cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k36n4
title: Data from: Paternal personality and social status influence offspring activity in zebrafish

description: Background: Evidence for the transmission of non-genetic information from
 father to offspring is rapidly accumulating. While the impact of chemical
 and physical factors such as toxins or diet on the fitness of the parents
 and their offspring have been studied extensively, the importance of
 behavioural and social circumstances has only recently been recognised.
 Behavioural traits such as personality characteristics can be relatively
 stable, and partly comprise a genetic component but we know little about
 the non-genetic transmission of plastic behavioural traits from parents to
 offspring. We investigated the relative effect of personality and of
 social dominance as indicators at the opposite ends of the plasticity
 range on offspring behaviour in the zebrafish (Danio rerio). We assessed
 male boldness, a behavioural trait that has previously been shown
 previously to possess genetic underpinnings, and experimentally
 manipulated male social status to assess the association between the two
 types of behaviour and their correlation with offspring activity. Results:
 We found a clear interaction between the relatively stable and putative
 genetic effects based on inherited differences in personality and the
 experimentally induced epigenetic effects from changes in the social
 status of the father on offspring activity. Conclusions: Our study shows
 that offspring behaviour is determined by a combination of paternal
 personality traits and non-genetic effects derived from the social status
 of the father.
description: DominanceStatusDominance status for each male over both experimental rounds.MalePCsData from PCAs to combine behavioural parametersOffspringActivityRaw data on offspring activity from video recordingsReadMe Zajitschek etal BMCEvolBiol 2017Information in data filters appliedSpermLongevityData on sperm longevity for each maleSpermMotilityData on sperm motility (% motile sperm ) for all malesSpermVelocityData on sperm velocity (VCL, VSL, VAP etc.) for all males
DOI: 10.5061/dryad.m457d
title: Data from: DNA taxonomy in the timber genus Milicia: evidence of unidirectional introgression in the West African contact zone

description: DNA-based techniques are helpful in characterising hybridisation patterns
 in plant species. To be efficient in disentangling species boundaries and
 interspecific gene flow, it is recommended to combine various
 methodologies and types of markers. Here, we used different analytical
 tools (algorithms implemented in Structure, Tess, NewHybrids and HIest,
 and the haploweb approach) and three nuclear genetic markers (7 nuclear
 simple sequence repeat loci (SSRs), 62 single-nucleotide polymorphism loci
 (SNPs) and a single-copy gene region, At103) to revisit hybridisation
 patterns in the commercially important African tree genus Milicia. Samples
 were collected in the natural ranges of Milicia regia and Milicia excelsa
 in West Africa. Using real data sets, simulated purebreds and hybrid
 genotypes, we found that SNPs yielded results more consistent than SSRs;
 outputs from the Bayesian and maximum-likelihood analyses differed
 significantly using the SSRs, whereas they were perfectly congruent using
 SNPs. A proportion of 12.4% hybrids were detected amongst the SNP genotype
 samples. A haploweb analysis of At103 gene sequences confirmed the
 existence of interspecific hybrids. There was also a clear evidence of
 advanced generations of hybrids (backcrossed individuals) but only towards
 M. regia. Although more investigation is required for understanding the
 mechanisms responsible for this asymmetric introgression, we suggest that
 it may be due to the differences in flowering time between species and
 between sexes, combined with a maternal inheritance of flowering time.
description: Chromatograms of
 length-variant heterozygotes in Milicia at At103This Sequencher file
 contains, for each length-variant heterozygote, (i) the forward and
 reverse At103 chromatograms which were assembled into contigs: the double
 peaks were called either using the "Call secondary function" or
 manually; (ii) the two haplotypes (a and b) reconstructed by combining the
 information carried by the forward and reverse chromatograms using the
 program Champuru (http://jfflot.mnhn.fr/champuru/). These samples of the
 genus Milicia were sequenced at the nuclear region
 At103.At103MiliciaLVHchromato.SPFSNP_and_SSR_Milicia_genotypesThis file presents the genotypes (at 7 nuclear SSR and 62 nuclear SNP) of Milicia samples collected in West Africa.
DOI: 10.17632/7vd77m6rnw
title: Nurses on the Frontlines of Climate-Related Health Challenges: A Global Scoping Review of Competencies, Preparedness, and Educational Gaps in Planetary Health

description: Data Matrix for Nurses on the Frontlines of Climate-Related Health Challenges: A Global Scoping Review of Competencies, Preparedness, and Educational Gaps in Planetary Health
DOI: 10.17632/7vd77m6rnw.1
title: Nurses on the Frontlines of Climate-Related Health Challenges: A Global Scoping Review of Competencies, Preparedness, and Educational Gaps in Planetary Health

description: Data Matrix for Nurses on the Frontlines of Climate-Related Health Challenges: A Global Scoping Review of Competencies, Preparedness, and Educational Gaps in Planetary Health
DOI: 10.5061/dryad.m41g1
title: Data from: Importance of antecedent environmental conditions in modeling species distributions

description: Although species distributions can change in an unexpectedly short period
 of time, most species distribution models (SDMs) use only long-term
 averaged environmental conditions to explain species distributions. We
 aimed to demonstrate the importance of incorporating antecedent
 environmental conditions into SDMs in comparison to long-term averaged
 environmental conditions. We modeled the presence/absence of 18 fish
 species captured across 108 sampling events along a 50-km length of the
 Sagami River in Japan throughout the 1990s (one to four times per site at
 45 sites). We constructed and compared the two types of SDMs: (1) a
 conventional model that uses only long-term averaged (10-year)
 environmental conditions; and (2) a proposed model that incorporates
 environmental conditions 2 years prior to a sampling event (antecedent
 conditions) together with long-term averages linked to life-history
 stages. These models both included geomorphological, hydrological, and
 sampling conditions as predictors. A random forest algorithm was applied
 for modeling and quantifying the relative importance of the predictors.
 For seven species, antecedent hydrological conditions were more important
 than the long-term averaged hydrological conditions. Furthermore, the
 distributions of two species with low prevalence could not be predicted
 using long-term averaged hydrological conditions but only using antecedent
 hydrological conditions. In conclusion, incorporating antecedent
 environmental factors linked with life-history stages at appropriate time
 scales can better explain changes in species distribution through time.
description: Fish and environmental
 data on Sagami River (1993-99)Presence-absence of 18
 fish species obtained from a monitoring program conducted in the Sagami
 River basin in Japan by the Kanagawa Prefectural Fisheries Technology
 Center, Freshwater Experimental Station. Various explanatory variables
 (geographic, hydrologic, sampling, spatial) are also included for modeling
 species distributions.Data.xlsx
DOI: 10.5061/dryad.7ft57
title: Data from: Linking the wintering and breeding grounds of warblers along the Pacific Flyway

description: Long-distance migration is a behavior that is exhibited by many animal
 groups. The evolution of novel migration routes can play an important role
 in range expansions, ecological interactions, and speciation. New
 migration routes may evolve in response to selection in favor of reducing
 distance between breeding and wintering areas, or avoiding navigational
 barriers. Many migratory changes are likely to evolve gradually and are
 therefore difficult to study. Here, we attempt to connect breeding and
 wintering populations of myrtle warblers (Setophaga coronata coronata) to
 better understand the possible evolution of distinct migration routes
 within this species. Myrtle warblers, unlike most other warblers with
 breeding ranges primarily in eastern North America, have two disjunct
 overwintering concentrations—one in the southeastern USA and one along the
 Pacific Coast—and presumably distinct routes to-and-from these locations.
 We studied both myrtle and Audubon's warblers (S. c. auduboni)
 captured during their spring migration along the Pacific Coast, south of
 the narrow region where these two taxa hybridize. Using stable hydrogen
 isotopes and biometric data, we show that those myrtle warblers wintering
 along the southern Pacific Coast of North America are likely to breed at
 high latitudes in Alaska and the Yukon rather than in Alberta or further
 east. Our interpretation is that the evolution of this wintering range and
 migration route along the Pacific Coast may have facilitated the breeding
 expansion of myrtle warblers into northwestern North America. Moreover,
 these data suggest that there may be a migratory divide within genetically
 similar populations of myrtle warblers.
description: Isomap Assignment Output
 FilesIsoMAP output files in
 .asc format for each feather. Directory substructure represents species
 (Audubon's versus myrtle) and is further divided by molt, with
 "alt" (alternate feather) versus basic (basic
 feather).isomap_output.zipRaw hydrogen isotope values and bird measurementsyrwa_migration_isotope.csv
DOI: 10.5061/dryad.mk8ns
title: Data from: Gene expression stasis and plasticity following migration into a foreign environment

description: Selection against migrants is key to maintaining genetic differences
 between populations linked by dispersal. However, migrants may mitigate
 fitness costs by proactively choosing among available habitats, or by
 phenotypic plasticity. We previously reported that a reciprocal transplant
 of lake and stream stickleback (Gasterosteus aculeatus) found little
 support for divergent selection. Here, we revisit that experiment to test
 whether phenotypic plasticity in gene expression may have helped migrants
 adjust to unfamiliar habitats. We measured gene expression profiles in
 stickleback via TagSeq and tested whether migrants between lake and stream
 habitats exhibited a plastic response to their new environment that
 allowed them to converge on the expression profile of adapted natives. We
 report extensive gene expression differences between genetically divergent
 lake and stream stickleback, despite gene flow. But for many genes,
 expression was highly plastic. Fish transplanted into the adjoining
 habitat partially converged on the expression profile typical of natives
 from their new habitat. This suggests that expression plasticity may
 soften the impact of migration. Nonetheless, lake and stream fish differed
 in survival rates and parasite infection rates in our study, implying that
 expression plasticity is not fast or extensive enough to fully homogenize
 fish performance.
description: Lohman_et_al_2017_SupplementaryDataR scripts, R data files, and CSV files with raw data for counts, meta data, parasite data,Lohman_et_al_2017_Supplementary_Data.zip
DOI: 10.5061/dryad.101h0
title: Data from: Stochastic evolutionary demography under a fluctuating optimum phenotype

description: Many natural populations exhibit temporal fluctuations in abundance that
 are consistent with external forcing by a randomly changing environment.
 As fitness emerges from an interaction between the phenotype and the
 environment, such demographic fluctuations probably include a substantial
 contribution from fluctuating phenotypic selection. We study the
 stochastic population dynamics of a population exposed to random (plus
 possibly directional) changes in the optimum phenotype for a quantitative
 trait that evolves in response to this moving optimum. We derive simple
 analytical predictions for the distribution of log population size over
 time both transiently and at stationarity under Gompertz density
 regulation. These predictions are well matched by population- and
 individual-based simulations. The log population size is approximately
 reverse gamma distributed, with a negative skew causing an excess of low
 relative to high population sizes, thus increasing extinction risk
 relative to a symmetric (e.g., normal) distribution with the same mean and
 variance. Our analysis reveals how the mean and variance of log population
 size change with the variance and autocorrelation of deviations of the
 evolving mean phenotype from the optimum. We apply our results to the
 analysis of evolutionary rescue in a stochastic environment and show that
 random fluctuations in the optimum can substantially increase extinction
 risk by both reducing the expected growth rate and increasing the variance
 of population size by several orders of magnitude.
description: Mathematica notebook for
 population-based simulationsThis notebook includes
 code to perform population-based simulations and plot their results, so as
 to reproduce figures 1 to 5 in the paper.stochastic EvoDemo _
 shared.nbSimulationsThis zip archive contains files to perform and analyze individual based simulations as done in the manuscript.
DOI: 10.17632/9wmbpf5kkj
title: DATA - Pasture Soils in the Southern Brazilian Highlands Are Net Methane (CH4) Sinks, Challenging Intergovernmental Panel on Climate Change (IPCC) Tier 1 Defaults

description: This dataset contains field measurements of soil–atmosphere methane (CH₄) exchange and associated soil environmental covariates across a pasture management intensification gradient in the Southern Brazilian Highlands (Lages, Santa Catarina, Brazil) during December 2019–December 2020. The study includes four grazing systems: natural grassland (NG), improved natural grassland (ING), cultivated perennial pasture (PP), and cultivated annual pasture (AP). Soil CH₄ fluxes were measured in 44 sampling campaigns using static chambers coupled to gas chromatography (Shimadzu GC-2014, FID). In each system, four paddocks were monitored (n = 4 replicates per system), and three chambers were installed per paddock (48 chambers total). For each sampling campaign, paddock-level fluxes correspond to the mean of three chambers to avoid pseudoreplication.

At each campaign, soil mineral nitrogen and moisture status were quantified in the 0–10 cm layer, including ammonium (NH₄⁺–N) and nitrate (NO₃⁻–N) extracted with 1 M KCl and quantified by steam distillation, as well as gravimetric moisture and water-filled pore space (WFPS). Additional sampling campaigns were conducted after fertilization and major rainfall events to capture short-lived emission peaks. The dataset supports analyses of (i) annual CH₄ balances (sink/source behavior) by management system, (ii) seasonal “hot moments” associated with rewetting and nitrogen inputs, and (iii) non-linear environmental controls on CH₄ fluxes (e.g., optimum uptake at intermediate WFPS and inhibition of CH₄ oxidation under elevated NH₄⁺).

Files provided include analysis-ready data tables, metadata (variable definitions, units, and codes), and/or scripts required to reproduce the statistical analyses and figures reported in the associated manuscript “Pasture Soils in the Southern Brazilian Highlands Are Net Methane (CH₄) Sinks, Challenging IPCC Tier 1 Defaults”. This dataset is intended for reuse in greenhouse-gas inventories, pasture management and climate-mitigation assessments, and synthesis/meta-analysis of soil CH₄ flux drivers in subtropical grassland systems.
DOI: 10.17632/9wmbpf5kkj.1
title: DATA - Pasture Soils in the Southern Brazilian Highlands Are Net Methane (CH4) Sinks, Challenging Intergovernmental Panel on Climate Change (IPCC) Tier 1 Defaults

description: This dataset contains field measurements of soil–atmosphere methane (CH₄) exchange and associated soil environmental covariates across a pasture management intensification gradient in the Southern Brazilian Highlands (Lages, Santa Catarina, Brazil) during December 2019–December 2020. The study includes four grazing systems: natural grassland (NG), improved natural grassland (ING), cultivated perennial pasture (PP), and cultivated annual pasture (AP). Soil CH₄ fluxes were measured in 44 sampling campaigns using static chambers coupled to gas chromatography (Shimadzu GC-2014, FID). In each system, four paddocks were monitored (n = 4 replicates per system), and three chambers were installed per paddock (48 chambers total). For each sampling campaign, paddock-level fluxes correspond to the mean of three chambers to avoid pseudoreplication.

At each campaign, soil mineral nitrogen and moisture status were quantified in the 0–10 cm layer, including ammonium (NH₄⁺–N) and nitrate (NO₃⁻–N) extracted with 1 M KCl and quantified by steam distillation, as well as gravimetric moisture and water-filled pore space (WFPS). Additional sampling campaigns were conducted after fertilization and major rainfall events to capture short-lived emission peaks. The dataset supports analyses of (i) annual CH₄ balances (sink/source behavior) by management system, (ii) seasonal “hot moments” associated with rewetting and nitrogen inputs, and (iii) non-linear environmental controls on CH₄ fluxes (e.g., optimum uptake at intermediate WFPS and inhibition of CH₄ oxidation under elevated NH₄⁺).

Files provided include analysis-ready data tables, metadata (variable definitions, units, and codes), and/or scripts required to reproduce the statistical analyses and figures reported in the associated manuscript “Pasture Soils in the Southern Brazilian Highlands Are Net Methane (CH₄) Sinks, Challenging IPCC Tier 1 Defaults”. This dataset is intended for reuse in greenhouse-gas inventories, pasture management and climate-mitigation assessments, and synthesis/meta-analysis of soil CH₄ flux drivers in subtropical grassland systems.
DOI: 10.5061/dryad.5pt27
title: Data from: Lizards in pinstripes: morphological and genomic evidence for two new species of scincid lizards within Ctenotus piankai Storr and C. duricola Storr (Reptilia: Scincidae) in the Australian arid zone

description: The scincid lizard genus Ctenotus is one of the most species-rich genera
 of squamate reptiles, but few molecular phylogenetic studies have been
 undertaken on the group. Here we assess molecular and morphological
 variation within C. piankai and C. duricola, an arid-adapted pair of
 nominate species characterized by a pattern of thin pale longitudinal
 lines on a dark background that occur primarily in the western deserts and
 Pilbara region of Australia. We sequenced mitochondrial DNA and
 genome-wide restriction-site associated DNA (RAD) from geographically
 widespread samples of these lizard taxa, with particularly dense sampling
 from the Pilbara region. Phylogenetic analyses of the mitochondrial
 cytochrome B gene and approximately 5,000 nuclear loci identified four
 highly divergent lineages within the two taxa. The four
 genetically-defined populations were concordant with geography and are
 distinguishable based on multiple morphological and color pattern
 characters, despite appearing superficially similar in appearance. Despite
 limited mtDNA exchange between two lineages in the Pilbara, we found no
 evidence for ongoing gene flow across the nuclear genome. For the western
 desert lineages, there was no evidence of introgression for either mtDNA
 or nDNA in our data. To resolve the taxonomy of the group, we redescribe
 C. piankai and C. duricola, and recognize the two divergent lineages as
 new species: C. rhabdotus sp. nov., from the south-eastern Kimberley, Ord,
 Victoria River and northern Tanami Desert regions of Western Australia and
 the Northern Territory, and C. pallasotus sp. nov., from the western
 Pilbara and North West Cape regions of Western Australia.
description: Sequence data, character
 data, and phylogeniesData file includes RAD
 and mtDNA phylogenies for the Ctenotus piankai group, plus raw genetic
 data and pairwise RAD distance matrix for individuals. Also includes file
 with morphological characters for all individuals
 scored.rabosky_zootaxa.zip
DOI: 10.5061/dryad.7hr7f
title: Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

description: Past shifts in connectivity in riverine environments (for example,
 sea-level changes) and the properties of current drainages can act as
 drivers of genetic structure and demographic processes in riverine
 population of fishes. However, it is unclear whether the same river
 properties that structure variation on recent timescales will also leave
 similar genomic signatures that reflect paleodrainage properties. By
 characterizing genetic structure in a freshwater fish species
 (Hollandichthys multifasciatus) from a system of basins along the Atlantic
 coast of Brazil we test for the effects of paleodrainages caused by
 sea-level changes during the Pleistocene. Given that the paleodrainage
 properties differ along the Brazilian coast, we also evaluate whether
 estimated genetic diversity within paleodrainages can be explained by past
 riverine properties (i.e., area and number of rivers in a paleodrainage).
 Our results demonstrate that genetic structure between populations is not
 just highly concordant with paleodrainages, but that differences in the
 genetic diversity among paleodrainages correspond to the joint effect of
 differences in the area encompassed by, and the number of rivers, within a
 paleodrainage. Our findings extend the influence of current riverine
 properties on genetic diversity to those associated with past
 paleodrainage properties. We discuss how these findings may explain the
 inconsistent support for paleodrainages in structuring divergence from
 different global regions and the importance of taking into account past
 conditions for understanding the high species diversity of freshwater fish
 that we currently observe in the world, and especially in the Neotropics.
description: Whitelist_STACKSThis R script creates a whitelist to input into STACKS v. 1.35, by eliminating SNPs from the last bp positions, as well as loci with exceedingly high genetic diversity based on theta.Dataset_sumstats_r75_p10.vcfVCF file used to calculate summary statistics and outputted from STACKS v. 1.35 using the parameters -r 75 and -p 10Dataset_sumstats_t75_p10.vcf.zipDataset_Structure_25missingStructure input file allowing 25% missing data maximum.sampleDownGeno2SFS_MODPython script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Modified from Papadopoulou and Knowles 2015 (DOI: http://dx.doi.org/10.5061/dryad.23hs1)