cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.835dg31
title: Data from: Female resistance to sexual coercion can evolve to preserve the indirect benefits of mate choice

description: Sexual conflict over the indirect benefits of mate choice may arise when
 traits in one sex limit the ability of the other sex to freely choose
 mates but when these coercive traits are not necessarily directly harmful
 (i.e. forced fertilization per se). While we might hypothesize that
 females can evolve resistance in order to retain the indirect, genetic
 benefits (reflected in offspring attractiveness) of mating with attractive
 males, up to now it has been difficult to evaluate potential underlying
 mechanisms. Traditional theoretical approaches do not usually conceptually
 distinguish between female preference for male mating display and female
 resistance to forced fertilization, yet sexual conflict over indirect
 benefits implies the simultaneous action of all of these traits. Here we
 present an integrative theoretical framework that draws together concepts
 from both sexual selection and sexual conflict traditions, allowing for
 the simultaneous coevolution of displays and preferences, and of coercion
 and resistance. We demonstrate that it is possible for resistance to
 coercion to evolve in the absence of direct costs of mating to preserve
 the indirect benefits of mate choice. We find that resistance traits that
 improve the efficacy of female mating preference can evolve as long as
 females are able to attain some indirect benefits of mating with
 attractive males, even when both attractive and unattractive males can
 coerce. These results reveal new evolutionary outcomes that were not
 predicted by prior theories of indirect benefits or sexual conflict.
description: Supporting Mathematica
 model codeSupporting code,
 sections 1 though 5. Zip contains five Mathematica notebook (.nb) files.
 Original analysis was done in Mathematica Version 9.supporting_scripts_dryad.zip
DOI: 10.5061/dryad.9r5bv61
title: Data from: Genetic diversity in frogs linked to past and future climate change on the roof of the world

description: Mountains, representing storehouses of biodiversity, endemism, and
 threatened species, are biodiversity hotspots of great conservation
 importance. However, increasing evidence indicates that mountain species
 throughout the world are responding to climate change, past or
 contemporary, by shifting their geographic distributions and patterns of
 genetic diversity, potentially affecting their adaptive capacity and
 increasing risk of extinction. Using the iconic high‐elevation frog
 Nanorana parkeri as indicator, we showed how spatial analyses of climatic
 stability combined with genetic data allow unravelling amphibian responses
 to past and future climate changes on ‘the roof of the world’—the
 Qinghai‐Tibetan Plateau. We found that areas along the Yarlung Tsangpo
 Valley were climatically more stable relative to other regions, apparently
 serving as a large climatic refugium during Quaternary glaciations, but
 that these areas will likely be affected by future climate change. As
 populations closer to Quaternary refugia usually had higher genetic
 diversity, current genetic diversity can be explained in the largest part
 by distance to historically stable areas, outweighing other historical and
 contemporary factors. Along with the dynamics of suitable range, a
 fluctuating habitat fragmentation supported the pattern of historical
 changes in genetic diversity (Ne) over time. Our results emphasize strong
 relationships between amphibian genetic diversity, past range dynamics,
 and where to preserve suitable habitats in the face of future climate
 changes. More generally, our findings highlighted a central role of
 refugia during Quaternary climatic fluctuations, and how isolation from
 refugia may have modulated amphibian genetic diversity across the
 Qinghai‐Tibetan Plateau.
description: Data of occurrence
 recordsOccurrence records of
 Nanorana parkeri used for ecological niche models. Occurrences were
 gathered from the field expeditions, the literature, the Global
 Biodiversity Information Facility (GBIF), and georeferenced specimen
 records.Occurrence records of Nanorana
 parkeri used for ecological niche
 models.xlsxThe accession numbers of
 COI sequencesPartial sequences of
 cytochrome c oxidase subunit I (COI) were based on Zhou et al.
 (2014).accession numbers of COI
 sequences.xlsx
DOI: 10.5061/dryad.q15pc00
title: Data from: Empowering conservation practice with efficient and economical genotyping from poor quality samples

description: 1. Moderate to high density genotyping (100+ SNPs) is widely used to
 determine and measure individual identity, relatedness, fitness,
 population structure and migration in wild populations. 2. However, these
 important tools are difficult to apply when high-quality genetic material
 is unavailable. Most genomic tools are developed for high quality DNA
 sources from lab or medical settings. As a result, most genetic data from
 market or field settings is limited to easily-amplified mitochondrial DNA
 or a few microsatellites. 3. To enable genotyping in conservation
 contexts, we used next-generation sequencing of multiplex PCR products
 from very low-quality DNA extracted from feces, hair, and cooked samples.
 We demonstrated utility and wide-ranging potential application in
 endangered wild tigers and tracking commercial trade in Caribbean queen
 conch. 4. We genotyped 100 SNPs from degraded tiger samples to identify
 individuals, discern close relatives, and detect population
 differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild
 dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters
 and field-collected samples were used to test relatedness and detect
 population structure. 5. We provide proof-of-concept for a rapid, simple,
 cost-effective, and scalable method (for both samples and number of loci),
 a framework that can be applied to other conservation scenarios previously
 limited by low quality DNA samples. These approaches provide a critical
 advance for wildlife monitoring and forensics, open the door to
 field-ready testing, and will strengthen the use of science in policy
 decisions and wildlife trade.
description: Scripts for primer
 design for SNP targets and filtering SNP dataThis directory contains
 a folder with scripts to choose targets, and choose and design primers for
 multiplex PCR. These scripts were used to design primers for 192 SNPs from
 tigers (Panthera tigris). To begin with, a vcf file is required as input.
 The nextflow pipeline to LD-prune SNPs from the the input VCF and choose
 polymorphic and differentiating snps is the first step. These SNPs are
 submitted to the run_p3 pipeline to design primers. This pipeline selects
 50,000 SNPs and outputs a bed file. These are used to design primers and
 as a final steps, the primers are written out in a format suitable for
 ordering. In addition to this folder, there is a text file with scripts
 for calling and filtering SNPs from raw fastq files of data generated by
 these primers and Illumina sequencing. The fastq files generated using
 these primers have been submitted to NCBI, accession number
 PRJNA516037.MEE_scripts_upload.zip
DOI: 10.5061/dryad.t73c30m
title: Data from: Size‐dependent stress response in juvenile Arctic charr (Salvelinus alpinus) under prolonged predator conditioning

description: Predator conditioning can be used to improve post-release antipredator
 recognition of hatchery-reared salmonids. However, possible negative
 stress-related effects of prolonged predator conditioning on juvenile fish
 physiology are poorly understood. We studied the effects of prolonged (91
 days) predator odour exposure on whole-body cortisol level and spleen size
 in six full-sib families of juvenile hatchery-bred Arctic charr
 (Salvelinus alpinus). Chemical cues from water containing charr-fed
 pikeperch (Sander lucioperca) were used as the predator exposure stimuli,
 and lakewater was used as a chemical control. Our study revealed that
 juvenile body cortisol levels post-predator conditioning were affected by
 treatment, fish size and their interaction. Importantly, among the smaller
 (i.e. slowest growing) charr, the predator-exposed fish had higher
 cortisol levels than control fish, while the opposite pattern was true for
 the larger fish. These results suggest that chemical cues from charr-fed
 predators induce a prolonged stress response in juvenile charr. As
 prolonged predation exposure seems to elevate stress levels in a
 size-dependent manner, the larger, faster growing fish could possibly have
 intrinsically lower stress responses to predation threats than smaller,
 slower growing fish. Possible coupling between stress sensitivity and
 growth requires further attention due to the likely implications for the
 management of unintended domestication among captive-reared salmonids.
description: Arctic_charr_cortisol_data_DryadCortisol data
DOI: 10.5061/dryad.68tk49g
title: Data from: Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing

description: Oomycetes are eukaryotic plant pathogens that require health monitoring.
 High-throughput sequencing (HTS) methods replace progressively
 cultivation-based approaches in soil surveys of Oomycetes, but very little
 control has been done from synthetic communities. Indeed, several
 potential biases do exist and need to be assessed for Oomycetes
 communities. We created a mock community by mixing DNA from 24
 Phytophthora species. We amplified two barcode regions with
 Oomycete-specific primers before HTS. With this aim, we used three primer
 sets in nested PCR amplification, targeting the ITS-1 region or the RAS
 gene region. The three nested PCR strategies proved to be a reliable
 qualitative approach, identifying approximately 95% of the species after
 Illumina Miseq sequencing and bioinformatic analysis. However,
 quantitative proportions of each species showed distortions compared to
 the original mixture of the mock. In addition, we compared the two ITS
 primer sets on soil environmental DNA sampled from temperate forests. The
 ‘oom18S-ITS7/18ph2f-5.8S-1R’ primer set, more specific to Phytophthora,
 was able to detect seven Phytophthora species, confirming what was
 expected for temperate forests. Using the ‘DC6-ITS7/oom18S-ITS7’ primer
 set that covers the broader Peronosporaceans, we detected only one
 Phytophthora species among the dominance of Pythium and Phytopythium
 species. We concluded that ‘oom18S-ITS7/18ph2f-5.8S-1R’ primer set is a
 reliable tool for the qualitative description of environmental
 Phytophthora communities.
description: RAS sequences of 24
 Phytophthora speciesRAS-Ypt sequences of 24
 Phytophthora species used in a mock community. Sequences were obtained
 through Sanger sequencing of 24 isolates. "Phytophtora
 sp.neb_1543" is a putative new species isolated from French Guianan
 soils.seq_RAS.txt
DOI: 10.5061/dryad.7r3742r
title: Data from: Broad-scale patterns of soil carbon (C) pools and fluxes across semiarid ecosystems are linked to climate and soil texture

description: Dryland (semiarid and arid) ecosystems are responsible for most of the
 interannual variation in atmospheric CO2 concentrations and contain a
 considerable fraction of the globe’s soil carbon (C) stock. Despite their
 important contribution to the global land C sink, we have a poor
 mechanistic understanding of the processes that drive C cycling patterns
 in drylands. In this study in eastern Utah, we examined the natural
 variation of soil C pools and fluxes along semiorthogonal gradients of
 climate and soil texture in order to determine the pertinent environmental
 controls on soil C cycling dynamics. Our study revealed a high degree of
 collinearity among C stocks and fluxes, which were related to climate,
 vegetation, and soil clay content. Soil C pools were positively correlated
 with both soil clay content and precipitation, which in turn was linked to
 aboveground plant biomass. By contrast, enzyme activities were negatively
 associated with temperature. We observed a strong decoupling of C pools
 and fluxes (for example, total C, DOC, microbial biomass C, and
 respiration) from the enzyme activities involved in organic matter
 decomposition. Overall, our findings indicate that the within- and
 between-site variation of soil C pools across diverse dryland ecosystems
 was strongly linked to both climate and edaphic characteristics, but the
 high degree of local variability within sites could challenge
 interpretations of environmental controls at broader scales.
description: Smith&Waring_Ecosystems_datasoil biogeochemical data for Smith and Waring (2018) Ecosystems
DOI: 10.5061/dryad.99s9r6b
title: Data from: Nectary size is a pollination syndrome trait in Penstemon

description: Evolution of complex phenotypes depends on the adaptive importance of
 individual traits, and the developmental changes required to modify
 traits. Floral syndromes are complex adaptations to pollinators that
 include color, nectar, and shape variation. Hummingbird-adapted flowers
 have evolved a remarkable number of times from bee-adapted ancestors in
 Penstemon, and previous work demonstrates that color over shape better
 distinguishes bee from hummingbird syndromes. Here we examined the
 relative importance of nectar volume and nectary development in defining
 Penstemon pollination syndromes. We tested the evolutionary association of
 nectar volume and nectary area with pollination syndrome across nineteen
 Penstemon species. In selected species, we assessed cellular-level
 processes shaping nectary size. Within a segregating population from an
 inter-syndrome cross, we assessed trait correlations between nectar
 volume, nectary area, and the size of stamens on which nectaries develop.
 Nectar volume and nectary area displayed an evolutionary association with
 pollination syndrome. These traits were correlated within a genetic cross,
 suggesting a mechanistic link. Nectary area evolution involves parallel
 processes of cell expansion and proliferation. Our results demonstrate
 that changes to nectary patterning are an important contributor to
 pollination syndrome diversity, and provide further evidence that repeated
 origins of hummingbird adaptation involve parallel developmental processes
 in Penstemon.
description: R code for Evolutionary
 AssociationsContains the markdown
 file for the evolutionary associations. This has a list of the files used
 and the code used for the associations.averagesAverages for traits used in the evolutionary associationsCombined_data_for_paperRaw data for evolutionary associationspen06Un-pruned phylogeny used for the evolutionary associations.TrichomeSize5cellsCell width data.F2.avgs.KAP. kunthii x P. amphorellae F2 averages for correlations.F2.trait.corrsR script for P. kunthii x P. amphorellae F2 trait correlations.
DOI: 10.5061/dryad.tt15798
title: Data from: Experimentally enhanced performance decreases survival in nature

description: Superior locomotor performance confers advantages in terms of male combat
 success, survival, and fitness in a variety of organisms. In humans,
 investment in increased performance via the exercise response is also
 associated with numerous health benefits, and aerobic capacity is an
 important predictor of longevity. Although the response to exercise is
 conserved across vertebrates, no studies have tested whether non-human
 animals that invest in increased athletic performance through exercise
 realize a survival advantage in nature. Green anole lizards respond to
 exercise training, and enhanced performance drives trade-offs with
 reproduction and immunocompetence. We released sprint-trained,
 endurance-trained, and untrained-control male and female green anole
 lizards into an isolated, urban island in New Orleans, LA, USA and
 monitored their survival. Sedentary controls realized a significant
 survivorship advantage compared to trained lizards. Our results suggest
 that locomotor capacity is currently optimized to maximize survival in
 green anoles, and that forcing additional investment in performance moves
 them into a suboptimal phenotypic space relative to their current
 environmental demands.
description: Survival
 DataSurvival and phenotypic
 data for green anoles in a lab study.FinalSurvival.xlsx
DOI: 10.5061/dryad.607cq34
title: Data from: Predatory lizards perceive plant-derived volatile odorants

description: Many lizards are olfactory foragers and prey upon herbivorous arthropods,
 yet their responses to common herbivore‐associated plant volatiles remain
 unknown. As such, their role in mediating plant indirect defenses also
 remains largely obscured. In this paper, we use a cotton‐swab odor
 presentation assay to ask whether lizards respond to two
 arthropod‐associated plant‐derived volatile compounds: 2‐(E)‐hexenal and
 hexanoic acid. We studied the response of two lizard species, Sceloporus
 virgatusand Aspidoscelis exsanguis, because they differ substantially in
 their foraging behavior. We found that the actively foraging A.
 exsanguisresponded strongly to hexanoic acid, whereas the ambush foraging
 S. virgatus responded to 2‐(E)‐hexenal—an herbivore‐associated plant
 volatile involved in indirect defense against herbivores. These findings
 indicate that S. virgatus may contribute to plant indirect defense and
 that a species' response to specific odorants is linked with foraging
 mode. Future studies can elucidate how lizards use various compounds to
 locate prey and how these responses impact plant‐herbivore interactions.
description: aspi_volatile_swabsData regarding response of Aspidoscelis exsanguis to volatile odorants. Contains all variables analyzed in the publication as well as some additional non-significant variables that were not included. Also includes an individual not included inthe published manuscript as it was determined to be of a different species.virgatus_volatile_trialsData regarding the response of Sceloporus virgatus to volatile odorants. Contains the variables included in the publication as well as some non-significant variables not included.aspi_volatile_responseR Script used to analyze the Aspidoscelis exsanguis data included in the publicationvirgatus_volatile_analysisR Script used to analyze the Sceloporus virgatus volatile response data.
DOI: 10.5061/dryad.vd7d8v6
title: Data from: Space use and social association in a gregarious ungulate: testing the conspecific attraction and resource dispersion hypotheses

description: Animals use a variety of proximate cues to assess habitat quality when
 resources vary spatiotemporally. Two nonmutually exclusive strategies to
 assess habitat quality involve either direct assessment of landscape
 features or observation of social cues from conspecifics as a form of
 information transfer about forage resources. The conspecific attraction
 hypothesis proposes that individual space use is dependent on the
 distribution of conspecifics rather than the location of resource patches,
 whereas the resource dispersion hypothesis proposes that individual space
 use and social association are driven by the abundance and distribution of
 resources. We tested the conspecific attraction and the resource
 dispersion hypotheses as two nonmutually exclusive hypotheses explaining
 social association and of adult female caribou (Rangifer tarandus). We
 used location data from GPS collars to estimate interannual site fidelity
 and networks representing home range overlap and social associations among
 individual caribou. We found that home range overlap and social
 associations were correlated with resource distribution in summer and
 conspecific attraction in winter. In summer, when resources were
 distributed relatively homogeneously, interannual site fidelity was high
 and home range overlap and social associations were low. Conversely, in
 winter when resources were distributed relatively heterogeneously,
 interannual site fidelity was low and home range overlap and social
 associations were high. As access to resources changes across seasons,
 caribou appear to alter social behavior and space use. In summer, caribou
 may use cues associated with the distribution of forage, and in winter
 caribou may use cues from conspecifics to access forage. Our results have
 broad implications for our understanding of caribou socioecology,
 suggesting that caribou use season‐specific strategies to locate forage.
 Caribou populations continue to decline globally, and our finding that
 conspecific attraction is likely related to access to forage suggests that
 further fragmentation of caribou habitat could limit social association
 among caribou, particularly in winter when access to resources may be
 limited.
description: Space-use and social
 association in caribou data fileData used to generate
 linear mixed models and figures for social association networks, home
 range overlap networks, and home range area.final-dt-dryad.Rdsfinal-dt-site-fidelity-dryadData used for linear mixed model and figure for site fidelity in caribou.
DOI: 10.5061/dryad.66gc768
title: Data from: Grizzly bear response to fine spatial and temporal scale spring snow cover in Western Alberta

description: Snow dynamics influence seasonal behaviors of wildlife, such as denning
 patterns and habitat selection related to the availability of food
 resources. Under a changing climate, characteristics of the temporal and
 spatial patterns of snow are predicted to change, and as a result, there
 is a need to better understand how species interact with snow dynamics.
 This study examines grizzly bear (Ursus arctos) spring habitat selection
 and use across western Alberta, Canada. Made possible by newly available
 fine-scale snow cover data, this research tests a hypothesis that grizzly
 bears select for locations with less snow cover and areas where snow melts
 sooner during spring (den emergence to May 31st). Using Integrated Step
 Selection Analysis, a series of models were built to examine whether snow
 cover information such as fractional snow covered area and date of snow
 melt improved models constructed based on previous knowledge of grizzly
 bear selection during the spring. Comparing four different models fit to
 62 individual bear-years, we found that the inclusion of fractional snow
 covered area improved model fit 60% of the time based on Akaike
 Information Criterion tallies. Probability of use was then used to
 evaluate grizzly bear habitat use in response to snow and environmental
 attributes, including fractional snow covered area, date since snow melt,
 elevation, and distance to road. Results indicate grizzly bears select for
 lower elevation, snow-free locations during spring, which has important
 implications for management of threatened grizzly bear populations in
 consideration of changing climatic conditions. This study is an example of
 how fine spatial and temporal scale remote sensing data can be used to
 improve our understanding of wildlife habitat selection and use in
 relation to key environmental attributes.
description: R code and
 dataThe zipped file contains
 an RMD file and corresponding data used in this
 analysis.r_data_berman_et_al_2019.zip
DOI: 10.4119/unibi/3007385
title: 5mC data generated by DeepSignal-plant and methylation categorisation files for all genes and repeats

description: DeepSignal-plant returns two main outputs: (I) one file that comprises all methylation calls for every analysed cytosine on every read, and (II) a frequency file with a summary of methylation calls for each cytosine in the reference genome sequence. The frequency file output, containing the methylation probabilities ranging from 0 to 1, was used by 5mCartograph 1.0 for the identification of genome-wide and gene/repeat-specific 5mC profiles and by GbMine for the determination of gene body methylated genes.
The frequency cytosine methylation data generated by DeepSignal-plant in tsv format for each Beta vulgaris chromosme seperately, the methylation categorisation files for all genes and repeats and the list of detected gbM (candidate) genes are here accessible.