cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6p150kf
title: Data from: Limits to environmental masking of genetic quality in sexual signals

description: There is considerable debate over the value of male sexual ornaments as
 signals of genetic quality. Studies alternately report that environmental
 variation enhances or diminishes the genetic signal, or leads to crossover
 where genotypes perform well in one environment but poorly in another. A
 unified understanding is lacking. We conduct a novel experimental test
 examining the dual effects of distinct categories of genetic (inbred
 versus crossed parental lines) and environmental quality (low, through
 high to extreme larval food stress) on a condition-dependent male
 ornament. We find that differences in genetic quality signalled by the
 ornament (male eyespan in Diasemopsis meigenii stalk-eyed flies) become
 visible and are amplified under high stress but are overwhelmed in extreme
 stress environments. Variance among independent genetic lines increases
 with environmental stress in both genetic quality classes, but at a slower
 rate in high quality outcrossed flies. Individual genetic lines generally
 maintain their ranks across environments, except among high quality lines
 under low environmental stress, where low genetic variance among lines
 precludes differentiation between ranks. Our results provide a conceptual
 advance, demonstrating a unified pattern for how genetic and environmental
 quality interact. They show when environmental conditions lead to the
 amplification of differences in signals of genetic quality and thereby
 enhance the potential indirect genetic benefits gained by female mate
 choice.
description: GxE
 DatasetMain data set.
 Information on Genetic and Environmental Quality of individual files, from
 a set of inbred lines, with line information, used in the analyses
 presented in the paper, Howie et al. 2019.DATA-GxE.txt
DOI: 10.5061/dryad.1h6r4dn
title: Data from: Enough for all: no mating effort adjustment to varying mate availability in a gift-giving spider

description: Reproduction is costly and since males possess a finite energetic budget,
 resource allocation to one mating event may constrain investment in
 subsequent matings. Consequently, males of many species evolved to adjust
 their reproductive investment in response to mating opportunities. When
 female availability is high, males are predicted to partition their
 reproductive effort among multiple partners to avoid resource depletion
 before mating opportunities have ceased. We tested this prediction in
 males of the spider Pisaura mirabilis, which mate via costly nuptial gifts
 consisting of silk-wrapped prey and are known to respond to social cues
 (rivals’ presence) by adjusting their reproductive investment. We
 manipulated the number of females exposed to males to induce perception of
 high vs low mating opportunities, and scored male investment to pre-mating
 traits (time allocated to gift construction and courtship) and traits at
 mating (copulation duration) during interactions with a female. We
 expected males facing higher mating opportunities to reduce their
 investment in all measured traits, but instead found no differences in
 male trait expression. These findings indicate lack of resource
 partitioning in response to variation in female availability, as males may
 be able to draw resources from non-reproductive traits (growth or immune
 defense), or may increase their food intake at mating by partially
 consuming the nuptial gift. Hence, despite their associated costs, by
 providing a source of nutrition, nuptial prey gifts may weaken selection
 for adaptive plasticity in male reproductive investment.
description: Courtship and copulation
 investment in P. mirabilisData on reproductive
 investment of Pisaura mirabilis males as mating opportunities vary. Data
 obtained from the experimental manipulation of female
 availability.Magris_and_Tuni_2019_Reproductive_adjustments_to_mating_opportunities.xlsx
DOI: 10.15468/dl.yecg8y
title: Occurrence Download

description: A dataset containing 283 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "OccurrenceStatus is Present",
 "TaxonKey is Pelodytes atlanticus"
 ]
}

 The dataset includes 283 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001702-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1b1k1sm
title: Data from: A laterally transferred viral gene modifies aphid wing plasticity

description: Organisms often respond to changing environments by altering development
 of particular traits. These plastic traits exhibit genetic variation,
 i.e., genotypes respond differently to the same environmental cues.
 Theoretical studies have demonstrated the importance of this variation,
 which is targeted by natural selection, in adapting plastic responses to
 maximize fitness. However, little is known about the underlying genetic
 mechanisms. We identify two laterally transferred genes that contribute to
 variation in a classic example of phenotypic plasticity: the pea aphid’s
 ability to produce winged offspring in response to crowding. We discovered
 that aphid genotypes vary extensively for this trait, and that aphid genes
 of viral origin are upregulated in response to crowding solely in
 highly-inducible genotypes. We knocked-down expression of these genes to
 demonstrate their functional role in wing plasticity. Through phylogenetic
 analysis we found that these genes likely originated from a virus that
 infects rosy apple aphids and causes their hosts to produce winged
 offspring. The function of these genes has therefore been retained
 following transfer to pea aphids. Our results uncover a novel role for
 co-opted viral genes, demonstrating that they are used to modulate
 ecologically-relevant, plastic phenotypes. Our findings also address a
 critical question about the evolution of environmentally-sensitive traits:
 whether or not the genes that control the expression of plastic traits
 also underlie variation in plasticity. The genes we identify originated
 from outside aphids themselves, and thus our work shows that genes
 formerly unrelated to plasticity can fine-tune the strength of plastic
 responses to the environment.
description: Experimental_raw_data
DOI: 10.5061/dryad.gb5n156
title: Data from: Self-deception in nonhuman animals: weak crayfish escalated aggression as if they were strong

description: Humans routinely deceive themselves when communicating to others, but no
 one knows whether other animals do the same. We ask whether dishonest
 signaling between crayfish meets a condition required for self-deception:
 dishonest individuals and honest individuals escalate aggression according
 to their signals of strength rather than actual strength. Using game
 theory, we predicted how an animal’s knowledge of its strength should
 affect its decision to escalate aggression. At the evolutionary
 equilibrium, an animal that knows its strength should escalate aggression
 according to its strength, relative to the expected strength of its
 opponent. By contrast, an animal that knows only its size should escalate
 aggression according to its size, relative to the size of its opponent. We
 tested these predictions by staging encounters between male crayfish
 (Cherax dispar) of known sizes and strengths. Consistent with a model of
 self-deception, crayfish escalated aggression based on the sizes of their
 claws relative to those of their opponents, despite the fact that size
 poorly predicts strength. Males who were weak for their size escalated
 disputes less often, but their aggression far exceeded the level predicted
 by a model of self-awareness, suggesting these crayfish were largely
 ignorant of their deception. Animals that fail to recognize their own
 dishonest signals may win disputes with stronger opponents without
 engaging in costly combat. Our game-theoretical approach can be used to
 identify potential cases of self-deception in nonhuman animals, enabling
 comparative studies of this behavior.
description: PCA.dataSeven linear measurements of claw size and one estimate of maximal claw force for left and right claws of crayfishregression.dataoutcomes of staged encounters with crayfish of known size and strength. Variables are as follows: A) crayfish ID; B & C) mean.size estimated as a score for PC1 and mean.force of the focal crayfish's pair of claws; D) random effect of focal crayfish from model of force predicted by size; E) mean residual force of the pair of claws from a regression of force onto size; F & G) minimal and maximal residual force (i.e., residua strength of weaker and stronger claw, respectively); H) difference in residual strength of stronger and weaker claw; I) ID of opponent crayfish; J) random effect of opponent crayfish from model of force predicted by size; L) opponents size estimate as a score for PC1; M) force of opponent's claws expected from their mean size; N) outcome of encounter, where 0 means focal crayfish fled and 1 means it escalated aggression; O) difference in mean size between focal crayfish and its opponent; P) difference in mean force between focal crayfish and its opponent; Q) difference between mean force of focal crayfish and the expected force of its opponent, given the opponent's mean claw size;mixed.model.data.txt
DOI: 10.5061/dryad.bn64b7f
title: Data from: Male social plasticity influences transient dynamics of alternative mating systems in water striders

description: Animal mating systems are often studied with the goal of understanding why
 species, populations, or groups vary from one another in the system they
 display. Although these differences are often treated as basically stable,
 it is also known that these systems may shift over time (e.g. from one
 breeding season to the next). There has been some study of how ecological
 factors correlate with these changes; however, few, if any, studies have
 investigated how the phenotypic composition of a group governs the timing
 and probability of system transitions. Groups of stream water striders
 (Aquarius remegis) can demonstrate quick and flexible transitions in
 mating system dynamics, with many groups eventually transitioning to a
 system in which a single, large male monopolizes mating opportunities. We
 asked if variation in individual- and group-level traits associated with
 morphology and behavior (e.g. size of the largest individual, variance in
 activity behavioral types, and average social plasticity) could partially
 explain the variability in how rapidly groups make this transition, if
 they make it all. Our results show that the average social plasticity of
 males in a group has important effects on the emergence timing of mating
 systems dominated by a single male.
description: Group
 dataGroup data for all small
 pools used in analyses. Group characteristics come from data presented in
 an earlier publication (Montiglio et al. 2017; DOI:
 https://doi.org/10.5061/dryad.69dh9). Stable times were manually
 calculated using scan sample data from the same previous
 publication.striders.xlsxMale dominance stability dataData for replicating analysis of male stability. Proportion of times male remained dominant were manually calculated from scan samples presented in an earlier publication (Montiglio et al. 2017; DOI: https://doi.org/10.5061/dryad.69dh9)Stability.xlsx
DOI: 10.5061/dryad.s205vd8
title: Data from: Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment

description: Heterogeneous environments, such as mountainous landscapes, create
 spatially varying selection pressure that potentially affects several
 traits simultaneously across different life stages, yet little is known
 about the general patterns and drivers of adaptation in such complex
 settings. We studied silver fir (Abies alba Mill.) populations across
 Switzerland and characterized their mountainous landscape using downscaled
 historical climate data. We sampled 387 trees from 19 populations and
 genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate
 their demographic distances. Seedling morphology, growth and phenology
 traits were recorded in a common garden, and a proxy for water use
 efficiency was estimated for adult trees. We tested whether populations
 have more strongly diverged at quantitative traits than expected based on
 genetic drift alone in a multi-trait framework, and identified potential
 environmental drivers of selection. We found two main responses to
 selection: (i) populations from warmer and more thermally stable locations
 have evolved towards a taller stature, and (ii) the growth timing of
 populations evolved towards two extreme strategies, "start early and
 grow slowly" or "start late and grow fast", driven by
 precipitation seasonality. Populations following the "start early and
 grow slowly" strategy had higher water use efficiency and came from
 inner Alpine valleys characterized by pronounced summer droughts. Our
 results suggest that contrasting adaptive life-history strategies exist in
 silver fir across different life stages (seedling to adult), and that some
 of the characterized populations may provide suitable seed sources for
 tree growth under future climatic conditions.
description: Abies Alba SNP data from
 19 Swiss populations374 SNPs, 387 trees
 across Switzerland in GenePop formatAbiesAlba_374SNPs_387trees_CH_4genepop.csvAbies Alba delta13C from 19 Swiss populationsDelta13C of 197 silver fir trees determined from needles. Approximately 10 trees per population.delta13c_adult_CH.csv
DOI: 10.5281/zenodo.18391682
title: Data: Entre el mito de la 'Generación Dorada' y la crisis actual de la Selección Chilena de fútbol: Identificación de los hinchas ante el fracaso deportivo
DOI: 10.5281/zenodo.18391683
title: Data: Entre el mito de la 'Generación Dorada' y la crisis actual de la Selección Chilena de fútbol: Identificación de los hinchas ante el fracaso deportivo
DOI: 10.5061/dryad.70jt240
title: Data from: Knock-on community impacts of a novel vector: spillover of emerging DWV-B from Varroa-infested honeybees to wild bumblebees

description: Novel transmission routes can directly impact the evolutionary ecology of
 infectious diseases, with potentially dramatic effect on host populations
 and knock-on effects on the wider host community. The invasion of Varroa
 destructor, an ectoparasitic viral vector in Western honeybees, provides a
 unique opportunity to examine how a novel vector affects disease
 epidemiology in a host community. This specialist honeybee mite vectors
 deformed wing virus (DWV), an important re-emerging honeybee pathogen that
 also infects wild bumblebees. Comparing island honeybee and wild bumblebee
 populations with and without V. destructor, we show that V. destructor
 drives DWV prevalence and titre in honeybees and sympatric bumblebees.
 Viral genotypes are shared across hosts, with the potentially more
 virulent DWV-B overtaking DWV-A in prevalence in a current epidemic. This
 demonstrates disease emergence across a host community driven by the
 acquisition of a specialist novel transmission route in one host, with
 dramatic community level knock-on effects.
description: Prevalence of DWVA, DWVB
 and Nosema spp. across bee hostsVirus (DWVA and DWVB)
 and Nosema spp (N. apis, N. bombi and N. ceranae) prevalence determined by
 PCR using parasite-specific primers.Manley_et_al_2019_prevalence_DWVA_DWVB_Nosema_220519.csvDWVA_raw_qPCR_dataQuantitative qPCR data on DWV-A viral load. This file contains 'house-keeping' gene Cq values, and details of how we calculated an estimate of viral load in a whole bee from the qPCR data.DWVB_raw_qPCR_dataQuantitative qPCR data on DWV-B viral load. This file contains 'house-keeping' gene Cq values, and details of how we calculated an estimate of viral load in a whole bee from the qPCR data.viral_load_DWVAProcessed qPCR data on DWV-A viral load alongside environmental data for each sample for statistical analysis.Manley_et_al_viral_load_DWVA.csvviral_load_DWVBProcessed qPCR data on DWV-B viral load alongside environmental data for each sample for statistical analysis.Manley_et_al_viral_load_DWVB.csv
DOI: 10.5061/dryad.37g4f36
title: Data from: Holocene population decline and conservation implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae)

description: The Western Hercules beetle (Dynastes grantii) is endemic to the highland
 forest habitats of southwestern USA and northern Mexico. The habitats
 harbor many endemic species, but are being threatened by rapid climate
 change and urban development. In this study, the genetic structure of D.
 grantii populations from southwestern USA was investigated. Specifically,
 genomic data from double-digest RADseq (ddRADseq) libraries were utilized
 to test whether geographically distant populations from the Mogollon Rim
 (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are
 genetically structured. The study also estimated the effective population
 size of the Mogollon Rim populations based on genetic diversity. The
 results indicated that the two geographic populations from the Mogollon
 Rim were not genetically structured. A population size reduction was
 detected since the end of the last glacial period, which coincided with a
 reduction of forest habitat in the study area. The results implied that
 the connectivity and the size of highland forest habitats in the Mogollon
 Rim could have been the major factors shaping the population genetic
 structure and demographic history of D. grantii. The Western Hercules
 beetle could be a useful flagship species for local natural history
 education and to promote the conservation of highland forest habitats.
description: Huang_2019_JOH_DGrantii_dryadInput files, results, and associated R codes for plotting results for PCA, RADPainter, and Stairway plot analyses. Output files from pyRAD analysis: allele, loci, and str.
DOI: 10.5061/dryad.p6v01kd
title: Data from: Stomatal sensitivity to CO2 diverges between angiosperm and gymnosperm tree species

description: The response of tree leaf gas exchange to elevated CO2 concentrations has
 been investigated in numerous experiments along the past 30 years.
 Stomatal regulation is a major plant control over leaf gas exchange, and
 the response to the increasing CO2 will shape the biological activity of
 forests in the future. Here we collected 144 records from 57 species on
 stomatal conductance in CO2 manipulation experiments on trees (340-980 ppm
 CO2). CO2-induced stomatal downregulation was calculated as the slope of
 the linear regression between stomatal conductance and [CO2]. Among tree
 species, the slope (a) of change in stomatal conductance per 100 ppm CO2
 increase ranged between 0 and -151, indicating stomatal downregulation,
 and only four species showed upregulation. There was a significant
 divergence between evergreen gymnosperms (a = -3.6±1.0), deciduous
 angiosperms (a = -16.3±3.1), and evergreen angiosperms (a = -32.8±7.1).
 Gymnosperms were less sensitive to CO2 changes than deciduous angiosperms
 even when considering only field experiments. The significant role of tree
 functional group in predicting CO2-induced stomatal downregulation was
 detected in multiple mixed effect models, with P values ranging between
 0.0002 and 0.0295. The significantly higher stomatal sensitivity to CO2 of
 angiosperms vs. gymnosperms might be related to the overall higher
 stomatal conductance of angiosperms; their thinner leaves, in turn losing
 water faster; and the decreasing atmospheric [CO2] at the time of their
 taxa diversification. We conclude that species differences must be taken
 into account in forecasting future forest fluxes.
description: Klein & Ramon
 Database Table S1Table S1. Complete
 database, in an Excel spreadsheet.
DOI: 10.5061/dryad.fk560dg
title: Data from: Latitudinal divergence in a wide-spread amphibian: contrasting patterns of neutral and adaptive genomic variation

description: Stochastic effects from demographic processes and selection are expected
 to shape the distribution of genetic variation in spatially heterogeneous
 environments. As the amount of genetic variation is central for long-term
 persistence of populations, understanding how these processes affect
 variation over large-scale geographic gradients is pivotal. We
 investigated the distribution of neutral and putatively adaptive genetic
 variation, and reconstructed demographic history in the moor frog (Rana
 arvalis) using 136 individuals from 15 populations along a 1700 km
 latitudinal gradient from northern Germany to northern Sweden. Using
 ddRAD-seq we obtained 27590 SNPs, and identified differentiation outliers
 and SNPs associated with growing season length. Populations grouped into a
 southern and a northern cluster, representing two phylogeographical
 lineages from different post-glacial colonization routes. Hybrid index
 estimation and demographic model selection showed strong support for a
 southern and northern lineage and evidence of gene flow between regions
 located on each side of a contact zone. However, patterns of past gene
 flow over the contact zone differed between neutral and putatively
 adaptive SNPs. While neutral nucleotide diversity was higher along the
 southern than the northern part of the gradient, nucleotide diversity in
 differentiation outliers showed the opposite pattern suggesting
 differences in the relative strength of selection and drift along the
 gradient. Variation associated with growing season length decreased with
 latitude along the southern part of the gradient, but not along the
 northern part where variation was lower, suggesting stronger
 climate-mediated selection in the north. Outlier SNPs included loci
 involved in immunity and developmental processes.
description: barcodelist_processradtagsList of barcodes and indices for process_radtagsprocess_arvalisScript used to run process_radtagsdenovo_arvalis_noreplicExample script from parameter optimization in the denovomap pipelinepopmap_arvalis_noreplicatesPopulation map used for STACKS and main analysespopmap_arvalis_noreplicatesregions_demographicPopulation map used to create vcf file to crease mSFS in easySFS.easySFS_projectionDown projection results from easySFSRUN_easySFSExample command to run easySFSarvalis_latitudinal_MSFSmultidimensional folded SFS created by easySFS and used for demographic analysis in fsc26denovo_arvalis_noreplicScript used to run fsc26fsc2_runall.shBoot_fsc26Script used to bootstrap 95% CI around parameter estimate for the best model identified in fsc26fsc2_runallScript to run all models in fsc26batch_1.summary.sumstatsStacks summary ouputbatch_1.sumstatsStacks summary outputbatch_1Final filtered vcf file used for the main analyses.