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opencc-by-4.0Jun 2017View details →

Extended Data Figure 5 in Host and viral traits predict zoonotic spillover from mammals

Extended Data Figure 5 | Global distribution of viral and host species richness for wild even-toed ungulates (order Cetartiodactyla). a, Observed total viral richness (for n = 70 host spp.); b, predicted total viral richness given maximum research effort; c, missing viruses or predicted minus observed total viral richness; d, observed zoonotic viral richness (n = 70);e, predicted zoonotic viral richness given maximum research effort; f, missing zoonoses or predicted minus observed zoonotic viral richness (same as included in Fig. 3c); g, global host species richness for Cetartiodactyla (n = 229);h, host species richness for Cetartiodactyla in our database (n = 105);i, species of the order Cetartiodactyla with no described viruses in the literature. Warmer colours (larger values) in c and f highlight areas predicted to be of greatest value for discovering novel viruses or novel viral zoonoses, respectively, in even-toed ungulates. Red/pink colours in panel i highlight areas with poor viral surveillance in even-toed ungulates species to date. Hatched regions represent areas where model predictions deviate systematically for the collection of species in that grid cell (see Methods).

opencc-zeroApr 2022View details →

Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly

Condition is assumed to reflect both genes and environment, enabling condition-dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness-related traits and condition-dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly Telostylinus angusticollis. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment-dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition-dependent traits to function as signals of genetic quality.

opencc-by-4.0Mar 2021View details →

Forming Impressions from Self-Truncated Samples of Traits - Interplay of Thurstonian and Brunswikian Sampling Effects

Data sets for both experiments of the article "Forming Impressions from Self-Truncated Samples of Traits - Interplay of Thurstonian and Brunswikian Sampling Effects" published in Journal of Personality and Social Psychology. Additionally norms for the trait adjectives used as stimulus materials in Experiment 2.

Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes

Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations, it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulates traits. Here we assess lipid content, growth, weight, and length variation in full and hybrid F1 crosses of deep and shallow water sympatric lake charr ecotypes reared for nine years in a common garden experiment. Redundancy analysis (RDA) and quantitative-trait-loci (QTL) genomic scans are used to identify associations between genotypes at 19,714 single nucleotide polymorphisms (SNPs) aligned to the lake charr genome and individual phenotypes to determine the role that genetic inheritance plays in ecotype phenotypic diversity. Lipid content, growth, length, and weight differed significantly among lake charr crosses throughout the experiment suggesting that pedigree plays a large role in lake charr development. Polygenic scores of 15 SNPs putatively associated with lipid content and/or condition factor indicated that ecotype distinguishing traits are polygenically regulated and additive. A QTL identified on chromosome 38 contained >200 genes, some of which were associated with lipid metabolism and growth, demonstrating the complex nature of ecotype diversity. The results of our common garden study further indicate that lake charr ecotypes observed in nature are pre-determined at birth and that ecotypes differ fundamentally in lipid metabolism and growth.

Personality, sperm traits and a test for their combined dependence on male condition in guppies

There is evidence that animal personality traits can have spill-over effects for sexual selection, with studies reporting that male behavioural types are associated with success during pre- and post-copulatory sexual selection. Given these links between personality and sexual traits, and the evidence that their expression can depend on an individual's nutritional status (i.e. condition), a novel prediction is that changes in a male's diet should alter both the average expression of personality and sexual traits, and their covariance. We tested these predictions using the guppy Poecilia reticulata, a species previously shown to exhibit strong condition dependence in ejaculate traits and a positive correlation between sperm production and individual variation in boldness. Contrary to expectation, we found that dietary restriction – when administered in mature adult males – did not affect the expression of either behavioural (boldness and activity) or ejaculate traits, although we did find that males subjected to dietary stress exhibited a positive association between sperm velocity and boldness that was not apparent in the unrestricted diet group. This latter finding points to possible context-dependent patterns of covariance between sexually selected and personality traits, which may have implications for patterns of selection and evolutionary processes under fluctuating environmental conditions.

Climatic history, constraints, and the plasticity of phytochemical traits under water stress

Environmental stress can induce changes in organismal traits and in resulting intraspecific variation. The nature of such effects will depend on the plasticity of trait expression and on any ecological constraints to such expression. Plants can mitigate abiotic stress, like drought, by changing their chemistry, but the ability to induce costly metabolites may be under strong local selection and ecologically constrained. Here we asked whether climate at the seed source predicts plant chemical plasticity in response to water stress and what the consequences are for intraspecific variation in phytochemical traits. To this end, we used common gardens of two widespread species of western milkweed (Asclepias fascicularis and Asclepias speciosa) that had been collected from sites across an aridity gradient. Both species produce high concentrations of leaf flavonols, which are hypothesized to mitigate water stress by functioning as antioxidants. These compounds were found in higher constitutive concentrations in plants sourced from drier sites, and both species responded to water stress in the common garden by increasing leaf flavonol concentrations. Interestingly, flavonol plasticity was higher in plants sourced from wetter sites in A. fascicularis, with similar, but weaker, patterns in A. speciosa. These opposing patterns in constitutive and induced flavonol expression reduced the variation between populations in leaf flavonol concentrations under water stress. These results suggest that local adaptation in plants can shape phytochemical strategies for water limitation but that the cost of metabolite production may ultimately limit the range of phytochemical variation.

opencc-by-4.0May 2022View details →

Code and data for "Species traits associated with rapid shifts in elevational distributions of Swiss birds"

Abstract Global change in climate and land use have profound effects on species’ geographic and elevational distributions. In European birds, while species are predicted to track their climatic niches upslope, lowland agricultural intensification and high elevation land abandonment can drive elevational shifts. Species traits that can predict response to change in climate and land use can inform conservation, but thorough examination of their relationships with elevational shifts in European birds are lacking. We estimate change in the elevational distributions of 71 species from 1996 to 2016 in a region of the western Palearctic with wide elevational gradients (approximately 3,000 m) and large changes in temperature. We model the relationships between elevational shifts and species traits associated with resource preference and adaptive capacity at five reference points including the cool edge, warm edge, and the core of species’ elevational distributions. When intermediate reference points were removed changes to the results were negligible, indicating that three reference points are likely sufficient. We found significant upslope and downslope shifts in 56% and 23% of our study species, respectively. Asymmetric rates of shifts in the cool and warm edges caused significant contractions in elevational extent in 30% of our study species. The effect of elevational preference (i.e. midpoint elevation) was habitat dependent. Movement in alpine birds was unidirectionally upslope, with nearly half displaying significant or apparent elevational range contractions. In woodland birds, asymmetries of shifts in reference points led to expansions in extent in low elevation species and contractions in high elevation species. Generally, migrants, species with smaller mass, smaller relative brain size, smaller hand-wing index, and generalists in diet, habitat, and elevation had greater upslope shifts. While elevational shifts in European birds were heterogenous and species-specific, many were rapid, and species traits associated with resource preference and adaptive capacity were associated with common patterns of elevation.

Geographical variation in the trait-based assembly patterns of multitrophic invertebrate communities

It has been argued that the mechanisms structuring ecological communities may be more generalizable when based on traits than on species identities. If so, patterns in the assembly of community-level traits along environmental gradients should be similar in different places in the world. Alternatively, geographic change in the species pool and regional variation in climate might result in site-specific relationships between community traits and local environments. These competing hypotheses are particularly untested for animal communities. Here we test the geographic constancy of trait-based assembly patterns using a widespread multi-trophic community: aquatic macroinvertebrates within bromeliads. We used data on 615 invertebrate taxa from 1656 bromeliads in 26 field sites from Mexico to Argentina. We summarized invertebrate traits with four orthogonal axes, and used these trait axes to examine trait convergence and divergence assembly patterns along three environmental gradients: detrital biomass and water volume in bromeliads, and canopy cover over bromeliads. We found no overall signal of trait-based assembly patterns along any of the environmental gradients. However, individual sites did show trait convergence along detrital and water gradients, and we built predictive models to explore these site differences. Sites that showed trait convergence along detrital gradients were all north of the Northern Andes. This geographic pattern may be related to phylogeographic differences in bromeliad morphology. Bromeliads with low detritus were dominated by detritivorous collectors and filter feeders, where those with high detritus had more sclerotized and predatory invertebrates. Sites that showed the strongest trait convergence along gradients in bromeliad water were in regions with seasonal precipitation. In such sites, bromeliads with low water were dominated by soft-bodied, benthic invertebrates with simple life cycles. In less seasonal sites, traits associated with short-term desiccation resistance, such as hard exoskeletons, were more important. In summary, we show that there are strong geographic effects on the trait-based assembly patterns of this invertebrate community, driven by the biogeography of their foundational plant species as well as by regional climate. We suggest that inclusion of biogeography and climate in trait-based community ecology could help make it a truly general theory. (excerpted from Srivastava, DS et al. 2022. Geographical variation in the trait-based assembly patterns of multitrophic invertebrate communities. Functional Ecology)

Data from: Composition of a chemical signalling trait varies with phylogeny and precipitation across an Australian lizard radiation

The environment presents challenges to the transmission and detection of animal signalling systems, resulting in selective pressures that can drive signal divergence among populations in disparate environments. For chemical signals, climate is a potentially important selective force because factors such as temperature and moisture influence the persistence and detection of chemicals. We investigated an Australian lizard radiation (Heteronotia) to explore relationships between a sexually dimorphic chemical signalling trait (epidermal pore secretions) and two key climate variables: temperature and precipitation. We reconstructed the phylogeny of Heteronotia with exon capture phylogenomics, estimated phylogenetic signal in among-lineage chemical variation, and assessed how chemical composition relates to temperature and precipitation using multivariate phylogenetic regressions. High estimates of phylogenetic signal indicate that the composition of epidermal pore secretions varies among lineages in a manner consistent with Brownian motion; although there are deviations to this, with stark divergences coinciding with two phylogenetic splits. Accounting for phylogenetic non-independence, we found that among-lineage chemical variation is associated with geographic variation in precipitation but not temperature. This contrasts somewhat with previous lizard studies, which have generally found an association between temperature and chemical composition. Our results suggest that geographic variation in precipitation can affect the evolution of chemical signalling traits, possibly influencing patterns of divergence among lineages and species.

opencc-zeroJun 2022View details →

Trait functional diversity explains mixture effects on litter decomposition at the arid end of a climate gradient

Litter decomposition is controlled by climate, litter quality and decomposer communities. Because the decomposition of specific litter types is also influenced by the properties of adjacent types, mixing litter types may result in non-additive effects on overall decomposition rates. The strength of these effects seems to depend on the litter functional diversity. However, it is unclear which functional traits or combination of traits explain litter mixture effects and if these depend on the range of trait values and the ecosystems involved. These uncertainties hamper our ability to predict decomposition in plant communities. We aimed at understanding whether and how functional diversity (measured as functional dispersion, FDis) influences litter decomposition, and how this influence varies among different climates and across decomposition stages. We calculated FDis based on litter traits related to nutrient concentrations or to litter recalcitrance, and tested whether these diversity measures and climatic parameters (soil moisture and temperature) explained litter mixture effects on decomposition. Additive mixture effects (i.e. decomposition of mixtures equalling the mean decomposition of the single litter types) were common in most of the evaluated climates. Non-additive, negative effects were mainly restricted to the driest and warmest sites, and decreased with time. Non-additive effects increased in magnitude with the mixtures' FDis, with positive effects being related to FDis in nutrient traits and negative effects being related to FDis in recalcitrance traits. Synthesis: Litter mixing did not have strong effects on decomposition rates across the studied climatic gradient overall, and the direction and intensity of the mixture effects were context-dependent. The effects were stronger and more negative in the dryer ecosystems. Where effects were found, functional diversity calculated from selected groups of traits (related to nutrients or litter recalcitrance) predicted mixture effects, especially where trait ranges were broad, though much of the variation remains unexplained. We propose that functional diversity metrics based on litter traits that are mechanistically relevant, applied to diverse site-specific litter mixtures in different climates, can help to better understand under which conditions and in which direction litter diversity affects decomposition.

opencc-by-4.0Dec 2021View details →

Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Data and code from: "Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana" published at Annals of Botany PLANTS. This is a dataset on phenotypic traits of Arabidopsis in response to different abiotic stresses and a reproducible R script to generate all figures and tables in the publication.

opencc-zeroJun 2022View details →

Data from: Plant host traits mediated by foliar fungal symbionts and secondary metabolites

Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2–370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, LASSO regression identified 12 metabolites that explained from 14–43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.

opencc-by-4.0Jun 2022View details →

Dataset: Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards

Dataset and R code associated with the following publication: Badiane et al. (2022), Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards. Journal of Animal Ecology, in press This dataset includes the following files: - An excel file containing the reflectance spectra of all individuals from all the study populations - An excel file containing the variables collected at the individual and population levels - Two R scripts corresponding to the analyses performed in the publication

opencc-zeroJul 2022View details →

Data from: Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands

This dataset contains data and code that support the results in Weil, S.-S., Martinez-Almoyna, C., Piton, G., Renaud, J., Boulangeat, L., Foulquier, A., ... & Thuiller, W. (2021) Strong links between plant traits and microbial activities but different abiotic drivers in mountain grasslands (accepted in Journal of Biogeography). We used an extensive plant-soil dataset that covers 14 elevational gradients (between 1500 and 2800 m of elevation) distributed over the whole French Alps to analyse the spatial co-dependencies between the plant and soil compartments. We ran a Graphical Lasso that extracts the direct and indirect linkages between plant functional composition, soil microbial activities, and environmental conditions (local climate and soil properties). Our main results are 1) that plant traits are tightly associated with microbial activities, the former being driven by climate and the latter by soil properties; 2) that the dominance of specific plant traits was more important than their diversity to determine plant-soil linkages; and 3) that soil microbes invested strongly in nutrient acquisition in sites with conservative plant traits and reduced organic matter quality.

The FloRes Database: A floral resources trait database for pollinator habitat-assessment generated by a multistep workflow

Background The decline of pollinating insects in agricultural landscapes proceeds due to intensive land use and the associated loss of habitat and food sources. The feeding of those insects depends on the spatial and temporal distribution of nectar and pollen as food resources. Hence, to protect insect biodiversity a spatio-temporal assessment of food quantity of their habitats is necessary. Therefore, sufficient data on traits of floral resources are required. New information Because floral resources' traits of plants are important to quantify food availability, we present two databases, the FloRes Database (Floral Resources Database) and the raw database, where FloRes was derived from. Both databases contain the plant traits (1) flowering period, (2) floral-unit density per day, (3) nectar volume per floral unit per day, (4) sugar content per floral unit, (5) sugar concentration in nectar, (6) pollen mass or volume per floral unit and per day, (7) protein content of pollen and (8) corolla depth. All traits are sampled from literature and online databases. The raw database consists of 702 specified plant species, 138 unspecified species 37 species (spec., sp), 22 species pluralis (spp) and for 79 only the genus was identified) and two species complexes (agg.). Those 842 taxa belong to 488 genera and 102 families. Finally, only 27 taxa have a complete set of traits, too less for a sufficient assessment of spatio-temporal availability of floral food resources. Because information of floral resources is scattered throughout many publications with different units, we also present our multistep workflow implemented in five consecutive R-scripts. The multistep workflow standardizes the trait units of the raw database to comparable entities with identical units and aggregates them on a reasonable taxonomic level into the second application database, the FloRes Database. Finally, the FloRes Database contains aggregated information of traits for 42 taxa and, when corolla depth is excluded, for 70 taxa. This is the first attempt to gather these eight traits from different literature sources in one database with a multistep workflow. The publication of the multistep workflow enables the users to extend the FloRes Database on their own demands with other literature data or newly gathered data to improve the quantification of food resources. Especially, the combination of pollen, nectar, and open flowers per square meter is, as far as we know, a novelty. The FloRes Database can be used to evaluate the quantity of food-resource habitats available for pollinators, e.g., to compare seed mixtures of agri-environmental measures, such as flower strips, considering flower phenology on a daily basis.

Functional traits and metacommunity theory reveal that habitat filtering and competition maintain bird diversity in a human shared landscape

Human shared landscapes cover much of Earth, yet their conservation value is contested. This controversy may persist because previous studies have examined species diversity, rather than the processes through which such diversity is maintained. For example, a site exhibiting high diversity may not actually bolster populations if the diversity is only maintained through net immigration. Recent research has begun to isolate the processes that maintain metacommunities and develop functional trait methods to identify these processes. However, the processes underlying bird communities remain obscure. Here, we leverage metacommunity theory, functional trait partitioning, and a Bayesian multispecies abundance model to assess whether a shared landscape – woody perennial polyculture farms – bolsters bird diversity. Such farms grow multiple species of food-producing woody perennials together with vegetative groundcover. We surveyed birds and their in situ functional traits across the US Midwest in traditional agriculture, woody perennial polyculture, prairie, and woods. We found that woody perennial polycultures exhibited the highest bird diversity and were the most preferred by many species (including threatened ones). Moreover, our functional trait analysis suggests that this diversity is maintained through habitat filtering and competition, rather than merely immigration. Thus, shared landscapes can likely conserve birds by providing a distinct habitat. These results suggest that woody perennial polyculture farms offer substantial potential to support bird populations in the US Midwest. Our study demonstrates the utility of in situ functional trait partitioning within a Bayesian framework to unmask ecological processes and help assess the conservation value of landscapes.

Changes in trait covariance along an orographic moisture gradient reveal the relative importance of light- and moisture-driven trade-offs in subtropical rainforest communities

• A range of functional trait-based approaches have been developed to investigate community assembly processes, but most ignore how traits covary within communities. • We combined existing approaches (community-weighted means [CWMs] and functional dispersion [FDis]) with a metric of trait covariance to examine assembly processes in five angiosperm assemblages along a moisture gradient in Australia's subtropics. In addition to testing hypotheses about habitat filtering along the gradient, we hypothesised that trait covariance would be strongest at both ends of the moisture gradient and weakest in the middle, reflecting trade-offs associated with light capture in productive sites and moisture stress in dry sites. • CWMs revealed evidence of climatic filtering, but FDis patterns were less clear. As hypothesised, trait covariance was weakest in the middle of the gradient, but unexpectedly peaked at the second driest site due to the emergence of a clear drought tolerance – drought avoidance spectrum. At the driest site, the same spectrum was truncated at the 'avoider' end, revealing important information about habitat filtering in this system. • Our focus on trait covariance revealed the nature and strength of trade-offs imposed by light and moisture availability, and complemented insights gained about community assembly from existing trait-based approaches.

Onthophagus babirussa sexual size dimporphism and male sexual trait files and R codes

Sexual size dimorphism (SSD) arises when natural selection and sexual selection act differently on males and females. Male-biased SSD is rare in insects and usually indicates strong selection pressure on a population or species. Patterns of SSD can also vary between populations of species that are exposed to different environmental conditions, such as differing resource availability and diversity. Here, we investigate intra-specific variation in SSD as well as relative investment in precopulatory (horn length) and postcopulatory traits (sperm length and testes weight) in a tropical rainforest dung beetle Onthophagus babirussa across Singapore and Peninsular Malaysia. Overall, three out of four populations displayed significant male-biased SSD and SSD was greater in populations with smaller overall body size. Average male body size was similar across all populations while female body size was significantly smaller in Singapore, suggesting that the pronounced SSD may also be due to stronger sexual selection on male body size in Singapore populations. All populations showed significant investment in horns as a weapon used in precopulatory competition, while postcopulatory traits showed no clear scaling relationship with body size, suggesting a higher priority on precopulatory sexual traits in the mating system of this species.

Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species

Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST-FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST-FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.