New Approaches for Inferring Phylogenies in the Presence of Paralogs

Abstract

The availability of whole genome sequences was expected to supply essentially unlimited data for phylogenetics. However, strict reliance on single-copy genes for this purpose has drastically limited the amount of data that can be used. Here, we review several approaches for increasing the amount of data used for phylogenetic inference, focusing on methods that allow for the inclusion of duplicated genes (paralogs). Recently developed methods that are robust to high levels of incomplete lineage sorting also appear to be robust to the inclusion of paralogs, suggesting a promising way to take full advantage of genomic data. We discuss the pitfalls of these approaches, as well as further avenues for research.

Keywords: duplication; incomplete lineage sorting; phylogenomics; polyploidy.