cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hb2bt
title: Data from: Can plants evolve tolerance mechanisms to heterospecific pollen effects? An experimental test of the adaptive potential in Clarkia species

description: Flowering plants do not occur alone and often grow in mixed-species
 communities where pollinator sharing is high and interactions via
 pollinators can occur at pre- and post-pollination stages. While the
 causes and consequences of pre-pollination interactions have been well
 studied little is known about post-pollination interactions via
 heterospecific pollen (HP) receipt, and even less about the evolutionary
 implications of these interactions. In particular, the degree to which
 plants can evolve tolerance mechanisms to the negative effects of HP
 receipt has received little attention. Here, we aim to fill this gap in
 our understanding of post-pollination interactions by experimentally
 testing whether two co-flowering Clarkia species can evolve HP tolerance,
 and whether tolerance to specific HP ‘genotypes’ (fine-scale local
 adaptation to HP) occurs. We find that Clarkia species vary in their
 tolerance to HP effects. Furthermore, conspecific pollen performance and
 the magnitude of HP effects were related to the recipient's history
 of exposure to HP in C. xantiana but not in C. speciosa. Specifically,
 better conspecific pollen performance and smaller HP effects were observed
 in populations of C. xantiana plants with previous exposure to HP compared
 to populations without such exposure. These results suggest that plants
 may have the potential to evolve tolerance mechanisms to HP effects but
 that these may occur not from the female (stigma, style) but from the male
 (pollen) perspective, a possibility that is often overlooked. We find no
 evidence for fine-scale local adaptation to HP receipt. Studies that
 evaluate the adaptive potential of plants to the negative effects of HP
 receipt are an important first step in understanding the evolutionary
 consequences of plant–plant post-pollination interactions. Such knowledge
 is in turn crucial for deciphering the role of plant–pollinator
 interactions in driving floral evolution and the composition of
 co-flowering communities.
description: Heterospecific pollen
 tolerance_Clarkia 2014 pollen tube dataClarkia 2014 pollen tube
 data.xlsx
DOI: 10.5061/dryad.p15br
title: Data from: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene

description: Loci that can be used to screen for sex in salmon can provide important
 information for study of both wild and cultured populations. Here, we
 tested for associations between sex and genotypes at thousands of loci
 available from a genotyping-by-sequencing (GBS) dataset to discover
 sex-associated loci in sockeye salmon (Oncorhynchus nerka). We discovered
 seven sex-associated loci, developed high-throughput assays for two loci,
 and tested the utility of these two assays in eight collections of sockeye
 salmon sampled throughout North America. We also screened an existing
 assay based on the master sex-determining gene in salmon (sdY) in these
 collections. The ability of GBS-derived loci to assign fish to their
 phenotypic sex varied substantially among collections suggesting that
 recombination between the loci that we discovered and the sex-determining
 gene has occurred. Assignment accuracy to phenotypic sex was much higher
 with the sdY assay but was still less than 100%. Alignment of sequences
 from GBS-derived loci to draft genomes for two salmonids provided strong
 evidence that many of these loci are found on the chromosome orthologous
 to the known sex chromosome in sockeye salmon. Our study is the first to
 describe the approximate location of the sex-determining region in sockeye
 salmon and indicates that sdY is also the master sex-determining gene in
 this species. However, discordances between sdY genotypes and phenotypic
 sex and the variable performance of GBS-derived loci warrant more
 research.
description: RAD genotypes at
 sex-associated loci for Wood River individualsRAD genotypes at seven
 sex-associated loci in 286 individuals from the Wood River basin. Some
 loci contain multiple SNPs (e.g. locus 30453). The position of the SNP in
 the RAD tag is found after the underscore in the locus designation (e.g
 designation 30453_92 contains genotypes for a SNP at position 92 in locus
 30453). Presence/absence loci do not contain SNPs. Individuals were
 sampled from six locations in the Wood River basin and each location is
 designated with a different code in the individuals
 column.RAD_genotypes_and_sex_for_wood_river_individuals.xlsxgenotype data from 5'-nuclease, sdY, and 18s assays in 8 collectionsGenotype data from two 5'-nuclease assays developed from RAD data (61628, 76412), sdY, and 18s assays. If 18s was absent, the genotype for sdY was considered a no call, even if an sdY band was present.5_prime_nuclease_sdy_and_18s_genotypes_all_collections.xlsx
DOI: 10.5061/dryad.c1d09
title: Data from: Weak olfaction increases seed scatter-hoarding by Siberian chipmunks: implication in shaping plant-animal interactions

description: Scatter-hoarding of seeds by animals plays an essential role in seed
 dispersal of plants and in shaping plant–animal interactions in forest
 ecosystems, but the function of scatter-hoarding behavior is still
 unclear. We hypothesize that weak olfactory cues between seeds and
 scatter-hoarding animals would increase scatter-hoarding. Using a
 rodent–plant system of Siberian chipmunks Tamias sibiricus and Korean
 pines Pinus koraiensis, we tested the effects on seed scatter-hoarding
 intensity by measuring and modifying the seed odor intensities and the
 abilities of the animals to detect seed odor. Siberian chipmunks seemed to
 scatter-hoard more seeds with weaker odor signals, and Siberian chipmunks
 with reduced olfactory ability scatter-hoarded more seeds, supporting our
 hypothesis. Our studies suggest that olfaction may have played an
 important role in the evolution of the strength of seed odor and
 scatter-hoarding behavior of animals, and in shaping plant–animal
 interactions.
description: Oikos
 data-Yi
DOI: 10.5061/dryad.b0r5q
title: Data from: Selective modulation of interhemispheric functional connectivity by HD-tACS shapes perception

description: Oscillatory neuronal synchronization between cortical areas has been
 suggested to constitute a flexible mechanism to coordinate information
 flow in the human cerebral cortex. However, it remains unclear whether
 synchronized neuronal activity merely represents an epiphenomenon or
 whether it is causally involved in the selective gating of information.
 Here, we combined bilateral high-density transcranial alternating current
 stimulation (HD-tACS) at 40 Hz with simultaneous electroencephalographic
 (EEG) recordings to study immediate electrophysiological effects during
 the selective entrainment of oscillatory gamma-band signatures. We found
 that interhemispheric functional connectivity was modulated in a
 predictable, phase-specific way: In-phase stimulation enhanced
 synchronization, anti-phase stimulation impaired functional coupling.
 Perceptual correlates of these connectivity changes were found in an
 ambiguous motion task, which strongly support the functional relevance of
 long-range neuronal coupling. Additionally, our results revealed a
 decrease in oscillatory alpha power in response to the entrainment of
 gamma band signatures. This finding provides causal evidence for the
 antagonistic role of alpha and gamma oscillations in the parieto-occipital
 cortex and confirms that the observed gamma band modulations were
 physiological in nature. Our results demonstrate that synchronized
 cortical network activity across several spatiotemporal scales is
 essential for conscious perception and cognition.
description: DataS1In accordance with the
 data policy at PloS Biology, the dataset used to reach the main
 conclusions drawn in this study is available as an Excel
 File.
DOI: 10.5061/dryad.44154
title: Data from: Human commercial models’ eye colour shows negative frequency-dependent selection

description: In this study we investigated the eye colour of human commercial models
 registered in the UK (400 female and 400 male) and Brazil (400 female and
 400 male) to test the hypothesis that model eye colour frequency was the
 result of negative frequency-dependent selection. The eye colours of the
 models were classified as: blue, brown or intermediate. Chi-square
 analyses of data for countries separated by sex showed that in the United
 Kingdom brown eyes and intermediate colours were significantly more
 frequent than expected in comparison to the general United Kingdom
 population (P&lt;0.001). In Brazil, the most frequent eye colour brown
 was significantly less frequent than expected in comparison to the general
 Brazilian population. These results support the hypothesis that model eye
 colour is the result of negative frequency-dependent selection. This could
 be the result of people using eye colour as a marker of genetic diversity
 and finding rarer eye colours more attractive because of the potential
 advantage more genetically diverse offspring that could result from such a
 choice. Eye colour may be important because in comparison to many other
 physical traits (e.g., hair colour) it is hard to modify, hide or
 disguise, and it is highly polymorphic.
description: Raw
 dataThe file contains
 spreadsheets of Brazilian and UK models eye colour, including columns for
 the agency.rarephenotype raw
 data.xlsx
DOI: 10.5061/dryad.74v52
title: Data from: Range contraction and increasing isolation of a polar bear subpopulation in an era of sea-ice loss

description: Climate change is expected to result in range shifts and habitat
 fragmentation for many species. In the Arctic, loss of sea ice will reduce
 barriers to dispersal or eliminate movement corridors, resulting in
 increased connectivity or geographic isolation with sweeping implications
 for conservation. We used satellite telemetry, data from individually
 marked animals (research and harvest), and microsatellite genetic data to
 examine changes in geographic range, emigration, and interpopulation
 connectivity of the Baffin Bay (BB) polar bear (Ursus maritimus)
 subpopulation over a 25-year period of sea-ice loss. Satellite telemetry
 collected from n = 43 (1991–1995) and 38 (2009–2015) adult females
 revealed a significant contraction in subpopulation range size (95%
 bivariate normal kernel range) in most months and seasons, with the most
 marked reduction being a 70% decline in summer from 716,000 km2 (SE
 58,000) to 211,000 km2 (SE 23,000) (p &lt; .001). Between the 1990s
 and 2000s, there was a significant shift northward during the on-ice
 seasons (2.6° shift in winter median latitude, 1.1° shift in spring median
 latitude) and a significant range contraction in the ice-free summers.
 Bears in the 2000s were less likely to leave BB, with significant
 reductions in the numbers of bears moving into Davis Strait (DS) in winter
 and Lancaster Sound (LS) in summer. Harvest recoveries suggested both
 short and long-term fidelity to BB remained high over both periods (83–99%
 of marked bears remained in BB). Genetic analyses using eight polymorphic
 microsatellites confirmed a previously documented differentiation between
 BB, DS, and LS; yet weakly differentiated BB from Kane Basin (KB) for the
 first time. Our results provide the first multiple lines of evidence for
 an increasingly geographically and functionally isolated subpopulation of
 polar bears in the context of long-term sea-ice loss. This may be
 indicative of future patterns for other polar bear subpopulations under
 climate change.
description: Laidre et al EcolEv
 genetic data FINALMicrosatellite data from
 four polar bear subpopulations in support of Laidre et al. Ecology and
 Evolution
DOI: 10.5061/dryad.53550
title: Data from: More for less: sampling strategies of plant functional traits across local environmental gradients

description: Ecologists use approaches based on plant functional traits to tackle
 several fundamental and applied questions. Although a perfect
 characterization of functional trait structure requires the measurement of
 all the individuals in communities, this is prohibitively
 resource-consuming. Consequently, the general practice is to average the
 trait values of a reduced number of individuals per species. However,
 there are different alternatives regarding the number, identity and
 spatial location of the individuals chosen to calculate species-averaged
 trait values. In this study, we compared different strategies for sampling
 functional traits, using community-weighted mean trait values (CWM) and
 the Rao index of functional diversity (FD). We intensively sampled the
 functional trait structure along a topographical gradient in a
 Mediterranean grassland, obtaining accurate estimations of the ‘real’
 values of these indices (CWMI and FDI) for three traits (height, leaf area
 and specific leaf area). We simulated three different sampling strategies
 differing in the spatial location of the individuals used to estimate
 species-mean trait: i) average of the whole gradient (GLO), ii) average of
 the sampling unit in which the abundances of species maximize (MAX) and
 iii) average of a reduced number of individuals per species and sampling
 unit (LOC). For each strategy, we simulated different sampling intensities
 (number of individuals sampled). For each trait, we examined the ability
 of each strategy and sampling intensity to accurately estimate CWMI and
 FDI, as well as their ability to detect changes in functional trait
 structure along the topographical gradient. LOC outperformed the other
 strategies in terms of accuracy and bias, and was much more efficient to
 describe changes along the gradient, regardless of the traits and
 indicators considered. Furthermore, LOC was the only strategy that
 improved consistently as sampling intensity increased, especially at low
 levels of intensity. Our results indicate that the impact of considering
 intraspecific variability in trait values can be greater than commonly
 assumed. Strategies that neglect this source of variability can result in
 inaccurate or biased estimations of the functional trait structure of
 plant communities. Most importantly, we show that intraspecific
 variability can be taken into consideration without any increases in the
 total number of individuals measured.
description: Traits per species and
 quadratData collected in the
 field including the proportional cover of each species in each sampling
 unit (20 x 20 cm quadrats). Sampling units are ordered according to its
 position in an environmental gradient. For each species and sampling unit,
 up to 10 individual plants were sampled and its functional traits measured
 (plant height, leaf area and specific leaf area)Species
 keyScientific names of the
 sampled species
DOI: 10.5061/dryad.2p303
title: Data from: Ex situ cultivation entails high risk of seed dormancy loss on short-lived wild plant species

description: 1. Changes in life-history traits such as seed dormancy during cultivation
 of wild plant species in ex situ facilities could jeopardise conservation
 actions such as revegetation and plant reintroductions, but the magnitude
 of these risks and their spread across different plant taxa is unknown. 2.
 In this study, we explored whether plants cultivated in the Botanic Garden
 Meise differ in seed germination characteristics from plants from natural
 populations. Using a Bayesian approach of a phylogenetically informed
 generalized linear mixed model, we analysed germination tests of 72
 herbaceous plant species from 27 plant families, originating from the
 cultivation beds in Meise as well as directly from wild populations. We
 investigated whether garden-collected seeds differ in germination
 percentage, seed dormancy and germination speed from wild-collected seeds.
 Furthermore, by analysing literature-collected information of 24
 life-history traits, we sought to identify potential selection pressures
 causing these germination changes in order to refine conservation
 protocols and practices. 3. We found a strong increase of germination
 percentage and a loss of seed dormancy in garden seeds compared to wild
 seeds across all species. However, these differences vanished with
 increasing storage time of the seeds as a result of decreased seed
 viability with seed aging over time. 4. Furthermore, traits associated
 with the life span of the species influenced the germination difference
 between cultivated and wild seeds, and short-lived species were
 particularly vulnerable to the loss of dormancy, while no difference could
 be detected between wild and cultivated perennial species. 5. Synthesis
 and applications: By the multi-species approach, we provide evidence that
 dormancy loss is a common phenomenon in ex situ collections of short-lived
 wild plant species. This has wide implications for the use and procedure
 of ex situ reared plant material for restoration and reintroduction
 measures. We suggest that effective dormancy breaking and temporal
 distribution of seedling plantation during propagation should be
 incorporated in restoration and reintroduction protocols to minimize
 unwanted changes in seed traits. Furthermore, we caution against the use
 of seeds from cultivated plants for basic seed ecology research such as
 germination requirements and seed storage behaviour.
description: Datafile_GerminationTestsDatafile of the germination tests of the species. A legend of the header is in the datafile
DOI: 10.5061/dryad.210mp
title: Data from: A three-stage symbiosis forms the foundation of seagrass ecosystems

description: Seagrasses evolved from terrestrial plants into marine foundation species
 around 100 million years ago. Their ecological success, however, remains a
 mystery because natural organic matter accumulation within the beds should
 result in toxic sediment sulfide levels. Using a meta-analysis, a field
 study, and a laboratory experiment, we reveal how an ancient three-stage
 symbiosis between seagrass, lucinid bivalves, and their sulfide-oxidizing
 gill bacteria reduces sulfide stress for seagrasses. We found that the
 bivalve–sulfide-oxidizer symbiosis reduced sulfide levels and enhanced
 seagrass production as measured in biomass. In turn, the bivalves and
 their endosymbionts profit from organic matter accumulation and radial
 oxygen release from the seagrass roots. These findings elucidate the
 long-term success of seagrasses in warm waters and offer new prospects for
 seagrass ecosystem conservation.
description: Experimental
 dataData from the
 Zostera-Loripes-Sulfide laboratory experiment.Experimental_data.xlsx
DOI: 10.5061/dryad.v31k428
title: Data from: Hosts do not simply outsource pathogen resistance to protective symbionts

description: Microbial symbionts commonly protect their hosts from natural enemies, but
 it is unclear how protective symbionts influence the evolution of host
 immunity to pathogens. One possibility is that ‘extrinsic’ protection
 provided by symbionts allows hosts to reduce investment in ‘intrinsic’
 immunological resistance mechanisms. We tested this idea using pea aphids
 (Acyrthosiphon pisum) and their facultative bacterial symbionts that
 increase host resistance to the fungal pathogen Pandora neoaphidis. The
 pea aphid taxon is composed of multiple host plant associated populations
 called biotypes, which harbour characteristic communities of symbionts. We
 found that biotypes that more frequently carry protective symbionts have
 higher, rather than lower, levels of intrinsic resistance. Within a
 biotype there was no difference in intrinsic resistance between clones
 that did and did not carry a protective symbiont. The host plant on which
 an aphid feeds did not strongly influence intrinsic resistance. We
 describe a simple conceptual model of the interaction between intrinsic
 and extrinsic resistance and suggest that our results may be explained by
 selection favouring both the acquisition of protective symbionts and
 enhanced intrinsic resistance in habitats with high pathogen pressure.
 Such combined protection is potentially more robust than intrinsic
 resistance alone.
description: Primary data from
 experiment 1 and 2File contains primary
 data of aphid survival and sporulation in experiment 1 and 2, and also
 data on symbiont field frequency taken from Henry et al 2013 and used for
 correlation with data from experiment 1.Hrcek_et_al_Evolution 2018
 _Primary_data_from_experiment_1_and_2.xls
DOI: 10.5061/dryad.k114944
title: Data from: Why do top predators engage in superpredation? From an empirical scenario to a theoretical framework

description: Lethal interactions can shape ecosystem structure, and consequently
 understanding their causes is ecologically relevant. To improve both
 empirical and theoretical knowledge on superpredation (i.e. predation on
 high-order predators), we studied an eagle owl population, including its
 main prey and mesopredators, and then we crossed these results with
 existing theories to provide a reasoning framework. We fitted our field
 data into four main causes explaining lethal interactions: food stress,
 opportunistic superpredation, removal of a competitor, and removal of a
 potential threat. Empirically, superpredation seemed to be mostly
 determined by the combination of the food-stress and
 opportunistic-superpredation hypotheses, which highlights the complexity
 of the factors triggering superpredation. Therefore, besides being a
 response to lower food availability, superpredation may also represent an
 effective mechanism to remove potential predators and/or competitors,
 either intentionally or not. Our theoretical framework focused on the
 decision-making process in superpredation, considering four inter-related
 stages: encountering; attacking; and capturing a mesopredator; as well as
 consuming a mesopredator once killed. Superpredation almost certainly
 results from a complex process of decision-making, accounting for costs
 and benefits assessed moment-to-moment and for each mesopredator
 individual. It is time to build bridges between theoretical and empirical
 studies to further understand the mechanisms driving complex interactions
 among top predators and mesopredators.
description: Data for eagle owl nest
 sitesData for eagle owl nest
 sites with: 1) the abundance of the main prey (rabbits); 2) the abundance
 of mesopredators (owls and raptors); 3) the percentage in the diet of main
 prey groups and mesopredatorsPAPER_DATA_DRYAD_NEST_SITES.xlsData on mesopredator speciesData on the ranks attributed to the species of mesopredators in terms of their abundance near eagle owl nest sites, their percentage in the diet of eagle owls, and their biomass ratio with the eagle owl.PAPER_DATA_DRYAD_SPECIES.xls