Orthologous repeats and mammalian phylogenetic inference.

TitleOrthologous repeats and mammalian phylogenetic inference.
Publication TypeJournal Article
Year of Publication2005
AuthorsBashir A, Ye C, Price AL, Bafna V
JournalGenome Res
Volume15
Issue7
Pagination998-1006
Date Published2005 Jul
ISSN1088-9051
KeywordsAnimals, Base Sequence, Computational Biology, DNA Transposable Elements, Humans, Mammals, Models, Biological, Molecular Sequence Data, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Alignment
Abstract

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.

DOI10.1101/gr.3493405
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/15998912?dopt=Abstract
PMCPMC1172044
Alternate TitleGenome Res.
PubMed ID15998912