62 Oral - Platform Session #6 Theory and Methods
Friday June 10, 11:35 AM - 11:50 AM
Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance
Authors: Mark Hibbins 1; Lara Breithaupt 1,2; Matthew Hahn 1,3
Affiliations: 1) Department of Biology, Indiana University, Bloomington, IN, USA; 2) Department of Statistical Science, Duke University, Durham, NC, USA; 3) Department of Computer Science, Indiana University, Bloomington, IN, USA
Keywords: Theory & Method Development
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for evolutionary inferences across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating species tree that describes this shared history. However, modern phylogenomic analyses have shown that genomes are often composed of a mosaic of different histories that can disagree both with the species tree and each other. These discordant gene trees describe shared histories among species that are not captured by their history of speciation, and therefore that are unaccounted for in standard comparative approaches. The application of standard methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one involves constructing a fuller phylogenetic variance-covariance matrix that includes branches not found in the species tree, while the other applies the pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Both approaches are agnostic to the biological cause of gene tree discordance, which may include incomplete lineage sorting and introgression. Using simulation, we demonstrate that our new approaches generate much more accurate estimates of evolutionary parameters than standard methods. Finally, by analyzing empirical data from a rapid radiation, we highlight how discordance can potentially lead to false inferences of clade-specific shifts in trait evolutionary rates.