Abstract
In this talk I will focus on two common sources of gene tree incongruence in phylogenomic studies: incomplete lineage sorting and gene tree estimation error. In prior theoretical work, both were studied extensively -- but separately. I will describe an analytical framework that bridges the gap by considering simultaneously the effect on reconstruction accuracy of the number of genes and of the number of sites per gene. Using this framework, I will discuss the inconsistency of concatenation methods, the advantages of sequence-based over topology-based methods and evidence that in this setting quantity trumps quality.
Joint work with Gautam Dasarathy, Elchanan Mossel, Rob Nowak, Mike Steel and Tandy Warnow.