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Methods

Orthologous repeats and mammalian phylogenetic inference

¹ Bioinformatics Program, University of California-San Diego, La Jolla, California 92093-0114, USA ² Computer Science Department, University of California-San Diego, La Jolla, California 92093-0114, USA

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, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.

³ Corresponding author.
E-mail abashir{at}ucsd.edu; fax (858) 534-7029.

[Supplemental material is available online at www.genome.org.]

⁴ In each case, there exist two clades whose union contains all species with the repeat clearly present and no species with the repeat clearly absent, supporting the hypothesis of two distinct repeat insertion events in the ancestor of each clade.

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