cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.19526
title: Data from: Evaluation of sex differences in the stopover behavior and postdeparture movements of wood-warblers

description: Sex differences in the behaviors underlying avian protandry, where males
 arrive at breeding areas earlier than females, are still poorly understood
 for most species. We tested for sex differences in stopover behavior,
 refueling rates, and post-departure movements during spring migration in
 two consecutive years in wood-warblers (Parulidae) at a coastal site on
 Lake Erie, Ontario, using automated radio telemetry (black-throated blue
 warblers Setophaga caerulescens and magnolia warblers S. magnolia) and
 analysis of plasma metabolites as indicators of refueling (magnolia
 warblers, American redstarts S. ruticilla and common yellowthroats
 Geothylpis trichas). We found no differences between sexes in stopover
 duration or refueling index, although we did find subtle sex differences
 in the onset and end of diel activity, with males beginning to forage
 earlier in the morning than females and male magnolia warblers ending diel
 activity later in the evening than female magnolia warblers. More obvious
 were annual differences in stopover duration and the timing of diel
 activity, with shorter stopovers and an earlier onset of diel activity in
 the year with a warmer spring. We also did not find any evidence that
 sexes differed in their post-departure ground speeds or migration routes.
 In wood-warblers, males and females can differ in some aspects of their
 stopover ecology, but these differences are likely context dependent and
 likely do not drive protandry in a consistent way.
description: morbey_LPBOmorbey_LPBO.csv This file has first capture dates for birds processed through the migration monitoring program at Long Point Bird Observatory. See readme.txt for further details.morbey_radioThis file contains information on birds in the radio telemetry study. Birds were released at Old Cut Research Station (42.584 N, 80.397 W). See readme.txt for details.morbey_tailwindThis file has extracted weather data from the RNCEP dataset. See readme.txt for details.morbey_bloodThis file has data for plasma metabolite study. Birds were captured at Old Cut Research Station (42.584 N, 80.397 W). See readme.txt for details.morbey_dielThis file has data for the analysis of onset and end of diel activity at Old Cut Research Station (42.584 N, 80.397 W). See readme.txt for details.morbey_flightsThis file has data on inter-tower flights after departure from the Old Cut region (within 20 km of 42.485 N, 80.397 W). See readme.txt for details.
DOI: 10.5061/dryad.hn356
title: Data from: Where are we now? Bergmann's Rule sensu lato in insects

description: Bergmann's rule states that individuals of a species/clade at higher
 altitudes or latitudes will be larger than species at lower ones. A
 systemic review of the known literature on inter- and intraspecific
 variation in insect size along latitudinal or altitudinal clines was done
 to see how often such clines appeared and if they reflected class-wide,
 species-specific, or experimentally biased tendencies. Nearly even numbers
 of studies showed Bergmann clines and Converse Bergmann clines, where
 insects get smaller as latitude/altitude increases. In fact, the majority
 of studies suggested no clines at all. Small ranges may have obscured
 certain clines, while giant ranges may have introduced artifacts.
 Researchers examining interspecific patterns found clines less frequently
 than those examining intraspecific patterns due to variation among species
 within the clades, which renders interspecific studies unhelpful.
 Bergmann's Rule does not apply to hexapods with nearly the same
 consistency as it does to endothermic vertebrates. The validity of
 Bergmann's Rule for any group and range of insects is highly
 idiosyncratic and partially depends on the study design. We conclude that
 studies of "Bergmann's Rule" should focus within species
 and look at widespread but contiguous populations to account for all
 sources of variation while minimizing error.
description: MShelomi-BergmannInsectsReview.txtThis file contains the data from the systematic review "Where Are We Now? Bergmann’s Rule sensu lato in Insects" in American Naturalist by Matan Shelomi (matanshelomi@yahoo.com). The data was collected from articles listed in the citations of the associated article. The first column lists the author and year of each entry, which can be compared with the references list. In the column "Sex," M=Male, F=Female, B=both. Under "Organs Checked," PCA=Principle Components Analysis and CVA=Canonical Variate Analysis, with the numbers in parentheses being the number of components analyzed. Under "units," PC=principle components. Lat=Latitude (Range measured in arc degrees) and Alt=Altitude (Range measured in meters elevation). Under "Results," + = Bergmann Cline observed, - = Converse Bergmann Cline observed, 0 = No cline observed, with additional descriptions for non-linear clines.forDRyad1.txt
DOI: 10.5061/dryad.t60n5
title: Data from: Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness

description: The effect of a mutation depends on its interaction with the genetic
 background in which it is assessed. Studies in experimental systems have
 demonstrated that such interactions are common among beneficial mutations
 and often follow a pattern consistent with declining evolvability of more
 fit genotypes. However, these studies generally examine the consequences
 of interactions between a small number of focal mutations. It is not
 clear, therefore, that findings can be extrapolated to natural
 populations, where new mutations may be transferred between genetically
 divergent backgrounds. We build on work that examined interactions between
 four beneficial mutations selected in a laboratory-evolved population of
 Escherichia coli to test how they interact with the genomes of diverse
 natural isolates of the same species. We find that the fitness effect of
 transferred mutations depends weakly on the genetic and ecological
 similarity of recipient strains relative to the donor strain in which the
 mutations were selected. By contrast, mutation effects were strongly
 inversely correlated to the initial fitness of the recipient strain. That
 is, there was a pattern of diminishing returns whereby fit strains
 benefited proportionally less from an added mutation. Our results
 strengthen the view that the fitness of a strain can be a major
 determinant of its ability to adapt. They also support a role for barriers
 of transmission, rather than differential selection of transferred DNA, as
 an explanation of observed phylogenetically determined patterns of
 restricted recombination among E. coli strains.
description: 1_Data_integrationR Script to load input files and collate into a single matched data frame containing fitness, growth rate, and genetic and biolog distance data2_mutation_effect_ANOVAR Script to perform ANOVA to: (i) examine variation in effect of each mutations over strains, (ii) examine variation in average effect of mutations per strain, and (iii) determine average effect of each mutation2a_Recipient strains on Broad phyloR Script to identify engineered strains in context of broader E. coli phylogeny3_PLSregression_&_correlationsScript to perform ANOVA testing for mutation effect variation over different recipient strains and to perform partial least squares (PLS) regression and plot contribution of independent variables to each component4_Phylo_contrastsR script to perform phylogenetic regression and calculate statistics of phylogenetic signalbiologBiolog profiles of engineered strainsfitness_estimatesFitness estimates of engineered strainsgrowth_ratesGrowth rate estimates of parent strains
DOI: 10.5061/dryad.14pp7
title: Data from: Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome

description: The von Hippel-Lindau (VHL) cancer syndrome is associated with mutations
 in the VHL gene. The pVHL protein is involved in response to changes in
 oxygen availability as part of an E3-ligase that targets the
 Hypoxia-Inducible Factor for degradation. pVHL has a molten globule
 configuration with marginal thermodynamic stability. The cancer-associated
 mutations further destabilize it. The Drosophila homolog, dVHL, has
 relatively low sequence similarity to pVHL, and is also involved in
 regulating HIF1-α. Using in silico, in vitro and in vivo approaches we
 demonstrate high similarity between the structure and function of dVHL and
 pVHL. These proteins have a similar fold, secondary and tertiary
 structures, as well as thermodynamic stability. Key functional residues in
 dVHL are evolutionary conserved. This structural homology underlies
 functional similarity of both proteins, evident by their ability to bind
 their reciprocal partner proteins, and by the observation that transgenic
 pVHL can fully maintain normal dVHL-HIF1-α downstream pathways in flies.
 This novel transgenic Drosophila model is thus useful for studying the VHL
 syndrome, and for testing drug candidates to treat it.
description: dVHLModelCoordinate file (PDB format) of the model structure of the Drosophila VHL protein.
DOI: 10.5061/dryad.8s8k6
title: Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.

description: In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene
 situated on chromosome 3H is recognised as an important source of
 resistance to the bymoviruses Barley yellow mosaic virus and Barley mild
 mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4
 and rym5, confer different isolate-specific resistances. In this study the
 sequence of eIF4E was analysed in 1090 barley landraces and non-current
 cultivars originating from 84 countries. An exceptionally high nucleotide
 diversity was evident in the coding sequence of eIF4E but not in either
 the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated
 on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in
 the coding sequence of eIF4E resulted in amino acid changes. A total of 47
 eIF4E haplotypes were identified and phylogenetic analysis using maximum
 likelihood provided evidence of strong positive selection acting on this
 barley gene. The majority of eIF4E haplotypes were found to be specific to
 distinct geographic regions. Furthermore, the eIF4E haplotype diversity
 (uh) was found to be considerably higher in East Asia, whereas SNP
 genotyping identified a comparatively low degree of genome-wide genetic
 diversity in 16 out of 17 tested accessions (each carrying a different
 eIF4E haplotype) from this same region. In addition, selection statistic
 calculations using coalescent simulations showed evidence of non neutral
 variation for eIF4E in several geographic regions, including East Asia,
 the region with a long history of the bymovirus-induced yellow mosaic
 disease. Together these findings suggest eIF4E may play a role in barley
 adaptation to local habitats.
description: SNP
 dataGenome-wide 383 SNP data
 for 70 barley accessions in GenAlex (Peakall & Smouse 2006)
 format
DOI: 10.5061/dryad.nq8h7
title: Data from: The price of associating with breeders in the cooperatively breeding chestnut-crowned babbler: foraging constraints, survival and sociality

description: Understanding the costs of living with breeders might offer new insights
 into the factors that counter evolutionary transitions from selfish
 individuals to cooperative societies. While selection on early dispersal
 is well-understood, it is less clear whether costs are also associated
 with remaining with family members during subsequent breeding; a
 pre-requisite to the evolution of kin-based cooperation. We propose and
 test the hypothesis that living in groups containing breeders is costly
 and that such costs are exacerbated by increasing group size. For example,
 in group-living central-place foragers, group members might suffer from
 resource depletion when foraging in a restricted area during breeding and
 significant costs of repeatedly travelling between foraging patches and
 the site of offspring. Using the cooperatively breeding chestnut-crowned
 babbler (Pomatostomus ruficeps), for which grouping during breeding is
 obligatory, we show that reproduction is associated with substantially
 reduced foraging areas and evidence of resource depletion, particularly in
 larger groups. Such effects largely persisted from the onset of incubation
 through to offspring independence 4-5 months later. All group members,
 irrespective of their breeder or helper status, lost significant body mass
 over this period, and, in males, mass loss was associated with reduced
 inter-annual survival. Although babblers are constrained from living
 outside of breeding groups due to high risks of predation and the poor
 success of breeding without helpers, we suggest that the effects we
 describe may generally select against group-living during breeding
 attempts in species where constraints to independent breeding and costs of
 dispersal are less acute.
description: Group home ranges,
 breeding and non-breedingproviding home range
 sizes of different groups, as well as potential explanatory
 variablesHRs breeding vs
 nonbreeding.csvInsects abundance -
 light-trap samplesInsects.csvranging behaviour_all yeargroup movement data over the entire year and potential predictorsranging behaviour_laying to dependent juvgroup movement data relative to the reproductive period, from egg laying to offspring independenceranging behaviour_ nestinggroup movement data relative to the active nestcondition, survival data-breeders and nonbreedersbody mass and survival data, including potential predictors (e.g sex, breeder vs non-breeder status, group size)
DOI: 10.5061/dryad.28524
title: Data from: Female lizards choose warm, moist nests that improve embryonic survivorship and offspring fitness

description: 1. The fitness consequence of maternal nest-site choice has attracted
 increasing scientific attention, but field studies identifying the
 long-term effects of nest-site choice on offspring survival and
 reproductive success are still rare in vertebrates. 2. To investigate the
 consequences of nest-site choice in lizards, we quantified the thermal and
 hydric conditions of nest sites that were chosen by female toad-headed
 agama (Phrynocephalus przewalskii) in the desert steppe of northern China.
 We also determined the effect of nest-site choice on embryonic development
 and survival and on offspring growth, survival, and maturity by comparing
 the embryos and offspring from maternally and randomly chosen nest sites.
 3. We found that female toad-headed agama chose warm and moist nest sites
 that improved the developmental rate and survivorship of embryos and
 promoted the post-hatching growth, sexual maturity, reproduction, and
 fitness of offspring, thereby improving their reproductive success. 4.
 Such studies on short-lived lizards across multiple stages of embryonic
 and postembryonic ontogeny are critical for fully understanding the
 fitness consequences of nest-site choice.
description: lizard nest environment
 and its influence on hatchling fitnessData of nest site
 selection.xls
DOI: 10.5061/dryad.72403
title: Data from: Evolution of the locomotory system in eels (Teleostei: Elopomorpha)

description: Background Living anguilliform eels represent a distinct clade of
 elongated teleostean fishes inhabiting a wide range of habitats.
 Locomotion of these fishes is highly influenced by the elongated body
 shape, the anatomy of the vertebral column, and the corresponding soft
 tissues represented by the musculotendinous system. Up to now, the
 evolution of axial elongation in eels has been inferred from living taxa
 only, whereas the reconstruction of evolutionary patterns and functional
 ecology in extinct eels still is scarce. Rare but excellently preserved
 fossil eels from the Late Cretaceous and Cenozoic were investigated here
 to gain a better understanding of locomotory system evolution in
 anguilliforms and, consequently, their habitat occupations in deep time.
 Results The number of vertebrae in correlation with the body length
 separates extinct and extant anguilliforms. Even if the phylogenetic
 signal cannot entirely be excluded, the analyses performed here reveal a
 continuous shortening of the vertebral column with a simultaneous increase
 in vertebral numbers in conjunction with short lateral tendons throughout
 the order. These anatomical changes contradict previous hypotheses based
 on extant eels solely. Conclusions The body curvatures of extant
 anguilliforms are highly flexible and can be clearly distinguished from
 extinct species. Anatomical changes of the vertebral column and
 musculotendinous system through time and between extinct and extant
 anguilliforms correlate with changes of the body plan and swimming
 performance and reveal significant shifts in habitat adaptation and thus
 behaviour. Evolutionary changes in the skeletal system of eels established
 here also imply that environmental shifts were triggered by abiotic rather
 than biotic factors (e.g., K/P boundary mass extinction event).
description: Table S1_Pfaff et
 al.Raw data, PCA, PIC,
 Pagel's lambda, Bloombergs-K-value
DOI: 10.15468/dl.t5n5bw
title: Occurrence Download

description: A dataset containing 1581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Pituophis deppei",
 "Year 1960-2026"
 ]
}

 The dataset includes 1581 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000842-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9s3k6
title: Data from: Trans-generational priming of resistance in wild flour beetles reflects the primed phenotypes of laboratory populations and is inhibited by co-infection with a common parasite

description: 1. Trans-generational priming renders offspring of immune-challenged
 parents less susceptible to disease-induced mortality, and has been
 demonstrated in a variety of arthropod taxa under controlled laboratory
 conditions. However, relatively little is known about the applicability of
 these laboratory results to priming in wild populations, especially in the
 context of environmental variables like maternal co-infection and
 potential trade-offs with other life history traits. 2. We performed
 nearly parallel trans-generational priming experiments on laboratory and
 wild strains of Tribolium beetles against the bacterial pathogen Bacillus
 thuringiensis (Bt). We investigated the impact of maternal immune
 challenge on offspring survival and development time, as well as the
 correlation between development and survival by priming status.
 Furthermore, we manipulated wild beetle parental co-infection with a
 gregarine parasite that was prevalent in the wild population in order to
 determine the impact of co-infection on the efficacy of trans-generational
 priming. 3. Trans-generational priming resulted in a large but birth
 order-dependent acceleration of offspring development time, and enhanced
 offspring survival against infection, in both laboratory and wild
 populations. However, adult parental co-infection with gut protozoa
 severely curtailed primed offspring survival against Bt infection. 4.
 These results suggest that shifts in life history traits associated with
 trans-generational priming in laboratory model systems extend to wild
 populations. These traits, including survival, development, and
 interference from co-infection, are important parameters for predicting
 the impact of priming on disease dynamics in the wild.
description: TgenBeetlesWildLab
DOI: 10.5061/dryad.589p0
title: Data from: Managing more than the mean: using quantile regression to identify factors related to large elk groups

description: 1. Animal group size distributions are often right-skewed, whereby most
 groups are small, but most individuals occur in larger groups that may
 also disproportionately affect ecology and policy. In this case, examining
 covariates associated with upper quantiles of the group size distribution
 could facilitate better understanding and management of large animal
 groups. 2. We studied wintering elk groups in Wyoming, where group sizes
 span several orders of magnitude, and issues of disease, predation and
 property damage are affected by larger group sizes. We used quantile
 regression to evaluate relationships between the group size distribution
 and variables of land use, habitat, elk density and wolf abundance to
 identify conditions important to larger elk groups. 3. We recorded 1263
 groups ranging from 1 to 1952 elk and found that across all quantiles of
 group size, group sizes were larger in open habitat and on private land,
 but the largest effect occurred between irrigated and non-irrigated land
 [e.g. the 90th quantile group size increased by 135 elk (95% CI = 42, 227)
 on irrigation]. 4. Only upper quantile group sizes were positively related
 to broad-scale measures of elk density and wolf abundance. For wolf
 abundance, this effect was greater on elk groups found in open habitats
 and private land than those in closed habitats or public land. If we had
 limited our analysis to mean or median group sizes, we would not have
 detected these effects. 5. Synthesis and applications. Our analysis of elk
 group size distributions using quantile regression suggests that private
 land, irrigation, open habitat, elk density and wolf abundance can affect
 large elk group sizes. Thus, to manage larger groups by removal or
 dispersal of individuals, we recommend incentivizing hunting on private
 land (particularly if irrigated) during the regular and late hunting
 seasons, promoting tolerance of wolves on private land (if elk aggregate
 in these areas to avoid wolves) and creating more winter range and varied
 habitats. Relationships to the variables of interest also differed by
 quantile, highlighting the importance of using quantile regression to
 examine response variables more completely to uncover relationships
 important to conservation and management.
description: Elk group sizes and
 covariatesgroups&covariates.csv
DOI: 10.15468/dl.upz7bk
title: Occurrence Download

description: A dataset containing 826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brunfelsia brasiliensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 826 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000843-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.