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opencc-by-4.0Jan 2023View details →

Plant functional traits and corresponding satellite multispectral data for two sites in the Czech Republic

This data set contains measurements of plant functional traits and corresponding satellite multispectral data for two sites in the Czech Republic – Lanžhot and &Scaron;títná throughout multiple campaigns. Plant functional traits were collected from representative trees selected at both study sites. At the Lanžhot site, a total of 16 trees of the following species were sampled: Quercus robur (4 trees), Quercus cerris L. (2 trees), Carpinus betulus (4 trees), Fraxinus angustifolia (4 trees), Tilia cordata (2 trees). At &Scaron;títná, a total of 10 Fagus sylvatica trees were sampled. Field campaigns were timed to cover different phenological stages of deciduous tree leaf development, from fresh leaf emergence, through full leaf development at the peak of the growing season, to autumn leaf senescence. In total, six field campaigns at Lanžhot during 2019 and 2020 and five field campaigns at &Scaron;títná during 2020 and 2021 were conducted.

Data from: Landscape variation in defense traits along gradients of multiple resources in a tropical savanna plant

Many plant species are widely distributed and consequently are exposed to multiple abiotic factors and diverse herbivores, each of which may distinctly affect the magnitude of different defense traits. Alternative theories for optimal allocation to plant defense traits predict both positive and negative associations between magnitude of defense and resource availability. These predictions may apply even within species. This suggests potential for a single species' patterns of association of defense traits and resources to vary with both the type of defense and identity of resource, but relatively few studies have explored intraspecific variation in multiple defense traits along several resource gradients simultaneously. In order to address this gap, especially in an ecosystem dominated by large mammalian herbivores, we assessed relationships between multiple resources (rainfall, soil N, and soil P) and plant defense traits (prickle density, phenolics, and lignin content) using a widely distributed tropical savanna herb, Solanum incanum, growing in naturally occurring resource gradients within the Serengeti National Park. We found substantial intraspecific variation in all three defense traits across sites (n =43). Variation in prickle density was positively associated with rainfall and soil P, but not soil N. In contrast to prickle density, phenolics and lignin were uncorrelated with all three resource gradients. This independent association of soil P with a carbon-based defense, prickle density, suggests potential for resources that are not components of defenses to influence allocation to defense traits. Such influence may reflect association between resource and herbivore abundance and/or preference. These varied patterns in resource-defense associations further emphasize the tremendous variation in anti-herbivore traits which may be influenced by different plant resources and highlight the need to consider multiple resource gradients in understanding evolution of plant traits.

Acer and Quercus root traits plasticity

Introduction: Plant nutrient acquisition strategies range along a spectrum from autonomous foraging to investment in cooperative foraging through mycorrhizal associations. However, in temperate ecosystems, many plant species encounter contrasted levels of symbiont availability in open fields versus closed forests. Little is known about how fungal partner availability may be associated with intraspecific variation in other root foraging traits in natural settings. Methods: Here, we addressed this issue by sampling saplings from two tree species: the arbuscular mycorrhizal (AM) Acer rubrum and the ectomycorrhizal (ECM) Quercus rubra from open fields (AM-dominated) and adjacent forest plots (ECM-dominated). For each species and environment, we measured morphological, architectural, and symbiotic root traits. Results: For the open field, Quercus had greater specific root length (SRL) while Acer had higher AM colonization and root diameter. In the closed forest, the opposite pattern was observed, namely Quercus had higher ECM colonization and Acer greater SRL. Discussion: Both species showed evidence of a shift toward autonomous root foraging in the habitat with low expected symbiont abundance (open field for Quercus and forest for Acer). Although the confounding effects of site abiotic properties could not be strictly controlled in this study, these results suggest that plants might adjust root foraging traits according to local habitat conditions. Synthesis: Our results shed new light on the intraspecific variation in plant position along the so-called "collaboration gradient", and suggest that mycorrhizal symbiont availability, along with other factors such as competition and site properties, may contribute to this variation.

To disperse or compete? Coevolution of traits leads to a limited number of reproductive strategies

Reproductive strategies are defined by a combination of behavioural, morphological, and life-history traits. Reproductive investment and offspring propagule size are two key traits defining reproductive strategies. While a substantial amount of work has been devoted to understanding the independent fitness effects of each of these traits, it remains unclear how coevolution between them ultimately affects the evolution of reproductive strategies, and how this might influence the relationship between dispersal and environmental factors. In this study, we explore how the evolution of reproductive strategies defined by these two coevolving traits is influenced by resource availability and spatial structuring of the environment using a simulation model. We find three possible equilibrium strategies across all scenarios: a competitor strategy with high reproductive investment (producing large propagules which disperse short distances), and two coloniser strategies differing in reproductive investment (both producing small propagules which disperse long distances). The possible equilibrium strategies for each scenario depended on starting conditions, spatial structure and resource availability. Evolutionary transitions between these equilibrium strategies were more likely in heterogeneous than homogeneous landscapes and at higher resource levels. Transition from coloniser strategy to competitor strategy was usually a two-step process, with changes in propagule size following initial evolution in investment. This highlights how the interaction between the two trait axes affects the evolution of reproductive strategies, particularly where fitness valleys preclude the simultaneous evolution of traits. Our results highlight the need to incorporate trait coevolution into evolutionary models to help develop a more integrative understanding of the structure of natural populations and how the interaction between traits constrains or hinders evolutionary processes.

opencc-by-4.0May 2023View details →

Data from: A framework to apply trait-based ecological restoration at large scales

R scripts and data to run the proposed framework at Coutinho, A. G., Carlucci, M. B., Cianciaruso, M. V. (2023) A framework to apply trait-based ecological restoration at large scales. Journal of Applied Ecology.

Data for: Traits help explain species' performance away from their climate niche centre

Aim: Climate change impacts on biota are variable across sites, among species, and throughout individual species' ranges. Niche theory predicts that population performance should decline as site climate becomes increasingly different from the species' climate niche centre, though studies find significant variation from these predictions. Here, we propose that predictions about climate responses can be improved by incorporating species' trait information. Location: Europe Methods: We used observations of plant species abundance change over time to assess variation in climate difference sensitivity (CDS), defined as how species performance (colonization, extinction, and abundance change) relates to the difference of site climate from the mean temperature and precipitation of each species' range. We then investigated if leaf economics, plant size, and seed mass traits were associated with the species' climate difference sensitivity. Results: Species that performed better (e.g., increased in abundance) towards sites progressively cooler than their niche centre were shorter and had more resource-acquisitive leaves (i.e., lower leaf dry matter content or LDMC) relative to species with zero or the opposite pattern of temperature difference sensitivity. This result supports the hypothesis that if sites cooler than niche centre are more stressful for a species, then shorter stature is advantageous compared to taller species. The LDMC result suggests the environment selects for more resource-acquisitive leaf strategies towards relatively cooler climates with shorter growing seasons, counter to expectations that conservative strategies would be favoured in such environments. We found few consistent relationships between precipitation difference sensitivities and traits. Main conclusions: The results supported key a priori foundations on how trait-based plant strategies dictate species responses to climate variation away from their niche centre. Further, plant height emerged as the most consistent trait that varied with species climate difference sensitivity, suggesting height will be key for theory development around species response to climate change.

opencc-by-4.0May 2023View details →

Exotic fish species traits across levels of establishment

Data for reproducing the results obtained by Bernery, Marino & Bellard (2023) in the paper "Relative importance of exotic species traits in determining invasiveness across levels of establishment: Example of freshwater fish" Data description and scripts for running the analyses are available at: https://github.com/claramarino/estab_levels_exotic_fish

The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions

Interspecific relationships between growth and survival are critical determinants of tree species diversity maintenance in forests. The trade-offs between growth and survival in co-occurring tree species are believed to arise along a continuum of life-history strategies. For example, co-occurring species range from those that grow slowly and survive well in resource-poor environments to those that grow quickly but have low survival rates in resource-rich environments. However, uncertainties remain regarding how growth-survival trade-offs are related to species traits, tree sizes, or environmental conditions. We examined how the relationships between species traits and growth–survival relationships shift in response to changes in stem sizes and across census periods with different climate conditions (frequency of strong winds, drought intensity) across 45 co-occurring tree species based on 23 years of growth and survival records in a warm temperate rain forest on Yakushima Island, Japan. We developed hierarchical Bayesian models of relative growth and survival rates, including leaf traits, wood density, and 95-percentile maximum stem diameter as explanatory variables. We tested the relationships between estimated trait-mediated growth–survival relationships and the intensities of climate events during five census periods. Each trait's effects on growth–survival relationships differed across the five census periods in response to climate conditions. Interspecific growth–survival relationships affected by a single trait axis for leaves or wood tended to be negative. In contrast, those affected by the maximum stem diameter tended to be positive. Such trends increased with more frequent strong winds or more intense droughts. The single-trait effects on growth–survival relationships were stronger for smaller sizes than for larger sizes. For all traits combined, we found a significant growth–survival trade-off only for small-sized stems in three of five census periods. Synthesis: Our results indicate that the effect of species traits on the growth–survival relationships depended on tree sizes, the census periods, or both in response to the frequency or intensity of climate events. We argue the importance of incorporating spatial and temporal variations in environmental conditions into long-term data from tree census to predict forest dynamics.

Amazonian Odonata trait bank

Discussion regarding the gaps of knowledge on Odonata is common in the literature. Such gaps are even greater when dealing with basic biological data for biodiverse environments like the Amazon Rainforest. Therefore, studies that address, classify and standardize functional traits allow the elaboration of a wide range of ecological hypotheses. Here, our main goal was to produce a database with 68 functional traits of 218 Odonata species that occur in the Brazilian Amazon. As a result, we provide a functional matrix and identified different functional patterns for the suborders, as well as a strong relationship between the different categories of traits. For this reason, we recommend choosing key traits that represent a set of functional variables, reducing the sampling efforts. In conclusion, we detect and discuss gaps in current literature and suggest possible paths to be taken or implement to increase our knowledge of odonate biology and ecology.

When the neighborhood matters: contextual selection on seedling traits in native and non-native California grasses

Plants interact extensively with their neighbors, but the evolutionary consequences of variation in neighbor identity are not well understood. Seedling traits are likely to experience selection that depends on the identity of neighbors because they influence competitive outcomes. To explore this, we evaluated selection on seed mass and emergence time in two California grasses, the native perennial Stipa pulchra and the non-native annual Bromus diandrus, in the field with six other native and non-native neighbor grasses in individual and mixed species treatments. We also quantified characteristics of each neighbor treatment to further investigate factors influencing their effects on fitness and phenotypic selection. Selection favored larger seeds in both focal species and this was largely independent of neighbor identity. Selection generally favored earlier emergence in both focal species, but neighbor identity influenced the strength and direction of selection on emergence time in S. pulchra but not B. diandrus. Greater light interception, higher soil moisture, and greater productivity of neighbors was associated with more intense selection for earlier emergence and larger seeds. Our findings suggest that changes in plant community composition can alter patterns of selection in seedling traits, and that these effects can be associated with measurable characteristics of the community.

Facilitation strength across environmental and beneficiary trait gradients in stream communities

Ecosystem engineers modify habitats in ways that facilitate other community members by ameliorating harsh conditions. The strength of such facilitation is predicted to be influenced by both beneficiary traits and abiotic context. One key trait of animals that could control the strength of facilitation is beneficiary body size because it should determine how beneficiaries fit within and exploit stress ameliorating habitat modifications. However, few studies have measured how beneficiary body size relates to facilitation strength along environmental gradients. We examined how the strength of facilitation by net-spinning caddisflies on invertebrate communities in streams varied along an elevation gradient and based on traits of the invertebrate beneficiaries. We measured whether use of silk retreats as habitat concentrated invertebrate density and biomass compared to surrounding rock-surface habitat and whether the use of retreat habitat varied across body sizes of community members along the gradient. We found that retreats substantially concentrated the densities of a diversity of taxa including eight different Orders, and this effect was greatest at high elevations. Caddisfly retreats also concentrated invertebrate biomass more as elevation increased. Body size of invertebrates inhabiting retreats was lower than that of surrounding rock habitats at low elevation sites, however body size between retreats and rocks converged at higher elevation sites. Additionally, the body size of invertebrates found in retreats varied within and across taxa. Specifically, caddisfly retreats functioned as a potential nursery for taxa with large maximal body sizes. However, the patterns of this taxa-specific nursery effect were not influenced by elevation unlike the patterns observed based on community level body size.Collectively, our results indicate that invertebrates use retreats in earlier life stages or when they are smaller in body size independent of life stage. Furthermore, our analysis suggests that facilitation strength intensifies as elevation increases within stream invertebrate communities. Further consideration of how trait variation and environmental gradients interact to determine the strength and direction of biotic interactions will be important as species ranges and environmental conditions continue to shift.

Trans-acting genotypes drive mRNA expression affecting metabolic and thermal tolerance traits

Evolutionary processes driving physiological trait variation depend on the underlying genomic mechanisms. Evolution of these mechanisms depends on whether traits are genetically complex (involving many genes) and how gene expression that impacts the traits is converted to phenotype. Yet, genomic mechanisms that impact physiological traits are diverse and context-dependent (e.g., vary by environment or among tissues), making them difficult to discern. Here we examine the relationships between genotype, mRNA expression, and physiological traits to discern the genetic complexity and whether the gene expression affecting the physiological traits is primarily cis or trans-acting. We use low-coverage whole genome sequencing and tissue-specific mRNA expression among individuals to identify polymorphisms directly associated with physiological traits and expressed quantitative trait loci (eQTL) driving variation in six temperature-specific physiological traits (standard metabolic rate, thermal tolerance, and four substrate-specific cardiac metabolic rates). Not surprisingly, there were few, only five, SNPs directly associated with physiological traits. Yet, by focusing on a select set of mRNAs belonging to co-expression modules that explain up to 82% of temperature specific (12°C or 28°C) metabolism and thermal tolerance, we identified hundreds of significant eQTL for mRNA whose expression affects physiological traits. Surprisingly, most eQTL (97.4% for heart and 96.7% for brain) of eQTL were trans-acting. This could be due to higher effect size or greater importance of trans versus cis-acting eQTLs for mRNAs that are central to co-expression modules. That is, we may have enhanced the identification of trans-acting factors by looking for SNPs associated with mRNAs in co-expression modules that are known to be correlated with the expression of 10s or 100s of other genes, and thus have identified eQTLs with widespread effects on broad gene expression patterns. Overall, these data indicate that the genomic mechanism driving physiological variation across environments is driven by trans-acting tissue-specific mRNA expression.

opencc-zeroJul 2023View details →

Beyond trait distances: Functional distinctiveness captures the outcome of plant competition

Functional trait distances between coexisting organisms reflect not only complementarity in the way they use resources, but also differences in their competitive abilities. Accordingly, absolute and relative trait distances have been widely used to capture the effects of niche dissimilarity and competitive hierarchies, respectively, on the performance of plants in competition. However, multiple dimensions of the plant phenotype are involved in these plant-plant interactions (PPI), challenging the use of relative trait distances to predict their outcomes. Furthermore, estimating the effects of competitive hierarchy on the performance of a group of coexisting plants remains particularly difficult since relative trait distances relate to the effects of a focal plant on another. We argue that trait distinctiveness, an emerging facet of functional diversity that characterizes the eccentric position of a species (or genotype) in a phenotypic space, can reveal the unique role played by a given individual plant in a group of competing plants . We used the model crop species Oryza sativa spp. japonica to evaluate the ability of trait distances and trait distinctiveness to predict the outcome of intraspecific PPI on the performance of single genotype and genotype mixtures. We performed a screening experiment to characterize the phenotypic space of 49 rice genotypes based on 11 aboveground and root traits. We selected nine genotypes with contrasting positions in the phenotypic space and grew them in pots following a complete pairwise interaction design. Relative distances and distinctiveness based on traits associated with light competition were by far the best predictors of the performance of single genotypes - taller genotypes that acquired resource faster being the best competitors - while absolute trait distances had no effect. These results indicate that competitive hierarchy for light dominates PPI in this experiment. Consistently, trait distinctiveness in plant height and age at flowering had the strongest, positive effects on mixture performance, confirming that functional distinctiveness captures the effects of trait hierarchies and asymmetric PPI at this scale. Our findings shed new light on the role of trait diversity in regulating PPI and ecosystem processes and call for a greater consideration of functional distinctiveness in studies of coexistence mechanisms.

Analysis Script of Prediction of Self-efficacy in Recognizing Deepfake based on HEXACO Personality Traits

Analysis Script (JASP) of Prediction of Self-efficacy in Recognizing Deepfake based on HEXACO Personality Traits

opencc-zeroJul 2023View details →

Diadromy drives elevated rates of trait evolution and ecomorphological convergence in Clupeiformes (herring, shad, and anchovies)

Migration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and non-diadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale, diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and non-diadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits, and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate traitspace and suggest these respective traitspaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome.

opencc-zeroDec 2022View details →

Inferring the evolutionary model of community-structuring traits with convolutional kitchen sinks: Code and data

When communities are assembled through processes such as filtering or limiting similarity acting on phylogenetically conserved traits, the evolutionary signature of those traits may be reflected in patterns of community membership. We show how the model of trait evolution underlying community-structuring traits can be inferred from community membership data using both a variation of a traditional eco-phylogenetic metric--the mean pairwise distance (MPD) between taxa--and a recent machine learning tool, Convolutional Kitchen Sinks (CKS). Both methods perform well across a range of phylogenetically informative evolutionary models, but CKS outperforms MPD as tree size increases. We demonstrate CKS by inferring the evolutionary history of freeze tolerance in angiosperms. Our analysis is consistent with a late burst model of freeze tolerance, suggesting it evolved recently. We suggest that data ordered on phylogenies such as trait values, species interactions, or community presence/absence are good candidates for CKS modeling because the generative models produce structured differences between neighboring points that CKS is well-suited for. We introduce the R package kitchen to perform CKS for generic application of the technique.

Fig. 8 in Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters

Fig. 8. Evolution of the most conserved morphological traits in Solanum with <10 transitions based on species-level analysis using stochastic character mapping. A, Pseudostipules; B, Enlarged anther connectives; C, Anther modifications; D, Pedicel insertion. Results from the best model are shown for each character (see Table 1 and suppl. Table S4 for details) based on 200 simulations. The topology used for mapping was derived from a supermatrix phylogeny with nine loci (two nuclear and seven plastid loci; Gagnon & al., 2022) with 725 species sampled and coded for each trait (58% of all species). All minor clades are labelled; tips reflect the crown nodes of each minor clade. Piecharts indicate likelihood of modelled ancestral states along the nodes, and frequency bars (tips) reflect proportion of species sampled within each clade with each state.

Fig. 4 in Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters

Fig. 4. Evolution of the most highly labile morphological traits in Solanum with>100 transitions based on species-level analysis using stochastic character mapping. A, Growth form; B, Sympodial unit structure; C, Glandular trichomes; D, Corolla shape; E, Corolla colour; F, Fruit colour. Results from the best model are shown for each character (see Table 1 and suppl. Table S4 for details) based on 200 simulations. The topology used for mapping was derived from a supermatrix phylogeny with nine loci (two nuclear and seven plastid loci; Gagnon & al., 2022) with 725 species sampled and coded for each trait (58% of all species). All minor clades are labelled; tips reflect the crown nodes of each minor clade. Piecharts indicate likelihood of modelled ancestral states along the nodes, and frequency bars (tips) reflect proportion of species sampled within each clade with each state.

opencc-zeroJul 2023View details →

Data from: Pre‐adaptation and adaptation shape trait‐environment matching in the Neotropics

The resources provided here comprise raw and final data sets used in our study 'Preadaptation and adaptation shape trait-environment matching in the Neotropics' (DOI: 10.1111/geb.13730) comprising curated geographic occurrences for 156 Swartzia taxa across its distribution in the Neotropics, phylogenetic information for 69 Swartzia taxa, and corresponding climatic (i.e. 19 climatic variables taken from WorldClim), soil (i.e. sand, nitrogen, and clay content taken from the SoilGrids 2.0 portal), and trait data for each taxa (i.e. trait measurements for lefleats, petals, and fruits). We also provide the script used to extract trait information from botanical monographs.

Impact of forest disturbance on microarthropod communities depends on underlying ecological gradient and species traits

Dataset and R scripts used in the publication "Impact of forest disturbance on microarthropod communities depends on underlying ecological gradient and species traits", PeerJ