Final Report Summary - PANDA (Phylogenetic ANalysis of Diversification Across the tree of life)
Understanding biodiversity as we see it around us today requires understanding its dynamics over millions of years of evolution. One approach to inferring such dynamics consists in formulating a set of models representing the key processes of speciation, extinction, and phenotypic evolution, and adjusting these models to the phylogenetic trees and phenotypes of present-day species.
The PANDA project aimed to significantly improve the models and inference machineries used for such phylogenetic inference, focusing on better accounting for the ecological context in which organisms evolve. It also aimed to use these tools across a wide variety of species groups, spanning macro and micro-organisms, to highlight general evolutionary patterns and processes.
We developed a comprehensive suite of models and phylogenetic tools than can be applied to present-day data in order to study long-term evolutionary dynamics. We made these tools available in a publicly-available and well-documented R package for use by the scientific community. More specifically, we developed models that can better account for the effect of past environmental changes, as well as interspecific interactions, on diversification and phenotypic evolution. We also developed a powerful Bayesian model that allows estimating species-level diversification rates, which allows testing the link between a variety of characteristics of the species (e.g. phenotypes, genotypes, habitats, ecologies, life-history traits) and diversification. Finally, we developed tools specifically designed to study the evolution of highly-dimensional traits, such as those collected with modern 3-dimensional morphometric techniques.
We applied our new models and tools to a variety of questions and biological systems. Past environmental changes and evolutionary dynamics. We found that rates of body-size evolution tend to be faster during cold rather than warm geological periods across birds and mammals; speciation rates tend to decline through time across tetrapods, and part of this decline may be linked to cooling temperatures during the Cenozoic. Climatic variations also impacted the diversification of plant mycorrhizal symbionts by modulating niche availability. In diatoms, the effect of climatic variation and other abiotic and biotic environmental changes is highly clade dependent. Interspecific interaction and evolutionary dynamics. We found that interspecific competition left a detectable signal in the phenotypes of extant Anolis lizards, and that it modulated traits involved in resource use more so that traits involved in social signaling in tanagers. We also found no evidence across birds for the ‘biotic interaction hypothesis’, which stipulates that more intense biotic interactions in the tropics spurs trait and species diversification. Correlates of diversification We analyzed correlates of diversification that have been underexplored, such as genetic diversity and molecular rates. We found that speciation rates are significantly negatively correlated with intraspecific genetic diversity across mammals, and that speciation rates are positively correlated to rates of molecular evolution on mitochondrial, but not nuclear markers.
The PANDA project aimed to significantly improve the models and inference machineries used for such phylogenetic inference, focusing on better accounting for the ecological context in which organisms evolve. It also aimed to use these tools across a wide variety of species groups, spanning macro and micro-organisms, to highlight general evolutionary patterns and processes.
We developed a comprehensive suite of models and phylogenetic tools than can be applied to present-day data in order to study long-term evolutionary dynamics. We made these tools available in a publicly-available and well-documented R package for use by the scientific community. More specifically, we developed models that can better account for the effect of past environmental changes, as well as interspecific interactions, on diversification and phenotypic evolution. We also developed a powerful Bayesian model that allows estimating species-level diversification rates, which allows testing the link between a variety of characteristics of the species (e.g. phenotypes, genotypes, habitats, ecologies, life-history traits) and diversification. Finally, we developed tools specifically designed to study the evolution of highly-dimensional traits, such as those collected with modern 3-dimensional morphometric techniques.
We applied our new models and tools to a variety of questions and biological systems. Past environmental changes and evolutionary dynamics. We found that rates of body-size evolution tend to be faster during cold rather than warm geological periods across birds and mammals; speciation rates tend to decline through time across tetrapods, and part of this decline may be linked to cooling temperatures during the Cenozoic. Climatic variations also impacted the diversification of plant mycorrhizal symbionts by modulating niche availability. In diatoms, the effect of climatic variation and other abiotic and biotic environmental changes is highly clade dependent. Interspecific interaction and evolutionary dynamics. We found that interspecific competition left a detectable signal in the phenotypes of extant Anolis lizards, and that it modulated traits involved in resource use more so that traits involved in social signaling in tanagers. We also found no evidence across birds for the ‘biotic interaction hypothesis’, which stipulates that more intense biotic interactions in the tropics spurs trait and species diversification. Correlates of diversification We analyzed correlates of diversification that have been underexplored, such as genetic diversity and molecular rates. We found that speciation rates are significantly negatively correlated with intraspecific genetic diversity across mammals, and that speciation rates are positively correlated to rates of molecular evolution on mitochondrial, but not nuclear markers.