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Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.

ABSTRACT: Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.].

SUBMITTER: Adams RH

PROVIDER: S-EPMC8208806 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Seed size is a key trait for understanding and predicting ecological processes in a plant community. In a tropical forest, trees and lianas are major components driving ecosystem function and biogeochemical processes. However, seed ecological research on both components remains limited, particularly phylogenetic patterns and relationships with other traits. Here, we compiled a unique dataset of seed size (seed mass and geometrical size metrics) based on collections of more than 5,200 seeds of 196 woody plant species, covering >98 and 70% of tree and liana stems, respectively, located on a 30-ha plot in a tropical evergreen forest in central Thailand. We aimed to (1) develop allometric equations among seed size metrics to predict seed mass; (2) examine phylogenetic influence on seed size variation; and (3) examine relationships among seed traits and several other functional plant traits. Our allometric equations relating seed mass, seed volume, and width were well-fitted with data (R 2 = 0.94, 0.87 respectively). A phylogenetic signal test found that seed size was randomly distributed across the phylogeny. To study the functional trait relationships, we separately tested seed size data of the tree and liana communities (146 and 50 species, respectively), against mean body size of frugivores, successional niches, leaf, and structural traits. For the tree community, seed size was significantly related to mean body size of frugivores, which we believe is a basic driver of seed size because it is related to the gape width affecting dispersal effectiveness. Nearly all leaf traits were significantly positively correlated with seed size (p < 0.03). The significant positive correlation of leaf area and greenness suggested the high-energy demand of large-seeded species. We found a strong positive correlation between seed size and leaf toughness, suggesting a coordination between seed size and leaf defense. However, all these patterns disappeared in the same analysis applied to the liana community. Liana seed size variation was lower than that of trees, perhaps because lianas grow in relatively more uniform conditions in the forest canopy. Frugivore size was the strongest driver of seed size variation. Our study shows a surprising contrast between trees and lianas that is worth further investigation.

Dataset Information

Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.

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