Concatenation Analyses in the Presence of Incomplete Lineage Sorting

Incomplete lineage sorting (ILS), modelled by the multi-species coalescent, is a process that results in a gene tree being different from the species tree. Because ILS is expected to occur for at least some loci within genome-scale analyses, the evaluation of species tree estimation methods in the presence of ILS is of great interest. Performance on simulated and biological data have suggested that concatenation analyses can result in the wrong tree with high support under some conditions, and a recent theoretical result by Roch and Steel proved that concatenation using unpartitioned maximum likelihood analysis can be statistically inconsistent in the presence of ILS. In this study, we survey the major species tree estimation methods, including the newly proposed “statistical binning” methods, and discuss their theoretical properties. We also note that there are two interpretations of the term “statistical consistency”, and discuss the theoretical results proven under both interpretations.