Using phylogenetic information to impute missing functional trait values in ecological databases

Evidence of self-care tooling and phylogenetic modeling reveal parrot tool use is not rare

Putatively rare behaviors like tool use are difficult to study because absence of evidence can arise from a species' inability to produce the behavior or from insufficient research. We combine data from digital platforms and phylogenetic modeling to estimate rates of tool use in parrots. Videos on YouTube revealed novel instances of self-care tooling in 17 parrot species, more than doubling the number of tool-using parrots from 11 (3%) to 28 (7%). Phylogenetic modeling suggests 11-17% of extant parrot species may be capable of tool use and identifies likely candidates. These discoveries impact our understanding of the evolution of tool use in parrots, revealing associations with relative brain size and feeding generalism and indicating likely ancestral tool use in several genera. Our findings challenge the assumption that current sampling efforts fully capture the distribution of putatively rare animal behaviors and offer a fruitful approach for investigating other rare behaviors.

CoRRE Trait Data: A dataset of 17 categorical and continuous traits for 4079 grassland species worldwide

In our changing world, understanding plant community responses to global change drivers is critical for predicting future ecosystem composition and function. Plant functional traits promise to be a key predictive tool for many ecosystems, including grasslands; however, their use requires both complete plant community and functional trait data. Yet, representation of these data in global databases is sparse, particularly beyond a handful of most used traits and common species. Here we present the CoRRE Trait Data, spanning 17 traits (9 categorical, 8 continuous) anticipated to predict species' responses to global change for 4,079 vascular plant species across 173 plant families present in 390 grassland experiments from around the world. The dataset contains complete categorical trait records for all 4,079 plant species obtained from a comprehensive literature search, as well as nearly complete coverage (99.97%) of imputed continuous trait values for a subset of 2,927 plant species. These data will shed light on mechanisms underlying population, community, and ecosystem responses to global change in grasslands worldwide.

Latitudinal specificity of plant-avian frugivore interactions

Broad-scale assessments of plant-frugivore interactions indicate the existence of a latitudinal gradient in interaction specialization. The specificity (i.e. the similarity of the interacting partners) of plant-frugivore interactions could also change latitudinally given that differences in resource availability could favour species to become more or less specific in their interactions across latitudes. Species occurring in the tropics could be more taxonomically, phylogenetically and functionally specific in their interactions because of a wide range of resources that are constantly available in these regions that would allow these species to become more specialized in their resource usage. We used a data set on plant-avian frugivore interactions spanning a wide latitudinal range to examine these predictions, and we evaluated the relationship between latitude and taxonomic, phylogenetic and functional specificity of plant and frugivore interactions. These relationships were assessed using data on population interactions (population level), species means (species level) and community means (community level). We found that the specificity of plant-frugivore interactions is generally not different from null models. Although statistically significant relationships were often observed between latitude and the specificity of plant-frugivore interactions, the direction of these relationships was variable and they also were generally weak and had low explanatory power. These results were consistent across the three specificity measures and levels of organization, suggesting that there might be an interplay between different mechanisms driving the interactions between plants and frugivores across latitudes.

Species-level correlates of land-use responses and climate-change sensitivity in terrestrial vertebrates

Land-use and climate change are major pressures on terrestrial biodiversity. Species' extinction risk and responses to human pressures relate to ecological traits and other characteristics in some clades. However, large-scale comparative assessments of the associations between traits and responses to multiple human pressures across multiple clades are needed. We investigated whether a set of ecological characteristics that are commonly measured across terrestrial vertebrates (ecological traits and geographic range area) are associated with species' responses to different land-use types and species' likely sensitivity to climate change. We aimed to test whether generalizable patterns in response to these pressures arise across both pressures and across vertebrate clades, which could inform assessments of the global signature of human pressures on vertebrate biodiversity and guide conservation efforts. At the species level, we investigated associations between land-use responses and ecological characteristics with a space-for-time substitution approach, making use of the PREDICTS database. We investigated associations between ecological characteristics and expected climate-change sensitivity, estimated from properties of species realized climatic niches. Among the characteristics we considered, 3 were consistently associated with strong land-use responses and high climate-change sensitivity across terrestrial vertebrate classes: narrow geographic range, narrow habitat breadth, and specialization on natural habitats (which described whether a species occurs in artificial habitats or not). The associations of other traits with species' land-use responses and climate-change sensitivity often depended on species' class and land-use type, highlighting an important degree of context dependency. In all classes, invertebrate eaters and fruit and nectar eaters tended to be negatively affected in disturbed land-use types, whereas invertebrate-eating and plant- and seed-eating birds were estimated to be more sensitive to climate change, raising concerns about the continuation of ecological processes sustained by these species under global changes. Our results highlight a consistently higher sensitivity of narrowly distributed species and habitat specialists to land-use and climate change, which provides support for capturing such characteristics in large-scale vulnerability assessments.

New horizons for comparative studies and meta-analyses

Comparative analyses and meta-analyses are key tools to elucidate broad biological principles, yet the two approaches often appear different in purpose. We propose an integrated approach that can generate deeper insights into ecoevolutionary processes. Marrying comparative and meta-analytic approaches will allow for (i) a more accurate investigation of drivers of biological variation, (ii) a greater ability to account for sources of non-independence in experimental data, (iii) more effective control of publication bias, and (iv) improved transparency and reproducibility. Stronger integration of meta-analytic and comparative studies can also broaden the scope from species-centric investigations to community-level responses and function-valued traits (e.g., reaction norms). We illuminate commonalities, differences, and the transformative potential of combining these methodologies for advancing ecology and evolutionary biology.

Evaluating plant lineage losses and gains in temperate forest understories: a phylogenetic perspective on climate change and nitrogen deposition

Global change has accelerated local species extinctions and colonizations, often resulting in losses and gains of evolutionary lineages with unique features. Do these losses and gains occur randomly across the phylogeny? We quantified: temporal changes in plant phylogenetic diversity (PD); and the phylogenetic relatedness (PR) of lost and gained species in 2672 semi-permanent vegetation plots in European temperate forest understories resurveyed over an average period of 40 yr. Controlling for differences in species richness, PD increased slightly over time and across plots. Moreover, lost species within plots exhibited a higher degree of PR than gained species. This implies that gained species originated from a more diverse set of evolutionary lineages than lost species. Certain lineages also lost and gained more species than expected by chance, with Ericaceae, Fabaceae, and Orchidaceae experiencing losses and Amaranthaceae, Cyperaceae, and Rosaceae showing gains. Species losses and gains displayed no significant phylogenetic signal in response to changes in macroclimatic conditions and nitrogen deposition. As anthropogenic global change intensifies, temperate forest understories experience losses and gains in specific phylogenetic branches and ecological strategies, while the overall mean PD remains relatively stable.

Functional trait dataset of European groundwater Amphipoda: Niphargidae and Typhlogammaridae

Groundwater represents a vast, but mostly hidden and inaccessible ecosystem. Although often overlooked in freshwater research, groundwater organisms form a significant part of freshwater biodiversity, whereas their functions are crucial in different ecosystem processes. Knowledge on functional traits is generally lacking for most groundwater species worldwide, yet European groundwater amphipods, particularly the family Niphargidae, are an exception. They are well-researched and used as a model system in ecological and evolutionary studies. We focused on this group to assemble a first functional trait dataset dedicated to groundwater species. We gathered data for eight morphological functional traits quantified through 27 measurements for 1123 individuals which represent 180 species and 314 MOTUs. Besides functional trait data, every entry is accompanied with locality information, including habitat type, and DNA sequences if available. The structure of the dataset and data processing information provided along enable wide applicability and extension to other amphipod taxa. When coupled with phylogeny, the dataset may further enhance different aspects of groundwater research, including biodiversity patterns, community assembly processes, and trait evolution.

Conserving avian evolutionary history can effectively safeguard future benefits for people

Phylogenetic diversity (PD)-the evolutionary history of a set of species-is conceptually linked to the maintenance of yet-to-be-discovered benefits from biodiversity or "option value." We used global phylogenetic and utilization data for birds to test the PD option value link, under the assumption that the performance of sets of PD-maximizing species at capturing known benefits is analogous to selecting the same species at a point in human history before these benefits were realized. PD performed better than random at capturing utilized bird species across 60% of tests, with performance linked to the phylogenetic dispersion and prevalence of each utilization category. Prioritizing threatened species for conservation by the PD they encapsulate performs comparably to prioritizing by their functional distinctiveness. However, species selected by each metric show low overlap, indicating that we should conserve both components of biodiversity to effectively conserve a variety of uses. Our findings provide empirical support for the link between evolutionary history and benefits for future generations.

How do distinct facets of tree diversity and community assembly respond to environmental variables in the subtropical Atlantic Forest?

This study assessed the impact of altitude, precipitation, and soil conditions on species richness (SR), phylogenetic diversity (PD), and functional diversity (FD) standardized effect sizes in subtropical Brazilian Atlantic Forest tree communities. We considered specific trait information (FDs) for FD, reflecting recent adaptive evolution, contrasting with deeper phylogenetic constraints in FD. Three functional traits (leaf area-LA, wood density-WD, and seed mass-SM) were examined for their response to these gradients. Generalized least squares models with environmental variables as predictors and diversity metrics as response variables were used, and a fourth-corner correlation test explored trait-environmental relationships. SR decreased with altitude, while PD increased, indicating niche convergence at higher altitudes. Leaf area and seed mass diversity also decreased with altitude. For LA, both FD and FDs were significant, reflecting filtering processes influenced by phylogenetic inheritance and recent trait evolution. For SM, only the specific trait structure responded to altitude. LA and SM showed significant trait-environmental relationships, with smaller-leaved and lighter-seeded species dominant at higher altitudes. Soil gradients affect diversity. Fertile soils have a wider range of LA, indicating coexistence of species with different nutrient acquisition strategies. WD variation is lower for FDs. SM diversity has different relationships with soil fertility for FDs and FD, suggesting phylogeny influences trait variation. Soil pH influences WD and LA under acidic soils, with deeper phylogenetic constraints (FD). Environmental factors impact tree communities, with evidence of trait variation constraints driven by conditions and resources. Subtropical Atlantic forests' tree assemblies are mainly influenced by altitude, pH, and soil fertility, selecting fewer species and narrower trait spectra under specific conditions (e.g., higher altitudes, pH). Functional diversity patterns reflect both phylogenetic and recent evolution constraints, with varying strength across traits and conditions. These findings highlight the intricate processes shaping long-lived species assembly across diverse environments in the Southern Brazilian Atlantic Forest.

Assessing the representation of species included within the Canadian Living Planet Index

To effectively combat the biodiversity crisis, we need ambitious targets and reliable indicators to accurately track trends and measure conservation impact. In Canada, the Living Planet Index (LPI) has been adapted to produce a national indicator by both World Wildlife Fund-Canada (Canadian Living Planet Index; C-LPI) and Environment and Climate Change Canada (Canadian Species Index) to provide insight into the status of Canadian wildlife, by evaluating temporal trends in vertebrate population abundance. The indicator includes data for just over 50% of Canadian vertebrate species. To assess whether the current dataset is representative of the distribution of life history characteristics of Canadian wildlife, we analyzed the representation of species-specific biotic variables (i.e., body size, trophic level, lifespan) for vertebrates within the C-LPI compared to native vertebrates lacking LPI data. Generally, there was considerable overlap in the distribution of biotic variables for species in the C-LPI compared to native Canadian vertebrate species lacking LPI data. Nevertheless, some differences among distributions were found, driven in large part by discrepancy in the representation of fishes—where the C-LPI included larger-bodied and longer-lived species. We provide recommendations for targeted data collection and additional analyses to further strengthen the applicability, accuracy, and representativity of biodiversity indicators.

Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia, Cricetidae)

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip-based metrics of trait evolution - Transition Rates, Stasis Time, and Last Transition Time - which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip-based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.

Intensive human land uses negatively affect vertebrate functional diversity

Land-use change is the leading driver of global biodiversity loss thus characterising its impacts on the functional structure of ecological communities is an urgent challenge. Using a database describing vertebrate assemblages in different land uses, we assess how the type and intensity of land use affect the functional diversity of vertebrates globally. We find that human land uses alter local functional structure by driving declines in functional diversity, with the strongest effects in the most disturbed land uses (intensely used urban sites, cropland and pastures), and among amphibians and birds. Both tropical and temperate areas experience important functional losses, which are only partially offset by functional gains. Tropical assemblages are more likely to show decreases in functional diversity that exceed those expected from species loss alone. Our results indicate that land-use change non-randomly reshapes the functional structure of vertebrate assemblages, raising concerns about the continuation of ecological processes sustained by vertebrates.