Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis

There are two paradigms for the phylogenetic analysis of multi-locus sequence data: one which forces all genes to share the same underlying history, and another that allows genes to follow idiosyncratic patterns of descent from ancestral alleles. The first of these approaches (concatenation) is clearly a simplified model of the actual process of genome evolution while the second (species-tree methods) may be overly complex for histories characterized by long divergence times between cladogenesis. Rather than making an a priori determination concerning which of these phylogenetic models to apply to our data, we seek to provide a framework for choosing between concatenation and species-tree methods that treat genes as independently evolving lineages. We demonstrate that parametric bootstrapping can be used to assess the extent to which genealogical incongruence across loci can be attributed to phylogenetic estimation error, and demonstrate the application of our approach using an empirical dataset from 10 species of the Natricine snake sub-family. Since our data exhibit incongruence across loci that are clearly caused by a mixture of coalescent stochasticity and phyogenetic estimation error, we also develop an approach for choosing among species tree estimation methods that take gene trees as input and those that simultaneously estimate gene trees and species trees.