cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rq65c2j
title: Data from: Coping with the cold: energy storage strategies for surviving winter in freshwater fish

description: For many ectothermic animals, the acquisition, storage, and depletion of
 lipids is integral to successfully coping with reduced metabolic rates and
 activity levels associated with cold, winter periods. In fish, lipids are
 crucial for overwinter survival and successful reproduction. The timing
 and magnitude of seasonal lipid storage should therefore vary predictably
 among fish with different thermal preferences and spawn times. Small- and
 large-bodied fish should also face different constraints associated with
 season that influence lipid cycling. However, much work to date has been
 species- and location-specific and a general conceptual model for the
 seasonal energy budgets of freshwater fish is lacking. Here, we conducted
 a comprehensive literature review of seasonal lipid levels in freshwater
 fishes. We predicted that warm and cool water species would be more likely
 to demonstrate peak lipid levels during warm months than cold water
 species, and expected a larger magnitude of annual lipid cycling in warm
 and cool water compared to cold water fish. We also expected dampened
 lipid cycling in larger fish due to their lower mass-specific metabolic
 rates. Observed patterns in the timing and magnitude of lipid storage
 contradicted our prediction because lipid cycling was widespread across
 species, despite thermal guild, with peak lipid levels commonly occurring
 during warmer months, even in cold water fish. For body size effects,
 larger bodied fish species had dampened seasonal lipid cycling, as
 predicted. We developed a conceptual framework describing how the ‘scope’
 for variation in annual lipid cycling changes with body size both among
 and within species in order to guide future work. Together, our findings
 suggest that energy acquired during warm months is broadly important for
 overwinter survival and reproduction in fishes, and provide a new
 perspective on the differential constraints and physiological responses to
 seasonality among freshwater fish.
description: MonthlyData_LipidAll extracted and normalized monthly lipid values for all species, life stages, sexes, and tissues included in this review. All relevant details regarding short forms used are outlined in the attached legend.
DOI: 10.5061/dryad.tk23st2
title: Data from: Experimental evolution of response to anoxia in Drosophila: recovery of locomotion following CO2 or N2 exposure

description: Many insects enter coma upon exposure to anoxia, a feature routinely
 exploited by experimentalists to handle them. But the genetic and
 physiological bases of anoxic coma induction and recovery are only
 partially understood, as are the long-term consequences for the
 animal's performance. We examined three populations of Drosophila
 melanogaster (designated B) that have been inadvertently under selection
 for rapid recovery from CO2 exposure for nearly 40 years (around 1,000
 generations) resulting from routine maintenance practices. We contrasted
 CO2 and N2 (presumed a less reactive gas) knockdown and recovery times of
 these B flies with six populations of common ancestry (A and C
 populations) that were not exposed to CO2 over the same period. We found
 that B populations showed faster and more consistent locomotor recovery
 than A or C populations after CO2 knockdown, a result also observed with
 N2 knockdown. A and C populations showed much higher variance in recovery
 time after CO2 exposure than after N2 exposure, suggesting gas-specific
 effects on pathways associated with locomotor recovery. While these
 selection treatments result in considerable variation in life history
 attributes and body size, with the characteristic intermediacy of B
 populations, their superiority in resistance to gas exposure and locomotor
 recovery suggests that it is a direct consequence of prior repeated
 exposure to anoxia, broadly, and CO2, specifically. Hence we describe a
 powerful new evolutionary model for the genetic and physiological
 investigation of anoxic coma in insects.
description: JEXBIO199521_Data_IData associated with the publication: https://doi.org/10.1242/jeb.199521JEXBIO199521_Data.xlsx
DOI: 10.5061/dryad.421dq43
title: Data from: Hybridization and geographic distribution shapes the spatial genetic structure of two co-occurring orchid species

description: Multiple ecological and life-history traits shape the fine-scale spatial
 genetic structure (FSGS) of a given population. The occurrence in core
 versus peripheral populations, levels of outcrossing, pollen and seed
 dispersal, and hybridization are important biological properties that
 influence the kinship of individuals within populations. We examined
 spatial genetic structure within 15 populations of Epidendrum fulgens and
 E. puniceoluteum distributed along a linear gradient of Brazilian coastal
 vegetation, including both allopatric and sympatric populations where the
 two orchid species hybridize. We analyzed 581 mapped specimens using nine
 simple sequence repeat loci, aiming to investigate how geographic
 distribution and hybridization shape within-population FSGS. A significant
 increase in FSGS was found towards peripheral populations, compared to
 core populations. Analysis of short- and long-distance components of FSGS
 identified biparental inbreeding and higher levels of FSGS at peripheral
 populations, when compared to core populations. In contrast, the
 relatively high density of reproductive adults in core populations
 potentially leads to highly overlapping seed and pollen movement,
 decreasing FSGS. Hybridization was an important factor shaping
 within-population spatial genetic structure at sympatric sites, decreasing
 the FSGS observed in parental species. Our results indicate that different
 ecological forces act in concert to create a gradient of FSGS along
 species distribution ranges, shaped by extensive levels of intra- and
 interspecific gene exchange.
description: file containing SSR
 genotypes and geographic coordinatesThe file can be used in
 Spagedi to perform fine scale genetic structure analysis, as performed in
 our manuscriptSSR_genotypes.txt
DOI: 10.5061/dryad.km3109k
title: Data from: Contrasting evolution of virulence and replication rate in an emerging bacterial pathogen

description: Host resistance through immune clearance is predicted to favour pathogens
 that are able to transmit faster and are hence more virulent. Increasing
 pathogen virulence is, in turn, typically assumed to be mediated by
 increasing replication rates. However, experiments designed to test how
 pathogen virulence and replication rates evolve in response to increasing
 host resistance, as well as the relationship between the two, are rare and
 lacking for naturally-evolving host-pathogen interactions. We inoculated
 55 isolates of Mycoplasma gallisepticum collected over 20 years from
 outbreak, into house finches (Haemorhous mexicanus) from disease-unexposed
 populations, which have not evolved protective immunity to M.
 gallisepticum. We show using three different metrics of virulence (body
 mass loss, symptom severity and putative mortality rate) that virulence
 has increased linearly over &gt;150,000 bacterial generations since
 outbreak (1994-2015). By contrast, while replication rates increased from
 outbreak through to the initial spread of resistance (1994-2004), no
 further increases have occurred subsequently (2007-2015). Finally, as a
 consequence, we found that any potential mediating effect of replication
 rate on virulence evolution was restricted to the period when host
 resistance was initially increasing in the population. Taken together, our
 results show that pathogen virulence and replication rates can evolve
 independently, particularly after the initial spread of host resistance.
 We hypothesize that the evolution of pathogen virulence can be driven
 primarily by processes such as immune manipulation after resistance
 spreads in host populations.
description: Tardy et
 al_2019year of pathogen
 sampling, measures of virulence, replication rate, pathogen
 load
DOI: 10.5061/dryad.j51kt03
title: Data from: Maize-field complexity and farming system influence insectivorous birds’ contribution to arthropod herbivore regulation

description: The contribution of insectivorous birds to reducing crop damage through
 suppression of herbivory remains underappreciated, despite their role as
 cropland arthropod predators. We examined the roles of farming system crop
 cover pattern and structural configuration in influencing assemblage
 composition of insectivorous birds and their herbivorous arthropod prey
 across maize fields, and determined how bird exclusion affects crop
 herbivory levels. To achieve these objectives, data were collected across
 a sample of organic and conventional small-scale non-Bt maize farms in
 western Kenya. Assessments of abundance, diversity and richness of
 insectivorous birds, and abundance of their arthropod prey, were compared
 between organic and conventional small-scale non-Bt maize on monocultured
 and intercropped farms. We also employed bird exclusion experiments to
 assess impacts of bird predation on herbivorous arthropod abundance.
 Results showed that higher structural heterogeneity supported higher
 insectivorous bird richness, particularly under organic systems, dense
 trees, large woodlots and thick hedgerows. Bird abundance further
 increased with crop diversity but not in relation to cropping method,
 hedgerow type or percent maize cover per se. Conversely, herbivorous
 arthropod abundance and richness increased on conventional farms and those
 with higher percent maize cover, but were unaffected by cropping methods,
 tree or hedgerow characteristics. Birds’ arthropod prey were more abundant
 under completely closed compared to open or semi-closed plots, confirming
 a significant linkage between birds and herbivorous arthropod suppression.
 In this study, we demonstrate importance of structural heterogeneity in
 agricultural landscapes, including diverse croplands and on-farm trees to
 maximize insectivorous birds’ contribution to reducing crop arthropod
 herbivory.
description: Bird encounter incidents
 across the farms surveyedSpecies of insect-eating
 birds that were encountered across all farms. List includes generalist
 species that consume insects and other food typesEstimated global
 populations per hectare of bird species fro each farm from
 DistanceEstimated population of
 bird species across the entire collection of farms studied. Population
 estimate are per hectare and are derived from the DISTANCE protocol,
 projected from regional average estimates for each of the farms
 surveyed
DOI: 10.5061/dryad.4m8b580
title: Data from: Human recreation reduces clutch size in great tits Parus major regardless of risk-taking personality

description: Recreation negatively affects wildlife by influencing animal behaviour
 vital to reproduction and survival. Such non-consumptive effects of
 perceived predation risk are mainly studied in ground-breeding birds.
 However, if anti-predator responses characterize bird species generally,
 so should non-consumptive effects of perceived predation associated with
 human recreation. Moreover, as individuals consistently differ in
 behaviours linked to anti-predator responses, they should also differ in
 responses to recreation, with bolder birds being less affected. To test
 this key prediction, we quantified effects of human recreation pressure on
 a cavity-breeding passerine. We uniquely quantified human recreation
 pressure over a substantial (8-year) period within twelve nest-box
 populations of the great tit Parus major, assayed annually for
 reproductive parameters. We detected considerable spatial variation in
 recreation pressure. In plots with high recreation pressure, we found
 strong support for birds breeding further away from highly frequented
 paths and birds producing smaller clutches; we also found moderate support
 for birds producing fewer fledglings. These detrimental effects did not
 vary with behavioural proxies of an individual’s risk-taking phenotype
 (exploratory activity). This implies that effects of recreation pressure
 apply to the average bird, and extend to species (like forest birds) not
 previously considered.
description: Main Analysis
 DataIncludes occupancy,
 reproductive success and exploratory behaviorHutflussDingemanseBehEcoDataBaseMainDryad.xlsxNestling DataIncluding morphological measurements of nestlings of 14 days ageHutflussDingemanseBehEcoChicksDryad.xlsxDisturbance 1Including information on plot check, such as duration and number of observersHutflussDingemanseBehEcoDisturbanceMainDryad.xlsxDisturbance 2Including detailed information on location and number of pedestriansHutflussDingemanseBehEcoDisturbanceSubDryad.xlsxHabitat DescriptionIncluding information on vegetation around the nest boxesHutflussDingemanseBehEcoHabitatDescription_Dryad.xlsxDistancesIncluding information on the rectangular distance from each nest box to the main source of disturbanceHutflussDingemanseBehEcoDistancesDryad.xlsx
DOI: 10.5061/dryad.t83d372
title: Data from: MicroRNA gene regulation in extremely young and parallel adaptive radiations of crater lake cichlid fish

description: Cichlid fishes provide textbook examples of explosive phenotypic
 diversification and sympatric speciation, thereby making them ideal
 systems for studying the molecular mechanisms underlying rapid lineage
 divergence. Despite the fact that gene regulation provides a critical link
 between diversification in gene function and speciation, many genomic
 regulatory mechanisms such as miRNAs have received little attention in
 these rapidly diversifying groups. Therefore, we investigated the
 post-transcriptional regulatory role of miRNAs in the repeated sympatric
 divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater
 lakes. Using miRNA and mRNA sequencing of embryos from five Midas species,
 we first identified miRNA binding sites in mRNAs and highlighted the
 presences of a surprising number of novel miRNAs in these adaptively
 radiating species. Then, through analyses of expression levels, we
 identified putative miRNA/gene target pairs with negatively correlated
 expression level that were consistent with the role of miRNA in
 downregulating mRNA. Furthermore, we determined that several miRNA/gene
 pairs show convergent expression patterns associated with the repeated
 benthic/limnetic sympatric species divergence implicating these miRNAs as
 potential molecular mechanisms underlying replicated sympatric divergence.
 Finally, as these candidate miRNA/gene pairs may play a central role in
 phenotypic diversification in these cichlids, we characterized the
 expression domains of selected miRNAs and their target genes via in situ
 hybridization, providing further evidence that miRNA regulation likely
 plays a role in the Midas cichlid adaptive radiation. These results
 provide support for the hypothesis that extremely quickly evolving miRNA
 regulation can contribute to rapid evolutionary divergence even in the
 presence of gene flow.
description: Midas
 transcriptomeRNA-Seq reads from 3
 individuals of five Midas species (A. astorquii, A. zaliosus, A. amarillo
 A. sagittae, and A. citrinellus) sampled at 1 day post-hatching were
 generated. In addition,12 individuals sampled at 1 month post-hatching (1
 mph) (Franchini, et al. 2016) were combined to build the reference
 transcriptome. The 490.3 million raw RNA-Seq paired-end reads were trimmed
 by Trimmomatic. The combination of reference-guided assembly by Stringtie
 and de novo assembly by Trinity were generated as Midas
 transcriptome.Midas_transcriptome.fa.gz
DOI: 10.5061/dryad.ct8r61v
title: Data from: Flexible polyandry in female flies is an adaptive response to infertile males

description: Infertility is common in nature despite its obvious cost to individual
 fitness. Rising global temperatures are predicted to decrease fertility,
 and male sterility is frequently used in attempts to regulate pest or
 disease vector populations. When males are infertile, females may mate
 with multiple males to ensure fertilisation, and changes in female mating
 behaviour in turn could intensify selection on male fertility. Fertility
 assurance is a potentially wide-spread explanation for polyandry, but
 whether and how it actually contributes to the evolution of polyandry is
 not clear. Moreover, whether a drop in male fertility would lead to a
 genetic increase in polyandry depends on whether females respond
 genetically or through behavioural plasticity to male infertility. Here,
 we experimentally manipulate male fertility through heat-exposure in
 Drosophila pseudoobscura, and test female discrimination against infertile
 males before and after mating. Using isogenic lines, we compare the roles
 of behaviourally plastic versus genetically fixed polyandry. We find that
 heat-exposed males are less active and attractive, and that females are
 more likely to remate after mating with these males. Remating rate
 increases with reduced reproductive output, indicating that females use
 current sperm storage threshold to make dynamic remating decisions. After
 remating with fertile males, females restore normal fecundity levels. Our
 results suggest that male infertility could explain the evolution of
 adaptively flexible polyandry, but is less likely to cause an increase in
 genetic polyandry.
description: Polyandry and fecundity
 dataData on: 1) female
 mating behaviour, remating, and fecundity in response to male
 heat-exposure; 2) male survival of heat-exposure; 3) fertility and mating
 capacity of heat-exposed males2019_Sutter_etal_dryad.xlsx
DOI: 10.5061/dryad.18dv32q
title: Data from: Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian

description: Wildlife disease dynamics are strongly influenced by the structure of host
 communities and their symbiotic microbiota. Conspicuous amphibian declines
 associated with the waterborne fungal pathogen Batrachochytrium
 dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally.
 However, less attention has been given to cryptic terrestrial-breeding
 amphibians that have also been declining in tropical regions. By
 experimentally manipulating multiple tropical amphibian assemblages
 harboring natural microbial communities, we tested whether Bd spillover
 from naturally infected aquatic-breeding frogs could lead to Bd
 amplification and mortality in our focal terrestrial-breeding host: the
 pumpkin toadlet Brachycephalus pitanga. We also tested whether the
 strength of spillover could vary depending on skin bacterial transmission
 within host assemblages. Terrestrial-breeding toadlets acquired lethal
 spillover infections from neighboring aquatic hosts and experienced
 dramatic but generally non-protective shifts in skin bacterial composition
 primarily attributable to their Bd infections. In contrast,
 aquatic-breeding amphibians maintained mild Bd infections and higher
 survival, with shifts in bacterial microbiomes that were unrelated to Bd
 infections. Our results indicate that Bd spillover from even mildly
 infected aquatic-breeding hosts may lead to dysbiosis and mortality in
 terrestrial-breeding species, underscoring the need to further investigate
 recent population declines of terrestrial-breeding amphibians in the
 tropics.
description: Becker_DatasetFull dataset including pathogen infection load data and microbiome alpha and beta diversity metrics over the course of the experiment.
DOI: 10.15468/dl.66z4ug
title: Occurrence Download

description: A dataset listing the 467791 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is iNaturalist Research-grade Observations"
 ]
}

 The dataset's 467791 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001812-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t8q43fv
title: Data from: Sensitivity to AMF species is greater in late-successional than early-successional native or non-native grassland plants

description: Sensitivity of plant species to individual arbuscular mycorrhizal (AM)
 fungal species is of primary importance to understanding the role of AM
 fungal diversity and composition in plant ecology. Currently, we do not
 have a predictive framework for understanding which plant species are
 sensitive to different AM fungal species. In two greenhouse studies, we
 tested for differences in plant sensitivity to different AM fungal species
 and mycorrhizal responsiveness across 17 grassland plant species of North
 America that varied in successional stage, native status, and plant family
 by growing plants with different AM fungal treatments including eight
 single AM fungal isolates, diverse mixtures of AM fungi, and
 non-inoculated controls. We found that late successional grassland plant
 species were highly responsive to AM fungi and exhibited stronger
 sensitivity in their response to individual AM fungal taxa compared to
 non-native or early successional native grassland plant species. We
 confirmed these results using a meta-analysis that included 13
 experiments, 37 plant species, and 40 fungal isolates (from nine
 publications and two greenhouse experiments presented herein). Mycorrhizal
 responsiveness and sensitivity of response (i.e., variation in plant
 biomass response to different AM fungal taxa) did not differ by the source
 of fungal inocula (i.e., local or not local) or plant family. Sensitivity
 of plant response to AM fungal species was consistently correlated with
 the average mycorrhizal response of that plant species. This study
 identifies that AM fungal identity is more important to the growth of late
 successional plant species than early successional or non-native plant
 species, thereby predicting that AM fungal composition will be more
 important to plant community dynamics in late successional communities
 than in early successional or invaded plant communities.
description: Exp1_mixed model_plus_
 fes1-fes2.sasSAS code for analysis of
 greenhouse Experiment 1Exp2_mixed model
 plus_Fes1_Fes2_.sasSAS code for analysis of
 greenhouse Experiment 2.MetaAnalysis.sasSAS code for analysis of all studies included in the meta-analysisExp1_dataData file for greenhouse Experiment 1Exp2_dataDatafile for greenhouse Experiment 2MetaAnalysis_dataDatafile for meta-analysis