. 2.We tested if
 Wolbachia bacteria represents a potential ally to control this pest. These
 symbionts are naturally present in many insects and often induce a form of
 conditional sterility called Cytoplasmic Incompatibility (CI): the
 offspring of infected males die, unless the eggs are rescued by the
 compatible infection, inherited from the mother that protects the embryo.
 A long-recognised, a strategy called the Incompatible Insect Technique
 (IIT) makes use of the CI phenotype to control insect populations through
 the mass release of infected males. To implement this technique in D.
 suzukii, we used back and forth Wolbachia transfers between D. suzukii and
 D. simulans to identify Wolbachia strains that can sterilize D. suzukii
 females despite the presence of wSuz, a natural Wolbachia infection in
 this species. 3.We identified two Wolbachia strains as potential
 candidates for developing IIT in D. suzukii. Both induce a very high level
 of CI in this pest which is not attenuated by the presence of wSuz in
 females. Moreover, the newly transferred Wolbachia do not affect the
 fitness or the mating competitiveness of the sterilizing males.
 4.Synthesis and applications. Although several critical steps still need
 to be tested and developed outside the laboratory to achieve the control
 of Drosophila suzukii using Incompatible Insect Technique. By an
 experimental approach in large population cage, we showed that releases of
 transinfected males limits population size. Thus, we provide in this study
 the proof of concept that this technique can be a very promising approach
 to control D. suzukii populations.
description: CI data of mass crosses
 in D.simulansCI_data_mass_crosses_D.simulans.csvCI data of individual crosses in D.simulansCI_data_individual_crosses_D.simulans.csvCI data of individual crosses D.suzukiiCI_data_individual_crosses_D.suzukii.csvCI data of male age effect on CI levelCI_data_male_age_effect.csvCI data of sterilizing male competitivenessCI_data_male_competitiveness.csvdata of IIT simulationdata_IIT_simulation.csv
DOI: 10.5061/dryad.93351
title: Data from: Sexual selection on male body size, genital length and heterozygosity: consistency across habitats and social settings

description: 1. Spatial and temporal variation in environmental factors and the social
 setting can help to maintain genetic variation in sexually selected traits
 if it affects the strength of directional selection. A key social
 parameter which affects the intensity of, and sometimes predicts the
 response to, mating competition is the operational sex ratio (OSR; ratio
 of receptive males to females). 2. How the OSR affects selection for
 specific male traits is poorly understood. It is also unclear how sexual
 selection is affected by interactions between the OSR and environmental
 factors, such as habitat complexity, that alter key male-female
 interactions such as mate encounter rates. 3. Here, we experimentally
 manipulated the OSR and habitat complexity and quantified sexual selection
 on male mosquitofish (Gambusia holbrooki) by directly measuring male
 reproductive success (i.e. paternity). 4. We show that, despite a more
 equitable sharing of paternity (i.e. higher levels of multiple paternity)
 under a male-biased OSR, selection on focal male traits was unaffected by
 the OSR or habitat complexity. Instead, sexual selection consistently, and
 significantly, favoured smaller bodied males, males with higher genome
 wide heterozygosity (based on &gt;3000 SNP markers), and males with a
 relatively long gonopodium (intromittent organ).
description: Sexual selection on male
 gambusia holbrooki in different environmentsThis data file contains
 the raw data analysed in the associated paper. It contains two worksheets.
 The first - Sexual selection on males contains the data used in the
 analysis described under the same subheading in the associated paper.The
 second - Number of sires per brood contains the data used in the analysis
 described under this subheading in the associated paper. Column
 descriptors are provided in each worksheetKahnplexity_for_DRYAD.xlsx
DOI: 10.5061/dryad.848ks
title: Data from: Virus epidemics can lead to a population-wide spread of intragenomic parasites in a previously parasite-free asexual population

description: In a recent issue of Molecular Ecology the role of intragenomic parasites
 in maintaining sexual reproduction was both experimentally evaluated by
 Kraaijeveld et al. and discussed by Crespi and Schwander. The prevalence
 of sex is difficult to explain, due to its costs when compared with
 asexual reproduction. Yet, as reviewed by Crespi and Schwander, sex can be
 favorable in the presence of proliferating transposons. Transposons are
 similar to mutations, in that their integration to non-neutral loci is
 likely to have deleterious effects, and sexual recombination provides a
 potential mechanism to confine their accumulation.
description: Endogenous_retroviruses_simulatorA simulator program that can be used to simulate endogenous viruses and their accumulation in genomes within asexual and sexual populations.DefaultsDefault values for the simulator.
DOI: 10.5061/dryad.jd417
title: Data from: Non-glandular trichomes of Solanum carolinense deter feeding by Manduca sexta caterpillars and cause damage to the gut peritrophic matrix

description: Plant trichomes constitute a first line of defence against insect
 herbivores. The pre- and post-ingestive defensive functions of glandular
 trichomes are well documented and include direct toxicity, adhesion,
 antinutrition and defence gene induction. By contrast, the defensive
 functions of non-glandular trichomes are less well characterized, although
 these structures are thought to serve as physical barriers that impede
 herbivore feeding and movement. We experimentally varied the density of
 stellate non-glandular trichomes in several ways to explore their pre- and
 post-ingestive effects on herbivores. Larvae of Manduca sexta (Sphingidae)
 initiated feeding faster and gained more weight on Solanum carolinense
 (Solanaceae) leaves having lower trichome densities (or experimentally
 removed trichomes) than on leaves having higher trichome densities. Adding
 trichomes to artificial diet also deterred feeding and adversely affected
 caterpillar growth relative to controls. Scanning electron and light
 microscopy revealed that the ingestion of stellate trichomes by M. sexta
 caterpillars caused extensive damage to the peritrophic membrane, a gut
 lining that is essential to digestion and pathogen isolation. These
 findings suggest that, in addition to acting as a physical barrier to
 deter feeding, trichomes can inhibit caterpillar growth and development
 via post-ingestive effects.
description: Raw
 dataRaw data from all the
 experiments
DOI: 10.5061/dryad.tb850
title: Data from: Plant functional groups regulate soil respiration responses to nitrogen addition and mowing over a decade

description: 1. Nitrogen (N) deposition and land-use practice (e.g. mowing) could have
 profound effects on soil respiration. However, the changes in other
 ecosystem components, such as plant functional groups (PFGs), may control
 soil carbon (C) efflux response to long term global change. 2. A 10-year
 (2005-2014) field experiment was conducted with both N addition (10g N m-2
 yr-1) and mowing (once a year) in a northern Chinese temperate grassland.
 We collected continuous data on soil respiration over 10 years accompanied
 with data on abiotic and biotic factors, and attempted to determine (i)
 the temporal variation in soil respiration and its responses to N addition
 and mowing, (ii) the regulation of soil respiration by PFGs and the
 underlying long-term mechanisms of control. 3. Soil respiration varied
 significantly among years. This was mainly caused by changes in
 precipitation pattern (e.g. frequency and distribution) during the
 growing-season rather than total rainfall. N addition significantly
 suppressed soil respiration by 10.4% whereas mowing stimulated it by 8.4%
 over the 10 years. The interaction of N addition with mowing had little
 effect on soil respiration. However, the significant effects of both N
 addition and mowing appeared only in the third year and thereafter,
 indicating the differences between long- and short-term responses. These
 long-term effects of N addition and mowing were mainly caused by changes
 in the PFGs of covers (e.g. grasses and forbs) and in soil pH rather than
 in soil microclimate. Forb-dominant patches had greater soil respiration
 than grass patches owing to their higher litter quality and photosynthetic
 capacity. 4. Our results highlight that shifts in aboveground plant
 community could play an important role in regulating soil respiration
 responses to N addition and mowing in the long-term. This is potentially
 important for improving our understanding of the link between above- and
 belowground ecological processes.
description: All data for this
 studyFE-Du-Data
 S1.xlsx
DOI: 10.5061/dryad.2b549t4
title: Data from: A trade-off between thickness and length in the zebra finch sperm mid-piece

description: The sperm mid-piece has traditionally been considered to be the engine
 that powers sperm. Larger mid-pieces have therefore been assumed to
 provide greater energetic capacity. However, in the zebra finch
 Taeniopygia guttata, a recent study showed a surprising negative
 relationship between mid-piece length and sperm energy content. Using a
 multidimensional approach to study mid-piece structure, we tested whether
 this unexpected relationship can be explained by a trade-off between
 mid-piece length and mid-piece thickness and/or cristae density inside the
 mitochondrial helix. We used selective plane illumination microscopy to
 study mid-piece structure from three-dimensional images of zebra finch
 sperm and used high-resolution transmission electron microscopy to
 quantify mitochondrial density. Contrary to the assumption that longer
 mid-pieces are larger and therefore produce or contain a greater amount of
 energy, our results indicate that the amount of mitochondrial material is
 consistent across mid-pieces of varying lengths, and longer mid-pieces are
 simply proportionately ‘thinner’.
description: Zebra finch gyre number
 and mid-piece length dataData file containing
 mid-piece length and gyre number data collected from experimental males in
 Part 1 of the study using SPIM. Descriptions of variables are included in
 the R code file “Zebra-finch_mid-piece_analysis.r”Mendonca2018_Gyres.csvZebra finch sperm mid-piece cross-section measurement dataData file containing mean mid-piece length and cross-sectional diameter measurement data collected from experimental males in Part 2 of the study using TEM. Descriptions of variables are included in the R code file “Zebra-finch_mid-piece_analysis.r”Mendonca2018_Sperm_Cross-section.csvMitochondrial cristae density dataData file containing mean mid-piece length and cristae density measurement data collected from experimental males in part 2 of the study using TEM. Descriptions of variables are included in the R code file “Zebra-finch_mid-piece_analysis.r”Mendonca2018_Cristae_density.csvZebra finch mid-piece analysis R scriptR script of the analysis reported in the manuscript 'A trade-off between thickness and length in the zebra finch sperm mid-piece'.Zebra-finch_mid-piece_analysis.RREADMEREADME file for data files associated with the manuscript “A trade-off between thickness and length in the zebra finch sperm mid-piece”
DOI: 10.15468/dl.efxd9f
title: Occurrence Download

description: A dataset containing 266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyxidanthera barbulata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 266 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001140-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8tk6477
title: Data from: Re-association of an invasive plant with its specialist herbivore provides a test of the Shifting Defence Hypothesis

description: 1. The shifting defence hypothesis (SDH) predicts that after invasive
 plants are introduced to new ranges, they will evolve reduced resistance
 to specialist herbivores and increased resistance to generalist herbivores
 because they can escape from specialists but are still attacked by
 generalists in their non-native ranges. For this to be true, the
 subsequent introduction of native specialist herbivores should reverse the
 above evolutionary processes, but evidence collected so far is scarce. 2.
 Here, we address this research gap by comparing resistance to specialist
 and generalist herbivores and resistance-related traits in the invasive
 plant Ambrosia artemisiifolia from five populations with about a decade
 history of infestation by the accidentally introduced native specialist
 leaf beetle Ophraella communa (infested populations), and three
 populations without such infestation history (uninfested populations). 3.
 In common garden experiments, the specialist O. communa performed better
 on uninfested populations than on infested populations, whereas two
 generalist insects, Spodoptera litura and Helicoverpa armigera, performed
 better on infested populations. Chemical analyses showed that plants from
 infested populations had lower concentrations of chlorogenic acid, an
 anti-generalist secondary compound that can attract O. communa.
 Furthermore, across mother plants from all populations studied,
 chlorogenic acid content was negatively correlated with larval growth of
 S. litura and positively correlated with that of O. communa. Finally,
 quantitative defence traits did not differ between infested and uninfested
 populations. 4. Although our results are most consistent with rapid
 evolution caused by enemy re-association, we cannot exclude the
 possibility that observed differences in resistance result from multiple
 introductions or selections from other enviromental factors. 5. Synthesis.
 These results suggest that re-association with a specialist herbivore from
 the native range may result in a rapid evolution of increased resistance
 to specialist herbivores and reduced resistance to generalist herbivores
 in the introduced range, which is likely to be mediated by the reduced
 production of secondary chemicals that can deter generalists while
 attracting the introduced specialist. This study supports the SDH from a
 new viewpoint, emphasizing the importance of incorporating the impacts of
 both specialist and generalist herbivores when evaluating the long-term
 control effects of classical biological control programs.
description: Re-association of an
 invasive plant with its specialist herbivore provides a test of the
 Shifting Defence Hypothesis
DOI: 10.5061/dryad.dg49cj7
title: Data from: Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium

description: Research on mutualism seeks to explain how co-operation can be maintained
 when uncooperative mutants co-occur with cooperative kin. Gains and losses
 of the gene modules required for co-operation punctuate symbiont
 phylogenies and drive lifestyle transitions between cooperative symbionts
 and uncooperative free-living lineages over evolutionary time. Yet whether
 uncooperative symbionts commonly evolve from within cooperative symbiont
 populations or from within distantly related lineages with antagonistic or
 free-living lifestyles (i.e., third-party mutualism exploiters or
 parasites), remains controversial. We use genomic data to show that
 genotypes that differ in the presence or absence of large islands of
 symbiosis genes are common within a single wild recombining population of
 Mesorhizobium symbionts isolated from host tissues and are an important
 source of standing heritable variation in co-operation in this population.
 In a focal population of Mesorhizobium, uncooperative variants that lack a
 symbiosis island segregate at 16% frequency in nodules, and genome size
 and symbiosis gene number are positively correlated with co-operation.
 This finding contrasts with the genomic architecture of variation in
 co-operation in other symbiont populations isolated from host tissues in
 which the islands of genes underlying co-operation are ubiquitous and
 variation in co-operation is primarily driven by allelic substitution and
 individual gene gain and loss events. Our study demonstrates that
 uncooperative mutants within mutualist populations can comprise a
 significant component of genetic variation in nature, providing biological
 rationale for models and experiments that seek to explain the maintenance
 of mutualism in the face of non-cooperators.
description: Cooperation
 DataShoot mass and percent
 nitrogen in leaf tissue data for plants grown in the
 greenhousePorterCooperationData.xlsx
DOI: 10.5061/dryad.30vn6
title: Data from: Faster isn't always better: selection on growth rate fluctuates across the life history and environments

description: Growth rate is increasingly recognised as a key life-history trait that
 may affect fitness directly, rather than evolving as a by-product of
 selection on size or age. An ongoing challenge is to explain the abundant
 levels of phenotypic and genetic variation in growth rates often seen in
 natural populations, despite what is expected to be consistently strong
 selection on this trait. Such a paradox suggests limits to how
 contemporary growth rates evolve. We explored limits arising from
 variation in selection, based on selection differentials for age-specific
 growth rates expressed under different ecological conditions. We present
 results from a field experiment that measured growth rates and
 reproductive output in wild individuals of a colonial marine invertebrate
 (Hippopodina iririkiensis), replicated within and across the natural range
 of succession in its local community. Colony growth rates varied
 phenotypically throughout this range, but not all such variation was
 available for selection, nor was it always targeted by selection as
 expected. While the maintenance of both phenotypic and genetic variation
 in growth rate is often attributed to costs of growing rapidly, our study
 highlights the potential for fluctuating selection pressures throughout
 the life history and across environments to play an important role in this
 process.
description: Monro & Marshall
 2014 AmNatEstimates of relative
 growth rates and fecundity for 20 focal colonies replicated across 3
 stages of succession in the field.Monro&Marshalldata.xlsx
DOI: 10.5061/dryad.96m9r
title: Data from: Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters

description: Many North American river otter (Lontra canadensis) populations are
 threatened or recovering but are difficult to study because they occur at
 low densities, it is difficult to visually identify individuals, and they
 inhabit aquatic environments that accelerate degradation of biological
 samples. Single nucleotide polymorphisms (SNPs) can improve our ability to
 monitor demographic and genetic parameters of difficult to study species.
 We used restriction site associated DNA (RAD) sequencing to discover
 20,772 SNPs present in Montana, USA, river otter populations, including
 14,512 loci that were also variable in at least one other population
 range-wide. After applying careful filtering criteria meant to minimize
 ascertainment bias and identify high quality, highly heterozygous (H o =
 0.2–0.50) SNPs, we developed and tested 52 independent SNP qPCR genotyping
 assays, including 41 that performed well with diluted DNA. The 41 loci
 provided high power for population assignment tests with only 1
 misassignment (1.6 %) between closely neighboring populations. Our SNPs
 showed high power to differentiate individuals and assign them to
 population of origin, as well as strong concordance of genotypes from high
 and diluted concentrations of DNA, and between original RAD and the SNP
 qPCR array.
description: StetzEtAl_River_otter
 SNPs_COGR_siTable S1: Allelic
 diversity and heterozygosity of 52-locus SNP-array for North American
 river otters identified through RAD sequencing.