cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1m207
title: Data from: Fragile coexistence of a global chytrid pathogen with amphibian populations is mediated by environment and demography

description: Unravelling the multiple interacting drivers of host pathogen co-existence
 is crucial in understanding how an apparently stable state of endemism may
 shift towards an epidemic and lead to biodiversity loss. Here, we
 investigate the apparent co-existence of the global amphibian pathogen
 *Batrachochytrium dendrobatidis* (Bd) with *Bombina variegata* populations
 in the Netherlands over a seven-year period. We used a multi-season
 mark-recapture data set and assessed potential drivers of co-existence
 (individual condition, environmental mediation and demographic
 compensation) at the individual and population level. We show that even in
 a situation with a clear cost incurred by endemic Bd, population sizes
 remain largely stable. Current environmental conditions and an
 over-dispersed pathogen load likely stabilize disease dynamics, but as
 higher temperatures increase infection probability, changing environmental
 conditions, for example a climate change-driven rise in temperature, could
 unbalance the current fragile host-pathogen equilibrium. Understanding the
 proximate mechanisms of such environmental mediation and of site-specific
 differences in infection dynamics can provide vital information for
 mitigation actions.
description: 01_Spitzenetal2017_Juvenile_datayearly counts of juveniles per site02_Spitzenetal2017_CMR_data1st datasheet: CMR data for all dates including the mean minumum temperature for the week prior to survey. 0 = not seen, 1 = seen but clean, values = Bd GE/swab. RUnumbers are all individual toads. 2nd datasheet gives the body condition per individual toad (RUnrs) upon capture. In both sheets the last columns provide information on gender/age and site.
DOI: 10.5061/dryad.f9s4424
title: Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

description: Phenotypic plasticity is thought to impact evolutionary trajectories by
 shifting trait values in a direction that is either favored by natural
 selection (“adaptive plasticity”) or disfavored (“nonadaptive”
 plasticity). However, it is unclear how commonly each of these types of
 plasticity occurs in natural populations. To answer this question, we
 measured glucosinolate defensive chemistry and reproductive fitness in
 over 1,500 individuals of the wild perennial mustard Boechera stricta,
 planted in four common gardens across central Idaho, USA. Glucosinolate
 profiles—including total glucosinolate concentration as well as the
 relative abundances and overall diversity of different compounds—were
 strongly plastic both among habitats and within habitats. Patterns of
 glucosinolate plasticity varied greatly among genotypes. Plasticity among
 sites was predicted to affect fitness in 27.1% of cases; more often than
 expected by chance, glucosinolate plasticity increased rather than
 decreased relative fitness. In contrast, we found no evidence for
 within-habitat selection on glucosinolate reaction norm slopes (i.e.,
 plasticity along a continuous environmental gradient). Together, our
 results indicate that glucosinolate plasticity may improve the ability of
 B. stricta populations to persist after migration to new habitats.
description: raw_dataContains six tab-delimited files with all data used in this analysis. See README file for details.GSplasticity_codeR code to generate all figures and reproduce all analyses
DOI: 10.5061/dryad.rg051
title: Data from: 8-year trends in physical activity, nutrition, TV viewing time, smoking, alcohol and BMI: a comparison of younger and older Queensland adults

description: Lifestyle behaviours significantly contribute to high levels of chronic
 disease in older adults. The aims of the study were to compare the
 prevalence and the prevalence trends of health behaviours (physical
 activity, fruit and vegetable consumption, fast food consumption, TV
 viewing, smoking and alcohol consumption), BMI and a summary health
 behaviour indicator score in older (65+ years) versus younger adults
 (18-65 years). The self-report outcomes were assessed through the
 Queensland Social Survey annually between 2007-2014 (n=12,552). Regression
 analyses were conducted to compare the proportion of older versus younger
 adults engaging in health behaviours and of healthy weight in all years
 combined and examine trends in the proportion of younger and older adults
 engaging in health behaviours and of healthy weight over time. Older
 adults were more likely to meet recommended intakes of fruit and vegetable
 (OR=1.43, 95%CI=1.23-1.67), not consume fast food (OR=2.54,
 95%CI=2.25-2.86) and be non-smokers (OR=3.02, 95%CI=2.53-3.60) in
 comparison to younger adults. Conversely, older adults were less likely to
 meet the physical activity recommendations (OR=0.86, 95%CI= 0.78-0.95) and
 watch less than 14 hours of TV per week (OR=0.65, 95%CI=0.58-0.74).
 Overall, older adults were more likely to report engaging in 3, or at
 least 4 out of 5 healthy behaviours. The proportion of both older and
 younger adults meeting the physical activity recommendations (OR=0.97,
 95%CI=0.95-0.98 and OR=0.94, 95%CI=0.91-0.97 respectively), watching less
 than 14 hours of TV per week (OR=0.96, 95%CI=0.94-0.99 and OR=0.94,
 95%CI=0.90-0.99 respectively) and who were a healthy weight (OR=0.95,
 95%CI=0.92-0.99 and OR=0.96, 95%CI=0.94-0.98 respectively) decreased over
 time. The proportion of older adults meeting the fruit and vegetable
 recommendations (OR=0.90, 95%CI=0.84-0.96) and not consuming fast food
 (OR=0.94, 95%CI=0.88-0.99) decreased over time. Although older adults meet
 more health behaviours than younger adults, the decreasing prevalence of
 healthy nutrition behaviours in this age group needs to be addressed.
description: Physical Activity,
 Nutrition, TV Viewing Time, Smoking, Alcohol and BMI in Queensland Adults,
 2007-2014.Physical Activity,
 Nutrition, TV Viewing Time, Smoking, Alcohol and BMI in Queensland Adults
 between 2007-2014. Demographics (location, age, gender, education and
 employment) included.Data for
 dryad.sav
DOI: 10.5061/dryad.4vr37
title: Data from: Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat

description: Positive species-genetic diversity correlations (SGDCs) are often thought
 to result from the parallel influence of neutral processes on genetic and
 species diversity. Yet, confounding effects of non-neutral mechanisms have
 not been explored. Here, we investigate the impact of non-neutral genetic
 diversity on SGDCs in high Andean wetlands. We compare correlations
 between plant species diversity (SD) and genetic diversity (GD) calculated
 with and without loci potentially under selection (outlier loci). The
 study system includes 2188 specimens from five species (three common
 aquatic macroinvertebrate and two dominant plant species) that were
 genotyped for 396 amplified fragment length polymorphism loci. We also
 appraise the importance of neutral processes on SGDCs by investigating the
 influence of habitat fragmentation features. Significant positive SGDCs
 were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a
 few outlier loci were detected in each species, they resulted in
 significant decreases in GD and in SGDCs. This supports the hypothesis
 that neutral processes drive species-genetic diversity relationships in
 high Andean wetlands. Unexpectedly, the effects on genetic diversity of
 the habitat fragmentation characteristics in this study increased with the
 presence of outlier loci in two species. Overall, our results reveal
 pitfalls in using habitat features to infer processes driving SGDCs and
 show that a few loci potentially under selection are enough to cause a
 significant downward bias in SGDC. Investigating confounding effects of
 outlier loci thus represents a useful approach to evidence the
 contribution of neutral processes on species-genetic diversity
 relationships.
description: SGDC-Outlier-BertinUltR scripts used by Bertin et al to analyze the data.CarexAFLP05NARaw AFLP data for the species Carex gayana.PatosiaAFLP05NARaw AFLP data for the species Patosia clandestinaHyalellaAFLP05NARaw AFLP data for the species Hyallela fossamancinii.AndesiopsAFLP05NARaw AFLP data for the species Andesiops peruvianus.AustrelmisAFLP05NARaw AFLP data for the species Austrelmis sp.
DOI: 10.5061/dryad.272r9
title: Data from: Are extra-pair males different from cuckolded males? An empirical and meta-analytic examination

description: Traditional models for female extra-pair matings assume that females
 benefit indirectly from extra-pair mating behaviour. Under these so-called
 adaptive models, extra-pair males are hypothesized to have more compatible
 genotypes, larger body size, exaggerated ornaments or to be older than
 cuckolded males. Alternatively, (‘nonadaptive’) models that consider
 female extra-pair matings to be a by-product posit that female extra-pair
 mating can be maintained even if there is no benefit to females. This
 could happen if, for example, males gained fitness benefits from
 extra-pair mating, while female and male extra-pair mating behaviours were
 genetically correlated. Extra-pair males are also expected to be older and
 larger if this improves their ability to convince or coerce females to
 mate. We investigated whether a female's extra-pair mates differed
 from her cuckolded mate in both genetic and phenotypic traits by analysing
 data from an insular house sparrow population. We found that extra-pair
 males were older than cuckolded males, consistent with both models.
 However, in contrast to the expectations from from adaptive models,
 extra-pair and cuckolded males were of similar genetic relatedness, and
 hence expected compatibility, with the female, and had comparable body
 size and secondary sexual traits. We also updated previous meta-analyses
 examining differences between extra-pair and cuckolded males. The
 meta-analytic results matched results from our house sparrow case study.
 Although we cannot completely exclude indirect benefits for females,
 nonadaptive models may better explain female extra-pair matings. These
 neglected alternative models deserve more research attention, and this
 should improve our understanding of the evolution of mating systems.
description: Data from: Are
 extra-pair males different from cuckolded males? An empirical and
 meta-analytic examinationThe datasets used for
 the house sparrow case studyMEC-14-1029.Data.SubmitFeb2015.xlsx
DOI: 10.5061/dryad.pt240
title: Data from: The effect of roads on spider monkeys’ home range and mobility in a heterogeneous regenerating forest

description: Arboreal fauna living in tropical ecosystems may be particularly affected
 by roads given their dependency on forest cover and the high vulnerability
 of such ecosystems to changes. Over a period of four years, we followed
 subgroups of spider monkeys living in a regenerating dry tropical forest
 with 8.2 km of roads within their home range. We aimed to understand
 whether roads shaped the home range of spider monkeys and which road
 features affected their movement. Only 18 percent (3 km) of the spider
 monkeys’ home range perimeter bordered with roads; these roads had greater
 habitat disparity between road sides than roads inside the home range.
 Although monkeys were reluctant to be close to roads, and roadside habitat
 contained low proportions of mature forest, spider monkeys crossed roads
 at 69 locations (7.5 crossings per kilometer). The main road
 characteristic affecting crossings was canopy opening size, with greater
 probability of crossing where canopy openings were smaller. Our findings
 support the importance of canopy opening size for road crossing of
 arboreal taxa, but they also indicate the relevant role roadside forest
 structure may have. Minimizing canopy opening size and forest disturbance
 along roads can facilitate the movement of arboreal fauna and preserve the
 important role of spider monkeys and other arboreal taxa in seed dispersal
 and thus the maintenance and regeneration of forest diversity.
description: crossing locations
 infoThis file contains
 information on the places where spider monkeys crossed the road (given in
 X and Y coordinates, UTM zone 16N, datum WGS 84) and other info about the
 crossing (e.g. road width and gap).spider monkeys
 locationsThis file contains the
 locations of spider monkeys subgroups separated by 30min intervals from
 2005 to 2008. The x and y coordinates are given in UTM format 16N zone,
 WGS84 datum.Habitat
 types_ZIPThis is a compressed
 RASTER file (tiff and corresponding reference files) for ArcGIS containing
 4 habitat types: 1) primary forest, 2) secondary forest, 3) young
 secondary forest, 4) no forest. UTM format 16N, WGS 84.Habitat
 types1.ziproads_shapefile
 ZIPThis is a compressed
 shapefile (ArcGIS) of the paved and dirt roads covering the study area.
 UTM format 16N, WGS 84.
DOI: 10.5061/dryad.53873
title: Data from: Non-adaptive female pursuit of extra-pair copulations can evolve through hitchhiking

description: Mounting evidence has indicated that engaging in extra-pair copulations
 (EPCs) might be maladaptive or detrimental to females. It is unclear why
 such non-adaptive female behavior evolves. In this study, we test two
 hypotheses about the evolution of female EPC behavior using population
 genetic models. First, we find that both male preference for allocating
 extra-effort to seek EPCs and female pursuit behavior without costs can be
 maintained and remain polymorphic in a population via frequency dependent
 selection. However, both behaviors cannot evolve when females with pursuit
 behavior suffer from a decline in male parental care. Second, we present
 another novel way in which female pursuit behavior can evolve; indirect
 selection can act on this behavior through a ratchet-like mechanism
 involving oscillating linkage disequilibria between the target EPC pursuit
 locus and two other loci determining male mate choice and a female sexual
 signal. Although the overall positive force of such indirect selection is
 relatively weak, our results suggest that it may still play a role in
 promoting the evolution of female EPC behavior when this behavior is
 non-adaptive (i.e., it is neutral) or only somewhat maladaptive (e.g.,
 males only occasionally lower parental care when their mates pursue EPCs).
description: nonadaptive
 FEPC_eigenvaluesmaladaptive
 FEPC_eigenvaluesFEPC_three_locus_simulationFEPC_BT
DOI: 10.5061/dryad.116td
title: Data from: Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae)

description: Adaptive evolution requires both raw genetic material and an accessible
 path of high fitness from one fitness peak to another. In this study, we
 used an introgression line (IL) population to map quantitative trait loci
 (QTL) for leaf traits thought to be associated with adaptation to
 precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A
 QTL Sign Test showed that several traits likely evolved under directional
 natural selection. Leaf traits correlated across species do not share a
 common genetic basis, consistent with a scenario in which selection
 maintains trait covariation unconstrained by pleiotropy or linkage
 disequilibrium. Two large effect QTL for stomatal distribution colocalized
 with key genes in the stomatal development pathway, suggesting promising
 candidates for the molecular bases of adaptation in these species.
 Furthermore, macroevolutionary transitions between vastly different
 stomatal distributions may not be constrained when such large effect
 mutations are available. Finally, genetic correlations between stomatal
 traits measured in this study and data on carbon isotope discrimination
 from the same ILs, support a functional hypothesis that the distribution
 of stomata affects the resistance to CO2 diffusion inside the leaf, a
 trait implicated in climatic adaptation in wild tomatoes. Along with
 evidence from previous comparative and experimental studies, this analysis
 indicates that leaf traits are an important component of climatic niche
 adaptation in wild tomatoes, and demonstrates that some trait transitions
 between species could have involved few, large effect genetic changes,
 allowing rapid responses to new environmental conditions.
description: Alignments and PAML
 results from stomatal candidate gene analysisdryaddata.zip
DOI: 10.5061/dryad.t5c97
title: Data from: Anthropogenic ecosystem disturbance and the recovery debt

description: Ecosystem recovery from anthropogenic disturbances, either without human
 intervention or assisted by ecological restoration, is increasingly
 occurring worldwide. As ecosystems progress through recovery, it is
 important to estimate any resulting deficit in biodiversity and functions.
 Here we use data from 3,035 sampling plots worldwide, to quantify the
 interim reduction of biodiversity and functions occurring during the
 recovery process (that is, the ‘recovery debt’). Compared with reference
 levels, recovering ecosystems run annual deficits of 46–51% for organism
 abundance, 27–33% for species diversity, 32–42% for carbon cycling and
 31–41% for nitrogen cycling. Our results are consistent across biomes but
 not across degrading factors. Our results suggest that recovering and
 restored ecosystems have less abundance, diversity and cycling of carbon
 and nitrogen than ‘undisturbed’ ecosystems, and that even if complete
 recovery is reached, an interim recovery debt will accumulate. Under such
 circumstances, increasing the quantity of less-functional ecosystems
 through ecological restoration and offsetting are inadequate alternatives
 to ecosystem protection.
description: Ecosystem recovery
 databaseThis meta-analytical
 database includes data from 354 studies of ecosystems undergoing recovery
 worldwide. We include ecosystem recovering from agriculture, logging,
 eutrophication, mining, hydrological disruption, overfishing, oil spills,
 and one natural disturbance, hurricanes. We include studies reporting
 three measures, two in the recovering ecosystem and one in a reference
 site.Moreno, Jones
 database.xlsxEcosytem recovery R
 scriptsR scripts used to
 calculate the recovery debt values with the meta-analytical database.
 Includes generalized mixed models, heterogeneity tests, and variance
 adjustments to meet meta-analytical criteria.Rdebt
 models.R
DOI: 10.5061/dryad.8527
title: Data from: To be seen or to hide: visual characteristics of body patterns for camouflage and communication in the Australian giant cuttlefish, Sepia apama.

description: It might seem obvious that a camouflaged animal must generally match its
 background whereas to be conspicuous an organism must differ from the
 background. However, the image parameters (or statistics) that evaluate
 the conspicuousness of patterns and textures are seldom well-defined, and
 animal coloration patterns are rarely compared quantitatively to their
 respective backgrounds. Here we examine this issue in the Australian giant
 cuttlefish Sepia apama. We confine our analysis to the best-known and
 simplest image statistic, the correlation in intensity between
 neighbouring pixels. S. apama can rapidly change their body patterns from
 assumed conspicuous signaling to assumed camouflage, thus providing an
 excellent and unique opportunity to investigate how such patterns differ
 in a single visual habitat. We describe the intensity variance and spatial
 frequency power spectra of these differing body patterns, and compare
 these patterns to the backgrounds against which they are viewed. The
 measured image statistics of camouflaged animals closely resemble their
 backgrounds, while signaling animals differ significantly from their
 backgrounds. Our findings may provide the basis for a set of general rules
 for crypsis and signals. Furthermore, our methods may be widely applicable
 to the quantitative study of animal coloration.
description: S. apama image stats
 dataData from images
 collected in field for spatial frequency power spectra, resulting log-log
 slopes, and pixel intensity variance (PIV). Includes sheets for
 camouflaging animals, signaling animals, corresponding backgrounds, and
 control images.
DOI: 10.5061/dryad.14c73
title: Data from: Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis

description: Mycorrhizal symbiosis is a widespread association between plant roots and
 mycorrhizal fungi, which is thought to contribute to plant niche
 differentiation and expansion. However, this has so far not been
 explicitly tested. To address the effect of mycorrhizal symbiosis on
 plants’ realized niches, we addressed how mycorrhizal status (i.e. the
 frequency of occurrence of mycorrhizal symbiosis), flexibility (i.e. the
 ability to grow both with and without mycorrhizal symbiosis) and type of a
 plant species affect the realized niche optima, widths and volumes. For
 this, we used co-occurrence data from the flora of the Netherlands along
 soil fertility, moisture, pH, salinity, light and temperature gradients.
 Phylogenetic dependency of the species was taken into account using
 phylogenetic generalized least squares models. We show that facultatively
 and flexibly mycorrhizal plants have the widest niches compared to
 non-mycorrhizal and obligately mycorrhizal, and inflexible plants
 respectively. Among obligate plant symbionts, ecto- and ericoid
 mycorrhizal plants exhibited the widest niches compared to plants with
 other mycorrhizal types. Also, plants with different mycorrhizal statuses
 and types differed in their realized niche optima. Synthesis. Our results
 indicate that mycorrhizal symbiosis mediates plant niche differentiation
 and expansion, facilitating the understanding of current distribution
 patterns of plant species, as well as predicting shifts in plant
 distribution and dominance due to environmental changes.
description: Mycorrhizal trait data
 and niche characteristics for vascular plants in the Dutch
 floraFile includes updated
 mycorrhizal status, type and flexibility data with new additional
 references, and realized niche optima, widths and volumes along soil
 fertility, pH, moisture, salinity, light and temperature axes for the
 vascular plant species in the Dutch flora. Also, a legend is provided as a
 separate sheet in the file. More details can be found in the README
 file.Gerz_2017_JEcol_data.xlsx
DOI: 10.5281/zenodo.18218638
title: Dissertation Dataset (NARS Evolution)