Orthologous Repeats and Phylogenetic Inference

Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis. Here, we present a purely computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to the phylogeny of 28 mammals, obtaining encouraging results. With the set of species with partial sequence data available now rapidly expanding, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.