Reconstructing the Phylogeny of Mobile Elements

Abstract

The study of mobile element evolution yields valuable insights into the mechanism and history of genome rearrangement, and can help answer questions about our evolutionary history. However, because the mammalian genome contains millions of copies of mobile elements exhibiting a complex evolutionary history, traditional phylogenetic methods are ill-suited to reconstructing their history. New phylogenetic reconstruction algorithms which exploit the unique properties of mobile elements and handle large numbers of repeats are therefore necessary to better understand both mobile elements' evolution and our own. We describe a randomized algorithm for phylogenetic reconstruction that scales easily to a million or more elements. We apply our algorithm to human and chimpanzee Alu and L1 elements, and to SINE elements from 61 species, finding 32 new L1, 111 new SINE, and over 1000 new Alu subfamilies. Our results suggest that the history of mobile elements is significantly more complex than we currently understand.