Speaker: Jonathan Odumegwu

Title: When is it surprising that all gene tree topologies are unique?

Abstract: Multilocus phylogenetic studies often show a high degree of gene tree heterogeneity—  gene trees that have different topologies from each other as well as from the species tree topology. In some cases, this can lead to studies with hundreds of loci having a distinct gene tree topologies. The degree of heterogeneity is expected to increase when there is a high degree of incomplete lineage sorting due to short branches (as measured in coalescent units) in the species tree. Other potential sources of heterogeneity include other biological processes such as introgression, recombination within genes, ancestral population structure, gene duplication and loss, and horizontal gene transfer, as well as gene tree estimation error due to short DNA sequences or inadequate substitution models. Here we examine the relationships between speciation and extinction rates and gene tree heterogeneity with both gene tree estimation error and no gene tree estimation error. In particular, higher speciation rates lead to shorter branches in the species tree and therefore higher levels of incomplete lineage sorting. In many cases, it might not be surprising that every gene tree has a unique topology, even for data sets with 1000 gene trees. We also propose using the average pairwise Robinson-Foulds (RF) distance between gene trees as a measure of heterogeneity as opposed to using the average RF distance between gene trees and the true species tree.