cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.55724
title: Data from: Sex-specific fitness consequences of nutrient intake and the evolvability of diet preferences

description: The acquisition of nutrients is fundamental for the maintenance of bodily
 functions, growth, and reproduction in animals. As a result, fitness can
 be maximized only when animals are able to direct their attention to foods
 that reflect their current nutritional needs. Despite significant
 literature documenting the fitness consequences of nutrient composition
 and preference, less is known about the underlying genetic architecture of
 the dietary preferences themselves, specifically, the degree to which they
 can respond to selection. We addressed this by integrating evolutionary
 quantitative genetics and nutritional geometry to examine the shape of the
 sex-specific fitness surfaces and the availability of genetic variance for
 macronutrient preferences in the fruit fly Drosophila melanogaster.
 Combining these analyses, we found that the microevolutionary potential of
 carbohydrate and protein preference was above average in this population,
 because the expected direction of selection was relatively well aligned
 with the major axis of the genetic variance-covariance matrix, G. We also
 found that potential exists for sexually antagonistic genetic constraint
 in this system; macronutrient blends maximizing fitness differed between
 the sexes, and cross-sex genetic correlations for their consumption were
 positive. However, both sexes were displaced from their feeding optima,
 generating similar directional selection on males and females, with the
 combined effect being that minimal sex-specific genetic constraints
 currently affect dietary preferences in this population.
description: Experiment_1Individual level consumption of protein and carbohydrate (labeled as Pcons and Ccons in the data file) was measured in which flies where exposed to 1 of 24 diets. Competitive adult fitness assays were then used to estimate male and female fitness (Comp_fitness).Experiment_2Binary choice assay in which flies were given unrestricted access to two different foodstuffs. Individual level consumption of protein and carbohydrates (labeled here as Pcons and Ccons) were estimated. Which inbred line (IL) and replicate vial (Vial) the fly came from, and the fly's sex was also recorder.
DOI: 10.15468/dl.am3yff
title: Occurrence Download

description: A dataset containing 12544 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-114.28970 13.90204,-81.95835 13.90204,-81.95835 26.84593,-114.28970 26.84593,-114.28970 13.90204))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Syrphidae"
 ]
}

 The dataset includes 12544 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000639-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.48vq4
title: Data from: Risso' s dolphins plan foraging dives

description: Humans remember the past and use that information to plan future actions.
 Lab experiments that test memory for the location of food show that
 animals have a similar capability to act in anticipation of future needs,
 but less work has been done on animals foraging in the wild. We
 hypothesized that planning abilities are critical and common in
 breath-hold divers who adjust each dive to forage on prey varying in
 quality, location, and predictability within constraints of limited oxygen
 availability. We equipped Risso &' s dolphins with
 sound-and-motion-recording tags to reveal where they focus their attention
 through their externally observable echolocation and how they fine-tune
 search strategies in response to expected and observed prey distribution.
 The dolphins &' information was integrated with synoptic prey
 data obtained from echosounders on an underwater vehicle. At the start of
 the dives, whales adjusted their echolocation inspection ranges in ways
 that suggest planning to forage at a particular depth. Once entering a
 productive prey layer, dolphins reduced their search range comparable to
 the scale of patches within the layer, suggesting that they were using
 echolocation to select prey within the patch. On ascent, their search
 range increased, indicating that they decided to stop foraging within that
 layer and started searching for prey in shallower layers. Information
 about prey, learned throughout the dive, was used to plan foraging in the
 next dive. Our results demonstrated that planning for future dives was
 modulated by spatial memory derived from multi-modal prey sampling
 (echoic, visual, and capture) during earlier dives.
description: Grampus griseus acoustic
 dataAcoustic data recorded
 from 33 Grampus using Dtags off California, describing foraging and
 communication vocalizations.Grampus_audits.zip
DOI: 10.5061/dryad.t63qq52
title: Data from: Conspicuous plumage does not increase predation risk: a continent-wide test using model songbirds

description: The forces shaping female plumage color have long been debated but remain
 unresolved. Females may benefit from conspicuous colors but are also
 expected to suffer costs. Predation is one potential cost, but few studies
 have explicitly investigated the relationship between predation risk and
 coloration. The fairy-wrens show pronounced variation in female coloration
 and reside in a wide variety of habitats across Australasia. Species with
 more conspicuous females are found in denser habitats, suggesting that
 conspicuousness in open habitat increases vulnerability to predators. To
 test this, we measured attack rates on 3D printed models mimicking
 conspicuously colored males and females, and dull females, in eight
 different fairy-wren habitats across Australia. Attack rates were higher
 in open habitats, and at higher latitudes. Contrary to our predictions,
 dull female models were attacked at similar rates to the conspicuous
 models. Further, the probability of attack in open habitats increased more
 for both types of female model than for the conspicuous male model. Across
 models, the degree of contrast (chromatic and achromatic) to environmental
 backgrounds was unrelated to predation rate. These findings do not support
 the long-standing hypothesis that conspicuous plumage, in isolation, is
 costly due to increased attraction of predators. Our results indicate that
 conspicuousness interacts with other factors in driving the evolution of
 plumage coloration.
description: PlumagePredationDataDryad-uploadValues used in analyses for published results of main articleSiteAverages-dryad uploadSite averages used in Figures.
DOI: 10.5061/dryad.s1d18
title: Data from: No release for the wicked: enemy release is dynamic and not associated with invasiveness

description: The enemy release hypothesis predicts that invasive species will receive
 less damage from enemies, compared to co-occurring native and noninvasive
 exotic species in their introduced range. However, release operating early
 in invasion could be lost over time and with increased range size as
 introduced species acquire new enemies. We used three years of data, from
 61 plant species planted into common gardens, to determine whether (1)
 invasive, noninvasive exotic, and native species experience differential
 damage from insect herbivores and mammalian browsers, and (2) enemy
 release is lost with increased residence time and geographic spread in the
 introduced range. We find no evidence suggesting enemy release is a
 general mechanism contributing to invasiveness in this region. Invasive
 species received the most insect herbivory, and damage increased with
 longer residence times and larger range sizes at three spatial scales. Our
 results show that invasive and exotic species fail to escape enemies,
 particularly over longer temporal and larger spatial scales.
description: README Schultheis
 Berardi LauREADME file with
 metadata to accompany data files.Dryad_Data_FullExperimental data file.damageExperimental data file to be used with R code.R code for Dryad phylogenyR code for paper analysis
DOI: 10.5061/dryad.rj083bv
title: Data from: Combining fish and benthic communities into multiple regimes reveals complex reef dynamics

description: Coral reefs worldwide face an uncertain future with many reefs reported to
 transition from being dominated by corals to macroalgae. However, given
 the complexity and diversity of the ecosystem, research on how regimes
 vary spatially and temporally is needed. Reef regimes are most often
 characterised by their benthic components; however, complex dynamics are
 associated with losses and gains in both fish and benthic assemblages. To
 capture this complexity, we synthesised 3,345 surveys from Hawai‘i to
 define reef regimes in terms of both fish and benthic assemblages.
 Model-based clustering revealed five distinct regimes that varied
 ecologically, and were spatially heterogeneous by island, depth and
 exposure. We identified a regime characteristic of a degraded state with
 low coral cover and fish biomass, one that had low coral but high fish
 biomass, as well as three other regimes that varied significantly in their
 ecology but were previously considered a single coral dominated regime.
 Analyses of time series data reflected complex system dynamics, with
 multiple transitions among regimes that were a function of both local and
 global stressors. Coupling fish and benthic communities into reef regimes
 to capture complex dynamics holds promise for monitoring reef change and
 guiding ecosystem-based management of coral reefs.
description: Hawaii_regimesHawaii_regimes.csv is a comma-separated file containing data used to define reef regimes for the Hawaii Islands. The file includes metadata for 1027 replicates, 10 reef community metrics used to define regimes in a cluster analysis, and the resulting reef regime. Reef community metrics are averages of individual replicates grouped based on spatial proximity. Details of the analysis can be found in the accompanying publication. Parties interested in using this data for other purposes are asked to contact Mary Donovan (donovan.maryk@gmail.com).Hawaii_regime_timeseries_Hawaii_regime_timeseries.csv is a comma-separated file containing data used to investigate changes in regimes over time. The file includes metadata for 1279 replicates across multiple years, 10 reef community metrics used to define regimes in a cluster analysis, and the geographic location of the replicate. Details of the analysis can be found in the accompanying publication. Parties interested in using this data for other purposes are asked to contact Mary Donovan (donovan.maryk@gmail.com).Hawaii_regime_driversHawaii_regime_drivers.csv is a comma-separated file containing data used to understand relationships between regime transitions and local and global drivers. The file includes data on human population density and degree heating weeks for each replicate found in Hawaii_regime_timeseries.csv. Details of the analysis can be found in the accompanying publication. Parties interested in using this data for other purposes are asked to contact Mary Donovan (donovan.maryk@gmail.com).
DOI: 10.5281/zenodo.18237798
title: CARE checklist for: [An Unusual Case of Idiopathic Pulmonary Hemosiderosis in a School Aged Nepali Girl]

description: This file contains the completed CARE checklist for the case report titled“[An Unusual Case of Idiopathic Pulmonary Hemosiderosis in a School Aged Nepali Girl]”, submitted to Wellcome Open Research.
DOI: 10.5281/zenodo.18381936
title: CARE checklist for: [An Unusual Case of Idiopathic Pulmonary Hemosiderosis in a School Aged Nepali Girl]

description: This file contains the completed CARE checklist for the case report titled“[An Unusual Case of Idiopathic Pulmonary Hemosiderosis in a School Aged Nepali Girl]”, submitted to Wellcome Open Research.
DOI: 10.5061/dryad.g753g
title: Data from: Genotype-by-environment interactions underlie the expression of pre- and postcopulatory sexually selected traits in guppies

description: The role that genotype-by-environment interactions (GEIs) play in sexual
 selection has only recently attracted the attention of evolutionary
 biologists. Yet GEIs can have profound evolutionary implications by
 compromising the honesty of sexual signals, maintaining high levels of
 genetic variance underlying their expression, and altering patterns of
 genetic covariance among fitness traits. In this study, we test for GEIs
 in a highly sexually dimorphic freshwater fish, the guppy Poecilia
 reticulata. We conducted an experimental quantitative genetic study in
 which male offspring arising from a paternal half-sibling breeding design
 were assigned to differing nutritional ‘environments’ (either high or low
 feed levels). We then determined whether the manipulation of diet quantity
 influenced levels of additive genetic variance and covariance for several
 highly variable and condition-dependent pre- and postcopulatory sexual
 traits. In accordance with previous work, we found that dietary limitation
 had strong phenotypic effects on numerous pre- and postcopulatory sexual
 traits. We also report evidence for significant GEI for several of these
 traits, which in some cases (area of iridescence and sperm velocity)
 reflected a change in the rank order of genotypes across different
 nutritional environments (i.e. ecological crossover). Furthermore, we show
 that genetic correlations vary significantly between nutritional
 environments. Notably, a highly significant negative genetic correlation
 between iridescent colouration and sperm viability in the high food
 treatment broke down under dietary restriction. Taken together, these
 findings are likely to have important evolutionary implications for
 guppies; ecological crossover may influence sexual signal reliability in
 unstable (nutritional) environments and contribute towards the extreme
 levels of polymorphism in sexual traits typically reported for this
 species. Furthermore, the presence of environment-specific genetic
 covariance suggests that trade-offs measured in one environment may not be
 indicative of genetic constraints in others.
description: Evans et al. JEB
 2015Please see paper for
 details on data collection and experimental design.
DOI: 10.15468/dl.9d79xf
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arenga pinnata",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 82 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000640-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r51j7
title: Data from: Flickers of speciation? Sympatric color morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence-with-gene-flow

description: One of the primary challenges of evolutionary research is to identify
 ecological factors that favor reproductive isolation. Therefore, studying
 partially isolated taxa has the potential to provide novel insight into
 the mechanisms of evolutionary divergence. Our study utilizes an adaptive
 color polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to
 explore the evolution of reproductive barriers in the absence of
 geographic isolation. Dark and light morphs are ecologically partitioned
 into basaltic and coral microhabitats a few meters apart. To test whether
 ecological barriers have reduced gene flow among dark and light
 phenotypes, we evaluated genetic variation at 30 microsatellite loci and a
 nuclear exon (Mc1r) associated with melanistic coloration. We report low,
 but significant microsatellite differentiation among color morphs and
 stronger divergence in the coding region of Mc1r indicating signatures of
 selection. Critically, we observed greater genetic divergence between
 color morphs on the same reefs than between the same morphs in different
 geographic locations. We hypothesize that adaptation to the contrasting
 microhabitats is overriding gene flow and is responsible for the partial
 reproductive isolation observed between sympatric color morphs. Combined
 with complementary studies of hawkfish ecology and behavior, these genetic
 results indicate an ecological barrier to gene flow initiated by habitat
 selection and enhanced by assortative mating. Hence the arc-eye hawkfish
 fulfill theoretical expectations for the earliest phase of
 speciation-with-gene-flow.
description: LocationInformation-MicrosatelliteGenotypesSampling locations, morphological data and microsatellite genotypes for 264 Paracirrhites arcatus individuals from Hawaii Island (USA). Microsatellite loci gen bank accession#JN886952-JN886989.MicrosatelliteGenotypes_264ind_Parcatus_GenePop-formatMicrosatellite genotypes in GenePop file format (3 digit alleles), 000 = missing. 30 microsatellite loci, 264 individuals.HabitatVariables_Hawaii_Parcatus_2morphs_100indUsed for environmental variables in distance-based redundancy analysis. Habitat variables for 100 Paracirrhites arcatus individuals of two color morphs collected on Hawaii Island 2010.GeneticDistanceMatrix_Euclidean_Hawaii_Parcatus_2morphs_100indGenetic distance matrix (Euclidean distances) for distance-based redundancy analysis, calculated in Genodive using 30 microsatellite genotypes of 100 Paracirrhites arcatus (2 color morphs) from Hawaii Island.
DOI: 10.5061/dryad.69mk7
title: Data from: Antibody selection and amino acid reversions

description: Pathogens adapt to antibody surveillance through amino acid replacements
 in targeted protein regions, or epitopes, that interfere with antibody
 binding. However, such escape mutations may exact a fitness cost due to
 impaired protein function. Here, it is hypothesised that the recurring
 generation of specific neutralising antibodies to an epitope region as it
 evolves in response to antibody selection will cause amino acid reversions
 by releasing early escape mutations from immune selection. The
 plausibility of this hypothesis was tested with stochastic simulation of
 adaptation at the molecular sequence level in finite populations. Under
 the conditions of strong selection and weak mutation, the rates of allele
 fixation and amino acid reversion increased with population size and
 selection coefficients. These rates decreased with population size,
 however, if mutation became strong, because clonal interference reduced
 the rate of adaptation. The model successfully predicts the rate of
 reversion per allele fixation for an important human immunodeficiency
 virus type 1 (HIV-1) antibody epitope region. Therefore, antibody
 selection may generate complex adaptive dynamics.
description: epitope12Fortran 95 computer code used for simulations.samplesText file of amino acid sequences from HIV-1 V3. Sequences are organised by the patient from which they were sampled. Preceding the set of samples from each patient is the number of sequence samples for the patient and then the year (e.g. 1988 is "88") and the number of sequences for each sample. This is followed by the sequences in FastA format; sequences are labelled with the patient number and the year of the sample.
DOI: 10.5061/dryad.296h2
title: Data from: Energetic benefits and adaptations in mammalian limbs: scale effects and selective pressures

description: Differences in limb size and shape are fundamental to mammalian
 morphological diversity; however, their relevance to locomotor costs has
 long been subject to debate. In particular, it remains unknown if scale
 effects in whole limb morphology could partially underlie decreasing
 mass-specific locomotor costs with increasing limb length. Whole fore- and
 hindlimb inertial properties reflecting limb size and shape – moment of
 inertia (MOI), mass, mass distribution, and natural frequency – were
 regressed against limb length for 44 species of quadrupedal mammals. Limb
 mass, MOI, and center of mass position are negatively allometric, having
 strong potential for lowering mass-specific locomotor costs in large
 terrestrial mammals. Negative allometry of limb MOI results in a 40%
 reduction in MOI relative to isometry for our largest sampled taxa.
 However, fitting regression residuals to adaptive diversification models
 reveals that co-diversification of limb mass, limb length, and body mass
 likely results from selection for differing locomotor modes of running,
 climbing, digging, and swimming. The observed allometric scaling does not
 result from selection for energetically beneficial whole limb morphology
 with increasing size. Instead, our data suggest that it is a consequence
 of differing morphological adaptations and body size distributions among
 quadrupedal mammals, highlighting the role of differing limb functions in
 mammalian evolution.
description: Limb Inertial Properties
 of Individual Limbs from Sampled MammalsSpreadsheet containing
 data on limb mass, length, center of mass position, moment of inertia,
 natural frequency, and radius of gyration of individual limbs for each
 specimen sampled. Within the file, 'COM' denotes center of mass
 position, 'MOI' denotes moment of inertia, 'NF'
 denotes natural frequency, and 'RG' denotes radius of gyration.
 'Rel. COM' denotes the relative center of mass position, the
 center of mass position expressed as a percentage of limb length.
 Likewise, 'Rel. RG' denotes relative radius of gyration, the
 radius of gyration expressed as a percentage of limb
 length.Limb_Inertial_Properties_All_Individuals.xlsMean Values of Limb Inertial Properties for Sampled SpeciesSpreadsheet containing mean values of inertial properties for each sampled species, in addition to mean values of body mass. These values were used in our analyses. Within the file, 'COM' denotes center of mass position, 'MOI' denotes moment of inertia, 'NF' denotes natural frequency, and 'RG' denotes radius of gyration. 'Rel. COM' denotes the relative center of mass position, the center of mass position expressed as a percentage of limb length. Likewise, 'Rel. RG' denotes relative radius of gyration, the radius of gyration expressed as a percentage of limb length.Limb_Inertial_Properties_Species_Means.xls