cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.np92nm2
title: Data from: Diverging phenological responses of Arctic seabirds to an earlier spring

description: The timing of annual events such as reproduction is a critical component
 of how free-living organisms respond to ongoing climate change. This may
 be especially true in the Arctic, which is disproportionally impacted by
 climate warming. Here, we show that Arctic seabirds responded to climate
 change by moving the start of their reproduction earlier, coincident with
 an advancing onset of spring and that their response is phylogenetically
 and spatially structured. The phylogenetic signal is likely driven by
 seabird foraging behavior. Surface-feeding species advanced their
 reproduction in the last 35 years while diving species showed remarkably
 stable breeding timing. The earlier reproduction for Arctic
 surface-feeding birds was significant in the Pacific only, where spring
 advancement was most pronounced. In both the Atlantic and Pacific,
 seabirds with a long breeding season had a greater response to the
 advancement of spring than seabirds with a short breeding season. Our
 results emphasize that spatial variation, phylogeny, and life-history are
 important considerations in seabird phenological response to climate
 change and highlight the key role played by the species’ foraging
 behavior.
description: PhenologyStudy_DataforDryadHatching dates of Arctic seabirds and estimated spring onset timing (1982-2016)
DOI: 10.7910/dvn/ciosaq
title: PICNIC Blur Data

description: Blur data for PICNIC subjects available as of October 2024.
DOI: 10.5061/dryad.6h661t9
title: Data from: Warm bodies, cool wings: regional heterothermy in flying bats

description: Many endothermic animals experience variable limb temperatures, even as
 they tightly regulate core temperature. The limbs are often cooler than
 the core at rest, but because the large locomotor muscles of the limbs
 produce heat during exercise, they are thought to operate at or above core
 temperature during activity. Bats, small-bodied flying mammals with
 greatly elongated forelimbs, possess wings with large surfaces lacking any
 insulating fur. We hypothesized that during flight the relatively small
 muscles that move the elbow and wrist operate below core body temperature
 because of elevated heat loss. We measured muscle temperature continuously
 in the small fruit bat Carollia perspicillata before and during wind
 tunnel flights, and discretely in diverse bats at rest in Belize. We found
 that bats maintained high rectal temperatures, but that there was a steep
 proximal-to-distal gradient in wing muscle temperature. Forearm muscles
 were 4–6ºC cooler than rectal temperature at rest and ~12ºC cooler during
 flights at an air temperature of 22ºC. These findings invite further study
 into how bats and other endotherms maintain locomotor performance in
 variable environments, when some muscles may be operating at low
 temperatures that are expected to slow contractile properties.
description: rummel_etal_2019
DOI: 10.5061/dryad.5p78n31
title: Data from: Experience modulates an insect’s response to anthropogenic noise

description: In response to anthropogenic noise, vertebrates express modified acoustic
 communication signals either through individual plasticity or local
 population adaptation. In contrast, how insects respond to this stressor
 is poorly studied. Field crickets Gryllus bimaculatus use acoustic signals
 to attract and locate mates and are commonly found in noisy roadside
 environments, offering a powerful system to study the effects of
 anthropogenic noise on insect communication. Rapid repetition of sexual
 calls (chirps) is essential to attract females, but calling incurs
 energetic costs and attracts predators. As a result, males are predicted
 to reduce calling rates when background noise is high. Here, we combine
 observations and experimental playbacks to show that the responses of
 Field cricket males to anthropogenic noise also depend on their previous
 experience with passing cars. First, we show that males living on highway
 edges decrease their chirp rate in response to passing cars. To assess
 whether this behavioural response depends on previous exposure to car
 noise, we then broadcast recordings of car noise to males located at
 different distances from the road and, therefore, with different previous
 exposure to car noise. Although all tested individuals responded to
 broadcasted traffic noise, males closest to the road decreased their chirp
 rate less than individuals calling further from the road. These results
 suggest that regular exposure to anthropogenic noise may decrease
 individuals' sensitivity and behavioural responses to noise, allowing
 them to maintain effective signalling rates. Behavioural plasticity
 modulated by experience may thus allow some insect species to cope with
 human-induced environmental stressors.
description: Gallego-Abenza et al.
 dataset_Experience modulates...2019The dataset contains
 Observational data from 2016, Experimental data from playback experiments
 2018 and the noise-distance gradient measurements.
DOI: 10.5061/dryad.4b10j7q
title: Data from: The fitness cost of mismatch repair mutators in Saccharomyces cerevisiae: partitioning the mutational load

description: Mutational load is the depression in a population's mean fitness that
 results from the continual influx of deleterious mutations. Here, we
 directly estimate the mutational load in a population of haploid
 Saccharomyces cerevisiae that are deficient for mismatch repair. We
 partition the load in haploids into two components. To estimate the load
 due to nonlethal mutations, we measure the competitive fitness of hundreds
 of randomly selected clones from both mismatch repair-deficient and
 -proficient populations. Computation of the mean clone fitness for the
 mismatch repair-deficient strain permits an estimation of the nonlethal
 load, and the histogram of fitness provides an interesting visualization
 of a loaded population. In a separate experiment, in order to estimate the
 load due to lethal mutations (i.e. the lethal mutation rate), we
 manipulate thousands of individual pairs of mother and daughter cells and
 track their fates. These two approaches yield point estimates for the two
 contributors to load, and the addition of these estimates is nearly equal
 to the separately measured short-term competitive fitness deficit for the
 mismatch repair-deficient strain. This correspondence suggests that there
 is no need to invoke direct fitness effects to explain the fitness
 difference between mismatch repair-deficient and -proficient strains.
 Assays in diploids are consistent with deleterious mutations in diploids
 tending towards recessivity. These results enhance our understanding of
 mutational load, a central population genetics concept, and we discuss
 their implications for the evolution of mutation rates.
description: Short term strain vs
 strain fitness competition dataThis is data for figs 2
 and 4. Strain numbers are as follows: 3531: haploid reference GFP+ strain;
 3533: haploid GFP- strain; 3534: haploid mutator (mmr-) GFP- strain; 3633:
 diploid reference GFP+ strain; 3634: diploid GFP- strain; 3643: diploid
 mutator (mmr-) GFP- strainstrain_v_strain_fitness_competitions.csvclone_fitness_competitionsThis is the data for the clone fitness competitions (Figs 3 and S2). frozen.plate is an internal ID for a group of up to 90 clones. plate.date is a unique identifier for a given batch, consisting of the plate ID and the date of the run. s.0.24.adj is the mode-adjusted selection coefficient as described in the methods. If the field include is set to "n", that clone was not used because of poor or no growth. If the field include is set to "r", that is a "reference" competition (not a clone). If the field include is set to "y", that data is used. Strain numbers: 3531 is haploid GFP+ reference, 3533 is haploid wild type, 3534 is haploid mmr- mutator. 3633, 3634, and 3643 are diploid versions of each, respectively.
DOI: 10.5061/dryad.p6k0mq3
title: Data from: Selfing ability and drift load evolve with range expansion

description: Colonization at expanding range edges often involves few founders,
 reducing effective population size. This process can promote the evolution
 of self-fertilization, but implicating historical processes as drivers of
 trait evolution is often difficult and requires an explicit model of
 biogeographic history. In plants, contemporary limits to outcrossing are
 often invoked as evolutionary drivers of self-fertilization, but
 historical expansions may shape mating system diversity, with leading-edge
 populations evolving elevated selfing ability. In a widespread plant,
 Campanula americana, we identified a glacial refugium in the southern
 Appalachian Mountains from spatial patterns of genetic drift among 24
 populations. Populations farther from this refugium have smaller effective
 sizes and fewer rare alleles. They also displayed elevated heterosis in
 among-population crosses, reflecting the accumulation of deleterious
 mutations during range expansion. While populations with elevated
 heterosis had reduced segregating mutation load, the magnitude of
 inbreeding depression lacked geographic pattern. The ability to
 self-fertilize was strongly positively correlated with the distance from
 the refugium and mutation accumulation—a pattern that contrasts sharply
 with contemporary mate and pollinator limitation. In this and other
 species, diversity in sexual systems may reflect the legacy of evolution
 in small, colonizing populations, with little or no relation to the
 ecology of modern populations.
description: Phenotypic data for f
 inbreeding depression and drift loadPopulation attributes
 and phenotypic data used to calculate stage-specific and cumulative
 inbreeding depression and drift load for 24 populations of Campanula
 americana. Column header descriptions are provided in the 'column
 header descriptions' tab.Koskietal_EvoLett_PhenotypicData_DriftLoad_InbreedingDepression.xlsxipyrad paramsParameter file associated with our processing of RADseq data in ipyradbellmergeAfter processing reads in ipyrad, the resulting data are stored in the variant call format (VCF) in bellmerge.vcf. These data can be analyzed with 3 R scripts to generate results presented in the paper.diversity R scriptExtracts estimates of the population mutation parameter and Tajima's Ddiversity.Rinbreeding coefficient R scriptCalculates observed and expected heterozygosity from genotypic data and the inbreeding coefficient of populations.inbreeding coefficient.RTDoA R scriptCalculates directionality statistics and identifies the geographic location of a recent range expansion. To properly run this file, one must set a filepath containing the files in the TDoA dependencies folder.TDoA.RREADME
DOI: 10.5061/dryad.04vk390
title: Data from: Genome-scale characterization of toxicity-induced metabolic alterations in primary hepatocytes

description: Context-specific Genome-scale Metabolic Network Reconstructions (GENREs)
 provide a means to understand cellular metabolism at a deeper level of
 physiological detail. Here, we use transcriptomics data from chemically
 exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism
 and predict biomarkers of liver toxicity using the Transcriptionally
 Inferred Metabolic Biomarker Response (TIMBR) algorithm. We profiled
 alterations in cellular hepatocyte metabolism following in vitro exposure
 to four toxicants (acetaminophen, carbon tetrachloride,
 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six hours.
 TIMBR predictions were compared with paired fresh and spent media
 metabolomics data from the same exposure conditions. Agreement between
 computational model predictions and experimental data led to the
 identification of specific metabolites and thus metabolic pathways
 associated with toxicant exposure. Here, we identified changes in the TCA
 metabolites citrate and alpha-ketoglutarate along with changes in
 carbohydrate metabolism and interruptions in ATP production and the TCA
 Cycle. Where predictions and experimental data disagreed, we identified
 testable hypotheses to reconcile differences between the model predictions
 and experimental data. The presented pipeline for using paired
 transcriptomics and metabolomics data provides a framework for
 interrogating multiple omics datasets to generate mechanistic insight of
 metabolic changes associated with toxicological responses.
description: Rawls_Supplementary_Data1Gene expression data for each treatment condition.Rawls_Supplementary_data2Gene enrichment categories from DAVID BioinformaticsRawls_Supplementary_data3Raw and normalized metabolomics data from the research study.Rawls_Supplementary_data4TIMBR production scores for metabolites in each of the treatment conditions.Rawls_Supplementary_data5Human Metabolome DataBase classifications for select TIMBR metabolites.Hepatocyte_Toxicology_Data_Supplement_081219Supplemental Information file containing figures and methods relevant to the manuscript, but not included in the main text.Rawls_Supplementary_data6Reaction ID numbers for metabolic reactions used to calculate TIMBR production scores.
DOI: 10.5061/dryad.vr300p0
title: Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology

description: Minimally-invasive sampling (MIS) is widespread in wildlife studies;
 however, its utility for massively parallel DNA sequencing (MPS) is
 limited. Poor sample quality and contamination by exogenous DNA can make
 MIS challenging to use with modern genotyping-by-sequencing approaches,
 which have been traditionally developed for high-quality DNA sources.
 Given that MIS is often more appropriate in many contexts, there is a need
 to make such samples practical for harnessing MPS. Here, we test the
 ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex
 amplicon sequencing approach, to effectively genotype minimally-invasive
 cloacal DNA samples collected from the Western Rattlesnake (Crotalus
 oreganus), a threatened species in British Columbia, Canada. As there was
 no previous genetic information for this species, an optimized panel of
 362 SNPs was selected for use with GT-seq from a de novo restriction-site
 associated DNA sequencing (RADseq) assembly. Comparisons of genotypes
 generated within and among RADseq and GT-seq for the same individuals
 found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and
 discordance (2.57%), the latter likely due to the different genotype
 calling models employed. GT-seq mean genotype discordance between blood
 and cloacal swab samples collected from the same individuals was also
 minimal (1.37%). Estimates of population diversity parameters were similar
 across GT-seq and RADseq datasets, as were inferred patterns of population
 structure. Overall, GT-seq can be effectively applied to low quality DNA
 samples, minimizing the inefficiencies presented by exogenous DNA
 typically found in minimally-invasive samples and continuing the expansion
 of molecular ecology and conservation genetics in the genomics era.
description: GTseq_311_41vcf file containing genotypic data for 41 Western rattlesnakes at 311 SNPs generated via GT-seqRADseq_9568_41vcf file containing genotypic data for 41 Western rattlesnakes at 9568 SNPs generated via RADseq
DOI: 10.5061/dryad.c1v64np
title: Data from: Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility

description: Terrestrial arthropods, including insects, commonly harbor maternally
 inherited intracellular symbionts that confer benefits to the host or
 manipulate host reproduction to favor infected female progeny. These
 symbionts may be especially vulnerable to thermal stress, potentially
 leading to destabilization of the symbiosis and imposing costs to the
 host. For example, increased temperatures can reduce the density of a
 common reproductive manipulator, Wolbachia, and the strength of its
 crossing incompatibility (cytoplasmic incompatibility, or CI) phenotype.
 Another manipulative symbiont, Cardinium hertigii, infects ~ 6-10% of
 Arthropods, and also can induce CI, but there is little homology between
 the molecular mechanisms of CI induced by Cardinium and Wolbachia. Here we
 investigated whether temperature disrupts the CI phenotype of Cardinium in
 a parasitic wasp host, Encarsia suzannae. We examined the effects of both
 warm (32°C day/ 29°C night) and cool (20°C day/ 17°C night) temperatures
 on Cardinium CI and found that both types of temperature stress modified
 aspects of this symbiosis. Warm temperatures reduced symbiont density,
 pupal developmental time, vertical transmission rate, and the strength of
 both CI modification and rescue. Cool temperatures also reduced symbiont
 density, however this resulted in stronger CI, likely due to cool
 temperatures prolonging the host pupal stage. The opposing effects of cool
 and warm-mediated reductions in symbiont density on the resulting CI
 phenotype indicates that CI strength may be independent of density in this
 system. Temperature stress also modified the CI phenotype only if it
 occurred during the pupal stage, highlighting the likely importance of
 this stage for CI induction in this symbiosis.
description: Doremusetal_PLoSPath2019_dataThis file contains data from crossing experiments using wasps (Encarsia suzannae, formerly E. pergandiella) infected with a heritable bacterium, Cardinium hertigii. These experiments tested the effect of exposure to different temperature regimens on a crossing incompatibility caused by C. hertigii between infected males and uninfected females, known as CI. CI is rescued when males mate with infected females (control or rescue cross in data file). Both male and female wasps were exposed to temperature stress in separate experiments, and a third experiment, using temperature "shocks" was also conducted using male hosts. The duration of pupal development and Cardinium density within the host are also included.
DOI: 10.5061/dryad.8nn2j46
title: Data from: Nut intake and non-alcoholic fatty liver disease risk

description: Abstract Objectives: Nut consumption has been associated with a lower risk
 of type 2 diabetes, metabolic syndrome, and insulin resistance. However,
 its effect on the risk of non-alcoholic fatty liver disease (NAFLD) is
 unknown. Therefore, we investigated the relationship between nut
 consumption and NAFLD risk. Setting and participants: We conducted a
 retrospective case-control study including 534 patients diagnosed with
 NAFLD and 534 controls matched by sex and age (± 5) from the Affiliated
 Nanping First Hospital of Fujian Medical University in China. Main outcome
 measures: Information on dietary intake was collected using a
 semi-quantitative food frequency questionnaires and nut consumption was
 calculated. Nut consumption was categorized using quartiles based on the
 distribution of daily nut intake of the controls. Binary logistic
 regression models were used to estimate odds ratio (ORs) and the 95%
 confidence intervals (CIs) for the association between nut consumption and
 NAFLD risk. Results: After adjusting for potential confounding variables,
 nut consumption was not associated with NAFLD risk in the overall sample.
 When the fully adjusted model was stratified by sex, a significant inverse
 association was found between high nut consumption and NAFLD only among
 the men in the highest quartile (OR = 0.43; 95% CI: 0.26–0.71; Ptrend =
 0.01). The inverse association of nut consumption with NAFLD risk in men
 remained significant after controlling for other known or suspected risk
 factors for NAFLD. Conclusions: Diets with a higher intake of nuts may be
 associated with a decreased risk of NAFLD, particularly in men.
description: nut intake and
 Non-alcoholic fatty liver disease risk
DOI: 10.5061/dryad.617744v
title: Data from: Linking genetic merit to sparse behavioral data: does behavior explain genetic variation for maternal care in Soay sheep?

description: Wild quantitative genetic studies have focused on a subset of traits
 (largely morphological and life-history), with others, such as behaviors,
 receiving much less attention. This is because it is challenging to obtain
 sufficient data, particularly for behaviors involving interactions between
 individuals. Here, we explore an indirect approach for pilot
 investigations of the role of genetic differences in generating variation
 in parental care. Variation in parental genetic effects for offspring
 performance is expected to arise from among-parent genetic variation in
 parental care. Therefore, we used the animal model to predict maternal
 breeding values for lamb growth and used these predictions to select
 females for field observation, where maternal and lamb behaviors were
 recorded. Higher predicted maternal breeding value for lamb growth was
 associated with greater suckling success, but not with any other measures
 of suckling behavior. Though our work cannot explicitly estimate the
 genetic basis of the specific traits involved, it does provide a strategy
 for hypothesis generation and refinement, that we hope could be used to
 justify data collection costs needed for confirmatory studies. Here
 results suggest that behavioral genetic variation is involved in
 generating maternal genetic effects on lamb growth in Soay sheep. Though
 important caveats and cautions apply, our approach may extend the ability
 to initiate more genetic investigations of difficult-to-study behaviours
 and social interactions in natural populations.
description: READMEThis file contains
 information on all the variables included in the 6 data files that
 accompany this manuscript.Growth_data_1985_to_2016Growth rate data for all lambs born between 1985 and 2016.GRM_1985_to_2012Genomic relatedness matrix containing genomic relatedness for all pairs of individuals in the study population.SNP_pedigree_1985_to_2016Single nucleotide polymorphism derived pedigree.Maternal_home_range_overlaps100% kernel home range overlaps (calculated using Bhattacharyya's affinity) for every pair of mothers with lamb growth information.Lamb_behavioural_dataInformation on all lamb behavioural traits studied.Maternal_behavioural_dataInformation for all maternal behavioural traits.