cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.77c4555
title: Data from: Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles

description: Whether sexual selection impedes or aids adaptation has become an
 outstanding question in times of rapid environmental change and parallels
 the debate about how the evolution of individual traits impacts on
 population dynamics. The net effect of sexual selection on population
 viability results from a balance between genetic benefits of “good genes”
 effects and costs of sexual conflict. Depending on how these facets of
 sexual selection are affected under environmental change, extinction of
 maladapted populations could either be avoided or accelerated. Here, we
 evolved seed beetles under three alternative mating regimes to disentangle
 the contributions of sexual selection, fecundity selection and male-female
 coevolution to individual reproductive success and population fitness. We
 compared these contributions between the ancestral environment and two
 stressful environments (elevated temperature and a host plant shift). We
 found evidence that sexual selection on males had positive genetic effects
 on female fitness components across environments, supporting good genes
 sexual selection. Interestingly, however, when males evolved under sexual
 selection with fecundity selection removed, they became more robust to
 both temperature and host plant stress compared to their conspecific
 females and males from the other evolution regimes that applied fecundity
 selection. We quantified the population-level consequences of this
 sex-specific adaptation and found evidence that the cost of socio-sexual
 interactions in terms of reduced offspring production was higher in the
 regime applying only sexual selection to males. Moreover, the cost tended
 to be more pronounced at the elevated temperature to which males from the
 regime were more robust compared to their conspecific females. These
 results illustrate the tension between individual-level adaptation and
 population-level viability in sexually reproducing species and suggest
 that the relative efficacies of sexual selection and fecundity selection
 can cause inherent sex-differences in environmental robustness that may
 impact demography of maladapted populations.
description: Raw
 dataRaw data of lifetime
 reproductive success (LRS), Fertility assays and Population fitness
 assays.
DOI: 10.5061/dryad.6mj52
title: Data from: Leisure-time physical activity and dementia risk: a dose-response meta-analysis of prospective studies

description: Background: Considerable evidences were indicative of favorable roles of
 physical activity (PA) in fighting against dementia. However, the shape of
 dose–response relationship has not been explored. Objective: To conduct a
 meta-analysis to quantitatively investigate the relationship of dementia
 with PA by metabolic equivalent of task (MET)-hour/week and kilocalorie
 (kcal)/week. Design: Prospective studies published from Jan 1, 1995 to
 August 2016 were searched in PubMed, EMBASE, Ovid and the Cochrane
 Library. Two meta-analyses were performed with the focus on exploring the
 dose-response relationship using two-stage generalized least squares
 regression. Results: The qualitative analysis showed a trend of
 dose-response relationship with all-cause of dementia (ACD), Alzheimer’s
 disease (AD) but not vascular dementia (VD). In the dose-response
 analysis, ACD (p-trend&lt;0.005; p-nonlinearity=0.87) and AD
 (p-trend&lt;0.005; p-nonlinearity= 0.10) exhibited a linear
 relationship with leisure-time PA (LTPA) over the observed range (0-2000
 kcal/week or 0–45 MET-h/week). Specifically, for every 500 kcal or 10
 MET-h increase per week, the decrement of risk is roughly 10% (95%CI,
 0.85-0.97) for ACD and 13% (95%CI, 0.79-0.96) for AD. Conclusions: We for
 the first time proved the dose-response relationship between LTPA and
 dementia/AD, which finding further supported the international PA
 guideline from a standpoint of dementia prevention.
description: Raw
 dataThe raw data file
 contains files relevant to data extraction, data analysis and other data
 relevant with contents in supplementary files
DOI: 10.5061/dryad.1d49q
title: Data from: Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

description: Background: Life history traits like developmental time, age and size at
 maturity are directly related to fitness in all organisms and play a major
 role in adaptive evolution and speciation processes. Comparative genomic
 or transcriptomic approaches to identify positively selected genes
 involved in species divergence can help to generate hypotheses on the
 driving forces behind speciation. Here we use a bottom-up approach to
 investigate this hypothesis by comparative analysis of orthologous
 transcripts of four closely related European Radix species. Results:
 Snails of the genus Radix occupy species specific distribution ranges with
 distinct climatic niches, indicating a potential for natural selection
 driven speciation based on ecological niche differentiation. We then
 inferred phylogenetic relationships among the four Radix species based on
 whole mt-genomes plus 23 nuclear loci. Three different tests to infer
 selection and changes in amino acid properties yielded a total of 134
 genes with signatures of positive selection. The majority of these genes
 belonged to the functional gene ontology categories “reproduction” and
 “genitalia” with an overrepresentation of the functions “development” and
 “growth rate”. Conclusions: We show here that Radix species divergence may
 be primarily enforced by selection on life history traits such as
 (larval-) development and growth rate. We thus hypothesise that life
 history differences may confer advantages under the according climate
 regimes, e.g., species occupying warmer and dryer habitats might have a
 fitness advantage with fast developing susceptible life stages, which are
 more tolerant to habitat desiccation.
description: ortholog
 clustersOrtholog gene clusters
 of four Radix species created with HaMStR. These clusters were used to
 infer selected loci with PAML and TreeSAAP.Phylogeny
 clustersorthologos gene clusters
 used for phylogenetic reconstruction of four Radix species plus
 Biomphalaria glabrata as outgroup
DOI: 10.5061/dryad.b98m6
title: Data from: Bioturbation determines the response of benthic ammonia oxidising microorganisms to ocean acidification

description: Ocean acidification (OA), caused by the dissolution of increasing
 concentrations of atmospheric carbon dioxide (CO2) in seawater, is
 projected to cause significant changes to marine ecology and
 biogeochemistry. Potential impacts on the microbially driven cycling of
 nitrogen are of particular concern. Specifically, under seawater pH levels
 approximating future OA scenarios, rates of ammonia oxidation (the
 rate-limiting first step of the nitrification pathway) have been shown to
 dramatically decrease in seawater, but not in underlying sediments.
 However, no prior study has considered the interactive effects of
 microbial ammonia oxidation and macrofaunal bioturbation activity, which
 can enhance nitrogen transformation rates. Using experimental mesocosms,
 we investigated the responses to OA of ammonia oxidizing microorganisms
 inhabiting surface sediments and sediments within burrow walls of the mud
 shrimp Upogebia deltaura. Seawater was acidified to one of four target pH
 values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT
 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were,
 on average, fivefold greater than in surface sediments. However, at all
 acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow
 sediments were significantly inhibited (by 79–97%; p &lt; 0.01),
 whereas rates in surface sediments were unaffected. Both bacterial and
 archaeal abundances increased significantly as pHT declined; by contrast,
 relative abundances of bacterial and archaeal ammonia oxidation (amoA)
 genes did not vary. This research suggests that OA could cause substantial
 reductions in total benthic ammonia oxidation rates in coastal bioturbated
 sediments, leading to corresponding changes in coupled nitrogen cycling
 between the benthic and pelagic realms.
description: Am_ox_ratesAmmonia oxidation rates from water column and sediment samples in a benthic mesocosm study. See ReadMe file for column headers and units.Gene_dataGene abundance data from a q-PCR study of bacterial and archaeal 16S rRNA and amoA genes in mesocosm sediments. See ReadMe file for column headings and units.CHN_dataData from elemental analyses showing the % carbon and nitrogen in sediments from a mesocosm study. See the ReadMe file for column headers and units.Phys_chem_dataPhysico-chemical data from monitoring overlying water paramaters within a benthic mesocosm; including pH, temp., salinity, nutrients and carbonate system outputs from CO2SYS. See the ReadMe file for column headers and units.
DOI: 10.5061/dryad.t6q1k5v
title: Data from: Effect of insect herbivory on plant community dynamics under contrasting water availability levels

description: 1. Diversity of plant communities is impacted by multiple global change
 drivers but also by altered biotic interactions with antagonist and
 mutualist organisms that can potentially affect species coexistence. 2.
 With a two-year outdoor mesocosm experiment in realistic mesic grassland
 communities, we explored the role of insect herbivory in impacting plant
 community dynamics under contrasting levels of water availability
 simulating altered rainfall regimes. We selected a grasshopper species
 (Calliptamus italicus) feeding predominantly on forbs while avoiding
 grasses. 3. High water availability reduced species coexistence, boosting
 productivity while decreasing individual plant survival. At the community
 level, herbivores were not able to promote species coexistence but
 asymmetrically influenced grasses and forbs, reducing forb biomass under
 high water availability. 4. Herbivores shaped individual plant responses
 to both abiotic conditions and individual-neighbours’ interactions.
 Herbivores influenced focal plant survival by altering the effect of
 neighbouring plants, mitigating the negative effect of high neighbour
 biomass at low water availability and exacerbating it at high level of
 water availability. 5. Synthesis: Altered rainfall has the capacity to
 change the relative strength of the plant-plant interactions and also to
 determine the effects of herbivores on grassland communities. The
 complexity of the interactions between plants and herbivores and the
 observed context-dependence indicate the need to incorporate multiple
 biotic and abiotic drivers to fully understand the mechanisms underlying
 plant dynamics and species coexistence in a changing world.
description: Tamburini et al. 2018
 DatasetPlant biomass and
 individual survival.
DOI: 10.5061/dryad.1g62f
title: Data from: Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System

description: Using a combination of population- and individual-based analytical
 approaches, we provide a comprehensive examination of genetic connectivity
 of Dungeness crab (Cancer magister) along ~1,200 km of the California
 Current System (CCS). We sampled individuals at 33 sites in 2012 to
 establish a baseline of genetic diversity and hierarchal population
 genetic structure, and then assessed inter-annual variability in our
 estimates by sampling again in 2014. Genetic diversity showed little
 variation among sites or across years. In 2012, we observed weak genetic
 differentiation among sites (FST range = -0.005 – 0.014) following a
 pattern of isolation by distance (IBD), and significantly high relatedness
 among individuals within nine sampling sites. In 2014, pairwise FST
 estimates were lower (FST range = -0.014 – 0.007), there was no spatial
 autocorrelation, and fewer sights had significant evidence of relatedness.
 Based on these findings, we propose that inter-annual variation in the
 physical oceanographic conditions of the CCS influence larval recruitment
 and thus gene flow, contributing to inter-annual variation in population
 genetic structure. Estimates of effective population size (Ne) were large
 in both 2012 and 2014. Together, our results suggest that Dungeness crab
 in the CCS may constitute a single evolutionary population, though
 geographically limited dispersal results in an ephemeral signal of
 isolation by distance. Furthermore, our findings demonstrate that
 populations of marine organisms may be susceptible to temporal changes in
 population genetic structure over short time periods, thus inter-annual
 variability in population genetic measures should be considered.
description: Genotypes_Jackson et
 al.See README.txt file for
 explanation of data.
DOI: 10.6084/m9.figshare.31151878
title: Diversity and Distributions Data

description: Data for paper
DOI: 10.6084/m9.figshare.31151878.v1
title: Diversity and Distributions Data

description: Data for paper
DOI: 10.6084/m9.figshare.31151878.v2
title: Diversity and Distributions Data

description: Data for paper
DOI: 10.5061/dryad.vv760
title: Data from: The influence of habitat accessibility on the dietary and morphological specialisation of an aquatic predator

description: Individual diet and habitat specialisation are widespread in animal taxa
 and often related to levels of predation and competition. Mobile consumers
 such as predatory fish can stabilise lake food webs by ranging over a
 larger area than their prey, thereby switching between habitats. Although,
 this switching assumes that the predator has equal preference for the
 available prey, individual diet specialisation and morphological
 adaptations to different habitats could potentially prevent individuals
 from switching between habitats. In this study, we assessed the niche
 width and individual specialisation in Eurasian perch (Perca fluviatilis)
 in response to a shift in habitat use by manipulating the ability for this
 top predator to couple habitats. We ran an 8-week pond experiment, to test
 the effect of habitat switching on diet and morphological specialisations.
 We show that habitat coupling influenced individual diet specialisation
 and niche use in expected directions where specialisation increased with
 decreasing habitat switching. In contrast to expectations, the
 morphological variation decreased with increasing diet specialisation. Our
 results expand on previous work and suggest that individual specialisation
 and niche width can impact the ability of mobile predators to couple
 habitats. Furthermore, it shows the importance of individual
 specialisations in relation to habitat coupling.
description: Diet of perch in
 experimentStomach content (%) of
 the perch at the end of the experiment.Stomach_content_Perch_Drottningholm 2013.xlsxMorphology_Drottningholm_2013_TPS_dataTPS file with digitised landmarks for each perch.Morphology_Drottningholm_2013_classifiersClassifiers for the TPS morphology file with details of Pond, Treatment and Habitats
DOI: 10.5061/dryad.76rc3
title: Data from: Intrinsic differences between males and females determine sex-specific consequences of inbreeding

description: Background Inbreeding increases homozygosity and exposes deleterious
 recessive alleles, generally decreasing the fitness of inbred individuals.
 Interestingly, males and females are usually affected differently by
 inbreeding, though the more vulnerable sex depends on the species and
 trait measured. Results We used the soil-dwelling nematode Caenorhabditis
 remanei to examine sex-specific inbreeding depression across nine
 lineages, five levels of inbreeding, and hundreds of thousands of progeny.
 Female nematodes consistently suffered greater fitness losses than their
 male counterparts, especially at high levels of inbreeding. Conclusions
 These results suggest that females experience stronger selection on genes
 contributing to reproductive traits. Inbreeding depression in males may be
 further reduced by sex chromosome hemizygosity, which affects the
 dominance of some mutations, as well as by the absence of sexual
 selection. Determining the relative contributions of sex-specific
 expression, genes on the sex chromosomes, and the environment they are
 filtered through—including opportunities for sexual selection—may explain
 the frequent though inconsistent records of sex differences in inbreeding
 depression, along with their implications for conservation and the
 evolution of mating systems.
description: Sex-specific inbreeding
 on offspring numberData is provided for
 male and female offspring production for different levels of inbreeding
 for nine different independently derived lineages. Columns give the sex of
 the focal individual (mated with an outbred control), the family/lineage
 ID, the level of inbreeding (F), the total number of offspring produced
 over an individuals lifespan, and the log transformation of offspring
 number.Ebel_offspring.xlsSex specific inbreeding on offspring production per dayData is provided for male and female offspring production for different levels of inbreeding for nine different independently derived lineages. Columns give the sex of the focal individual (mated with an outbred control), the family/lineage ID, the level of inbreeding (F), and columns for the day-specific offspring production for each individual.Ebel_offspringperday.xlsSex-specific inbreeding on egg survivorship/hatchingData is provided for male and female specific survivorship of eggs for different levels of inbreeding for nine different independently derived lineages. Columns give the sex of the focal individual (mated with an outbred control), the family/lineage ID, the level of inbreeding (F), the total number of eggs that were alive versus dead for a given replicate individual.Ebel_survivorship.xlsEffects of inbreeding on male mating successData is provided for male mating success across different levels of inbreeding for nine different independently derived lineages. Columns give the family/lineage ID, the level of inbreeding (F), mating rate of the focal male (in females per hour), and the log of the mating rate.Ebel_mating.xls
DOI: 10.5061/dryad.812mm
title: Data from: Chaotic genetic patchiness without sweepstakes reproduction in the shore crab Hemigrapsus oregonensis

description: Fine-scale spatial and temporal variation in the genetic composition of
 benthic recruits, known as chaotic genetic patchiness, is often observed
 in marine and estuarine species with planktonic larvae. Several
 explanations have been proposed for chaotic genetic patchiness, including
 sweepstakes reproductive success, variability in larval source and natural
 selection. In a survey of the green shore crab Hemigrapsus oregonensis in
 Bodega Bay, California, allele frequencies at a mitochondrial single
 nucleotide polymorphism were found to differ significantly among samples
 of first stage zoeae and between zoeae and adults. Sweepstakes
 reproductive success is unlikely to be responsible because the fecundity
 of this species is too low and there was no reduction in genetic diversity
 among zoeae. In principle, influxes of larvae from genetically distinct
 populations over 500 km to the north could have caused these differences;
 however, coalescent estimates indicated that gene flow from these distant
 populations has been very low and it is unlikely that first stage zoeae
 would have been transported such great distances. The possibility remains
 that natural selection, directly or indirectly, is responsible for the
 observed patchiness in mitochondrial allele frequencies.
description: haplotypeSequencesDNA sequences of partial cytochrome oxidase I sequences used for our analyses. These include both sequences from our study and those from Petersen (2007) doi:10.1007/s00227-006-0442-xtotalSnpCountsFor each sample of individuals, number individuals with each of the four different nucleotides at sequence position 461 (SNP-461). The first section of the table is for SNP genotypes determined by TaqMan probes, the second sequence is for SNP genotypes determined by sequencing, and the third section combines numbers from both methods of genotyping.totalSnpFrequenciesSNP-461 allele frequencies for SNP genotypes determined from TaqMan probes, sequencing, and totals for both methods combined.combinedSequencesAll partial COI sequences from this study and Petersen (2007), trimmed alignment.sequenceOrganizerPerl script to organize sequences in combinedSequences.pl. Finds all unique haplotypes, names them h1, h2, h3... and writes fasta file of all unique haplotypes, writes file with number of occurrences of each haplotype, writes file of counts of each haplotype in each sample, writes input file for the software Arlequin, writes input file for the software IMa2combineSnpsReads counts of SNPs alleles (A, T, C, or G) from one file with counts in samples for TaqMan genotyping and another file with counts in samples from sequence-based genotyping and combines them. Output SNP counts and SNP frequencies by location and an input file in Genepop format. Allows samples to be pooled into named aggregate collectionssequencesToSnpsReads sequences in fasta file, outputs SNP counts
DOI: 10.5061/dryad.c61q0
title: Data from: Social network analysis of mating patterns in American black bears (Ursus americanus)

description: Nonrandom mating can structure populations and has important implications
 for population-level processes. Investigating how and why mating deviates
 from random is important for understanding evolutionary processes as well
 as informing conservation and management. Prior to the implementation of
 parentage analyses, understanding mating patterns in solitary, elusive
 species like bears was virtually impossible. Here, we capitalize on a
 long-term genetic data set collected from black bears (Ursus americanus)
 (N = 2422) in the Northern Lower Peninsula (NLP) of Michigan, USA. We
 identified mated pairs using parentage analysis and applied logistic
 regression (selection) models that controlled for features of the social
 network, to quantify the effects of individual characteristics, and
 spatial and population demographic factors on mating dynamics. Logistic
 regression models revealed that black bear mating was associated with
 spatial proximity of mates, male age, the time a pair had coexisted, local
 population density and relatedness. Mated pairs were more likely to
 contain older males. On average, bears tended to mate with nearby
 individuals to whom they were related, which does not support the
 existence of kin recognition in black bears. Pairwise relatedness was
 especially high for mated pairs containing young males. Restricted
 dispersal and high male turnover from intensive harvest mortality of NLP
 black bears are probably the underlying factors associated with younger
 male bears mating more often with female relatives. Our findings
 illustrate how harvest has the potential to disrupt the social structure
 of game species, which warrants further attention for conservation and
 management.
description: Black bear data_Moore et
 alThis file contains
 information from black bear samples collected via harvest from the
 Northern Lower Peninsula of Michigan, USA. File includes bear ID, sex,
 estimated age at the time of harvest, geographic coordinates of harvest
 locations (the centroid of the township, range, and section reported by
 hunters), and the 12-locus microsatellite genotypes. See associated
 manuscript for specific details about sample collection, bear aging,
 sexing, geographic locations, and genotyping.