cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d8ts9
title: Data from: Environmental variation partitioned into separate heritable components

description: Trait variation is normally separated into genetic and environmental
 components, yet genetic factors also control the expression of
 environmental variation, encompassing plasticity across environmental
 gradients and within-environment responses. We defined four components of
 environmental variation: plasticity across environments, variability in
 plasticity, variation within environments, and differences in
 within-environment variation across environments. We assessed these
 components for cold tolerance across five rearing temperatures using the
 Drosophila melanogaster Genetic Reference Panel (DGRP). The four
 components were found to be heritable, and genetically correlated to
 different extents. By whole genome single marker regression, we detected
 multiple candidate genes controlling the four components and showed
 limited overlap in genes affecting them. Using the binary UAS-GAL4 system,
 we functionally validated the effects of a subset of candidate genes
 affecting each of the four components of environmental variation and also
 confirmed the genetic and phenotypic correlations obtained from the DGRP
 in distinct genetic backgrounds. We delineate selection targets associated
 with environmental variation and the constraints acting upon them,
 providing a framework for evolutionary and applied studies on
 environmental sensitivity. Based on our results we suggest that the
 traditional quantitative genetic view of environmental variation and
 genotype-by-environment interactions needs revisiting.
description: Supporting Table
 S1Line mean, standard
 error and number of replicates per trait for all DGRP
 linesSupplementary_Table_S1.xlsxSupporting Table S4Top SNPs associated with V(plast), V(v.plast), V(WE), and V(AE)Supplementary_Table_S4.xlsxOriginal CTmin dataCTmin for all five thermal rearing environments (17, 20, 23, 26, and 29 °C), with the grouping of each observation due to experimental factors, and with the indication of five major chromosomal inversions and Wolbachia infection statusevo_13391_data.csv
DOI: 10.5061/dryad.04pj7
title: Data from: Contrasting patterns of X-chromosome divergence underlie multiple sex-ratio polymorphisms in stalk-eyed flies

description: Sex-linked segregation distorters cause offspring sex ratios to differ
 from equality. Theory predicts that such selfish alleles may either go to
 fixation and cause extinction, reach a stable polymorphism, or initiate an
 evolutionary arms race with genetic modifiers. The extent to which a sex
 ratio distorter follows any of these trajectories in nature is poorly
 known. Here we used X-linked sequence and simple tandem repeat data for
 three sympatric species of stalk-eyed flies (Teleopsis whitei and two
 cryptic species of T. dalmanni) to infer the evolution of distorting X
 chromosomes. By screening large numbers of field and recently lab-bred
 flies we found no evidence of males with strongly female-biased sex ratio
 phenotypes (SR) in one species but high frequencies of SR males in the
 other two species. In the two species with SR males, we find contrasting
 patterns of X chromosome evolution. T. dalmanni - 1 shows chromosome-wide
 differences between sex-ratio (XSR) and standard (XST) X chromosomes
 consistent with a relatively old sex-ratio haplotype based on evidence
 including genetic divergence, an inversion polymorphism, and reduced
 recombination among XSR chromosomes relative to XST chromosomes. In
 contrast, we found no evidence of genetic divergence on the X between
 males with female-biased and non-biased sex ratios in T. whitei. Taken
 with previous studies that found evidence of genetic suppression of sex
 ratio distortion in this clade, our results illustrate that sex ratio
 modification in these flies is undergoing recurrent evolution with diverse
 genomic consequences.
description: Stalk Eyed Flies SR
 Genotyping PhenotypingContains offspring sex
 ratio phenotype data and X-linked STR genotype data for stalk-eyed flies
 (Teleopsis dalmanni and Teleopsis whitei). Also includes X-linked STR
 genotype data for a series of crosses in Teleopsis dalmanni used to make a
 genetic map of the X-chromosome.Teleopsis Sequence
 AlignmentsDRYAD_alignments_paczolt_2017.zip
DOI: 10.5061/dryad.1c990
title: Data from: Host-pathogen metapopulation dynamics suggest high elevation refugia for boreal toads

description: Emerging infectious diseases are an increasingly common threat to
 wildlife. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium
 dendrobatidis (Bd), is an emerging infectious disease that has been linked
 to amphibian declines around the world. Few studies exist that explore
 amphibian-Bd dynamics at the landscape scale, limiting our ability to
 identify which factors are associated with variation in population
 susceptibility and to develop effective in situ disease management.
 Declines of boreal toads (Anaxyrus boreas boreas) in the Southern Rocky
 Mountains are largely attributed to chytridiomycosis but variation exists
 in local extinction of boreal toads across this metapopulation. Using a
 large-scale historic dataset, we explored several potential factors
 influencing disease dynamics in the boreal toad-Bd system: geographic
 isolation of populations, amphibian community richness, elevational
 differences, and habitat permanence. We found evidence that boreal toad
 extinction risk was lowest at high elevations where temperatures may be
 sub-optimal for Bd growth and where small boreal toad populations may be
 below the threshold needed for efficient pathogen transmission. In
 addition, boreal toads were more likely to recolonize high elevation sites
 after local extinction, again suggesting that high elevations may provide
 refuge from disease for boreal toads. We illustrate a modeling framework
 that will be useful to natural resource managers striving to make
 decisions in amphibian-Bd systems. Our data suggest that in the southern
 Rocky Mountains high elevation sites should be prioritized for
 conservation initiatives like reintroductions.
description: boreal_toad_bd_historiesEncounter histories for boreal toads and Bd at 83 sites in the southern Rocky Mountains. Data are for 10 visits for each species from 2001-2010. Encounters are coded as 1s when boreal toads or Bd were detected, 0s if these species were not detected, and "." if no survey was conducted.boreal_toad_bd_covariatesSite and survey covariate information for 83 study sites in the southern Rocky Mountains and 100 survey dates. Site covariates include: elevation, habitat permanence, whether other amphibian species had been detected at the site in the past, and which region the site is located in. The only survey covariate used was day-of-year that the survey was conducted on.
DOI: 10.5061/dryad.dc1q8
title: Data from: Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska

description: For pathogens that infect multiple species the distinction between
 reservoir hosts and spillover hosts is often difficult. In Alaska, three
 variants of the arctic rabies virus exist with distinct spatial
 distributions. We test the hypothesis that rabies virus variant
 distribution corresponds to the population structure of the primary rabies
 hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (V. vulpes)
 in order to possibly distinguish reservoir and spill over hosts. We used
 mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess
 population structure in those two species. mtDNA structure did not
 correspond to rabies virus variant structure in either species.
 Microsatellite analyses gave varying results. Bayesian clustering found 2
 groups of arctic foxes in the coastal tundra region, but for red foxes it
 identified tundra and boreal types. Spatial Bayesian clustering and
 spatial principal components analysis identified 3 and 4 groups of arctic
 foxes, respectively, closely matching the distribution of rabies virus
 variants in the state. Red foxes, conversely, showed eight clusters
 comprising 2 regions (boreal and tundra) with much admixture. These
 results run contrary to previous beliefs that arctic fox show no
 fine-scale spatial population structure. While we cannot rule out that the
 red fox is part of the maintenance host community for rabies in Alaska,
 the distribution of virus variants appears to be driven primarily by the
 artic fox Therefore we show that host population genetics can be utilized
 to distinguish between maintenance and spillover hosts when used in
 conjunction with other approaches.
description: Goldsmith et al fox
 dataDNA sequence data and
 microsatellite genotypes for red and arctic foxes, a Newick tree file of
 rabies virus variants from Alaska, and two Arlequin project files for data
 analysis.Goldsmith_et_al_fox_data_12_15.zip
DOI: 10.5061/dryad.p85q4
title: Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size

description: Lithification, the transition of unconsolidated sediments to fully
 indurated rocks, can potentially bias estimates of species richness,
 evenness, and body size distribution derived from fossil assemblages.
 Fossil collections made from well-indurated rocks consistently exhibit
 lower species richness, lower evenness, and a specimen size distribution
 skewed towards larger specimens relative to collections made from
 unconsolidated sediments, even when collections are drawn from the same
 assemblage. This phenomenon is known as the lithification bias. While the
 bias itself has been demonstrated empirically, much less attention has
 been paid to its causes. Proposed causes include taphonomic processes
 (e.g., destruction of small specimens during early diagenesis) or
 methodological differences (e.g., sieving vs. counting specimens on
 outcrops, bedding surfaces, or mechanically split surfaces). Here we
 investigate the potential effects of preferential intersection that could
 also result in a methodologically related bias: the preferential sampling
 of larger specimens relative to smaller ones when fossils are counted on
 rock surfaces. We used an analog model to simulate preferential
 intersection (fossil collection via splitting fossiliferous rock) and
 compare the results to a random draw model that approximates the effects
 of sieving. The model was parameterized using nine different combinations
 of species abundance and species size distributions. The results show
 that, with rare exceptions, species richness is 5–23% lower, evenness
 5-25% lower, and average specimen size 24–150% higher in preferential
 intersection than in random draw simulations. We conclude that
 preferential intersection can impose a significant bias independent of
 other mechanisms (e.g., preferential destruction of smaller specimens
 during diagenetic or sampling processes), that the magnitude of this bias
 is partially dependent on the species abundance and size distributions,
 and that this bias alone does not fully account for empirically observed
 lithification bias on species richness (i.e., other sources of bias are
 also at work).
description: Matlab code and input
 datasets used for analysisThis file contains the
 Matlab code in association with the Hawkins et al. paper entitled
 "Breaking down the lithification bias: The effect of preferential
 sampling of larger specimens on the estimate of species richness,
 evenness, and average specimen size"Revision_SupplementalData.docxDryadSubmissionZippedThis is a zipped file containing the Matlab code in association with the Hawkins et al. paper entitled "Breaking down the lithification bias: The effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size"Supplementary Appendices I and IISupplementaryAppendices.docxSupplementaryAppendices.txt
DOI: 10.5061/dryad.d1c18
title: Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)

description: Coral reef fishes represent one of the most spectacularly diverse
 assemblages of vertebrates on the planet, but our understanding of their
 mode of diversification remains limited. Here we test whether the
 diversity of the damselfishes (Pomacentridae), one of the most
 species-rich families of reef-associated fishes, was produced by a single
 or multiple adaptive radiation(s) during their evolutionary history. Tests
 of the tempo of lineage diversification using a time-calibrated phylogeny
 including 208 species revealed that crown pomacentrid diversification has
 not slowed through time as expected under a scenario of a single adaptive
 radiation resulting from an early burst of diversification. Evolutionary
 modeling of trophic traits similarly rejected the hypothesis of early
 among-lineage partitioning of ecologically important phenotypic diversity.
 Instead, damselfishes are shown to have experienced iterative convergent
 radiations wherein subclades radiate across similar trophic strategies
 (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies.
 Regionalization of coral reefs, competition, and functional constraints
 may have fueled iterative ecological radiation and convergent evolution of
 damselfishes. Through the Pomacentridae, we illustrate that radiations may
 be strongly structured by the nature of the constraints on
 diversification.
description: TableS1List of studied species, with their ecological classifications (diet and farming behaviors) and their maximum standard length (SL). The origin of dissected specimens and Genbank number are also provided.TableS2Model specific parameters for best-fitting models to each morphological trait. In cases where there were multiple best-fitting models (∆AIC &lt; 2), parameters for all models are given.TableS3AIC scores and weights, and model specific parameters for models fitted to mandible and premaxilla shape data while accounting for measurement error.TableS4Results from multivariate analysis of variance (MANOVA) of shape across the three ecotypes of each major subclade (i.e. “Stegastinae + Lepidozigynae + Chrominae”, Abudefdufinae and Pomacentrinae).Figure_S1Consensus phylogenetic tree of damselfishes. Node numbers indicate posterior probabilities.Figure_S2TPS deformation grids depicting shape variation of (A) the mandible and (B) the premaxilla explained by the first three relative warps (minimal (-RW) and maximal (+RW) values)).Figure_S3Levels of shape disparity (Mean ± SE) within the main subclades of Pomacentridae. Letters refer to subclades: S, Stegastinae; L, Lepidoziginae; A, Abudefdufinae; C, Chrominae; P, Pomacentrinae.AppendixS1Descriptions of methods for molecular analyses and phylogenetic reconstruction.AppendixS2Descriptions of methods for modeling of trait evolution while accounting for measurement error and related major conclusions.
DOI: 10.5061/dryad.19np6
title: Data from: Sediment and turbidity associated with offshore dredging increase coral disease prevalence on nearby reefs

description: In recent decades, coral reef ecosystems have declined to the extent that
 reefs are now threatened globally. While many water quality parameters
 have been proposed to contribute to reef declines, little evidence exists
 conclusively linking specific water quality parameters with increased
 disease prevalence in situ. Here we report evidence from in situ coral
 health surveys confirming that chronic exposure to dredging-associated
 sediment plumes significantly increase the prevalence of white syndromes,
 a devastating group of globally important coral diseases. Coral health
 surveys were conducted along a dredging-associated sediment plume gradient
 to assess the relationship between sedimentation, turbidity and coral
 health. Reefs exposed to the highest number of days under the sediment
 plume (296 to 347 days) had two-fold higher levels of disease, largely
 driven by a 2.5-fold increase in white syndromes, and a six-fold increase
 in other signs of compromised coral health relative to reefs with little
 or no plume exposure (0 to 9 days). Multivariate modeling and ordination
 incorporating sediment exposure level, coral community composition and
 cover, predation and multiple thermal stress indices provided further
 confirmation that sediment plume exposure level was the main driver of
 elevated disease and other compromised coral health indicators. This study
 provides the first evidence linking dredging-associated sedimentation and
 turbidity with elevated coral disease prevalence in situ. Our results may
 help to explain observed increases in global coral disease prevalence in
 recent decades and suggest that minimizing sedimentation and turbidity
 associated with coastal development will provide an important management
 tool for controlling coral disease epizootics.
description: Prevalence of coral
 health and coverPrevalence of coral
 health and coverCoral_health_and_cover.xlsx
DOI: 10.5061/dryad.r11c0
title: Data from: Photosynthetic acclimation to warming in tropical forest tree seedlings

description: Tropical forests have a mitigating effect on man-made climate change by
 acting as a carbon sink. For that effect to continue, tropical trees will
 have to acclimate to rising temperatures, but it is currently unknown
 whether they have this capacity. We grew seedlings of three tropical tree
 species over a range of temperature regimes (TGrowth = 25, 30, 35 °C) and
 measured the temperature response of photosynthetic CO2 uptake. All
 species showed signs of acclimation: the temperature-response curves
 shifted, such that the temperature at which photosynthesis peaked (TOpt)
 increased with increasing TGrowth. However, although TOpt shifted, it did
 not reach TGrowth at high temperature, and this difference between TOpt
 and TGrowth increased with increasing TGrowth, indicating that plants were
 operating at supra-optimal temperatures for photosynthesis when grown at
 high temperatures. The high-temperature CO2 compensation point did not
 increase with TGrowth. Hence, temperature-response curves narrowed with
 increasing TGrowth. TOpt correlated with the ratio of the RuBP
 regeneration capacity over the RuBP carboxylation capacity, suggesting
 that at high TGrowth photosynthetic electron transport rate associated
 with RuBP regeneration had greater control over net photosynthesis. The
 results show that although photosynthesis of tropical trees can acclimate
 to moderate warming, carbon gain decreases with more severe warming.
description: SlotWinter_Photosynthesis_TemperatureResponseRaw temperature-response data of net photosynthesis of seedlings of three tropical tree species grown at three different temperature regimesSlotWinter_RespirationDark respiration rate and the temperature-sensitivity of dark respiration (Q10) for seedlings of three tropical tree species grown at 3 different temperatures.SlotWinter_RGRRelative growth rate data for three species grown at 3 different temperature regimesSlotWinter_VcmaxJmaxCalculated maximum rates of RuBP carboxylation (Vcmax) and RuBP regeneration (Jmax) for seedlings of three tropical tree species grown at three different temperature regimes
DOI: 10.6084/m9.figshare.31160614
title: Purcell-enhanced two-photon emission from a quantum dot via dark-state biexciton loading

description: Source data in .xlsx format for preparing the figures in the main text.
DOI: 10.6084/m9.figshare.31160614.v1
title: Purcell-enhanced two-photon emission from a quantum dot via dark-state biexciton loading

description: Source data in .xlsx format for preparing the figures in the main text.
DOI: 10.5281/zenodo.15376261
title: Phylogenomics unveil recent origin of morphological complexity in Coleochaetophyceae Dataset

description: Phylogenomics on Coleochaetophyceae: Assemblies, SuperTranscripts, BUSCO, Transdecoder, Decontamination, Orthofinder, OSG, PhyloPyPruner, COGS, Prequal, and concatenated Alignment.
DOI: 10.5281/zenodo.15881357
title: Phylogenomics unveil recent origin of morphological complexity in Coleochaetophyceae Dataset

description: Phylogenomics on Coleochaetophyceae: Assemblies, SuperTranscripts, BUSCO, Transdecoder, Decontamination, Orthofinder, OSG, PhyloPyPruner, COGS, Prequal, and concatenated Alignment.
DOI: 10.5061/dryad.mb342
title: Data from: Macronutrient signature of dietary generalism in an ecologically diverse primate in the wild

description: A question of considerable importance is why some animals are able to
 succeed on a wide range of diets while others are more tightly
 constrained. Theory predicts that generalists should show a flexible
 response for macronutrient acquisition in the face of ecologically-driven
 constraint on the nutritional balance of available foods, which in the
 modelling framework of nutritional geometry has been quantitatively
 characterized as an “equal distance” regulatory model. This prediction,
 which has empirical support from several laboratory studies on insects,
 has not been tested for any generalist animal in the wild, nor for any
 vertebrate. We performed the first such test, using 281 dawn-to-dusk focal
 animal observations over three years (2013-2015) of Rhesus macaques
 monkeys (Macaca mulatta tcheliensis), a primate that is second only to
 humans in ecological generalism. Results showed, as predicted, that
 macronutrient regulation conformed closely to the equal distance pattern,
 and differed markedly from the other, ecologically more-specialized
 primate species that have been studied to date. The same was independently
 true for lactating and non-lactating macaques, but lactating females had
 substantially higher intake of macronutrients, as well as the
 non-nutritional food components, indigestible fiber and tannins. This
 demonstrates that equal distance regulation by non-lactating monkeys was
 not an artefact of constraint such as restricted food availability or an
 upper limit to the ingestion of dietary fiber or plant tannins, but a
 strategic regulatory response to variation in dietary macronutrient
 balance. We discuss implications of our results for the most generalist
 primate of all, humans.
description: % of 3 year mean in AP,
 NP and TEPercentage of 3-year
 means for protein, non-protein energy and total energy intake in
 springNon-nutritional
 factorsSpring intakes of
 non-digestible fiber and tanninNutrients and energy
 intake in spring ACROSS 3 YEARSAbsolute macronutrient
 and energy spring intakes in 2013, 2014 and 2015Nutrient and energy intake in
 spring across 3 years.
 Final.xlsxSeeds density and
 contributions to diets on a dry metters basisAvailability estimates
 and intake measures of seeds over 24 monthsSeed density and contributions
 to diets Final.xlsx