Orthologous repeats and mammalian phylogenetic inference

Ali Bashir, Chun Ye, Alkes L. Price, Vineet Bafna

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


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.

Original languageEnglish
Pages (from-to)998-1006
Number of pages9
JournalGenome Research
Issue number7
StatePublished - Jul 2005
Externally publishedYes


Dive into the research topics of 'Orthologous repeats and mammalian phylogenetic inference'. Together they form a unique fingerprint.

Cite this