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Systematic Biology 2006 55(6):928-935; doi:10.1080/10635150600865419
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© 2006 Society of Systematic Biologists

SINEs of a Nearly Perfect Character

David A. Ray1, Jinchuan Xing2, Abdel-Halim Salem3 and Mark A. Batzer2

1 Department of Biology, West Virginia University PO Box 6057, Morgantown, West Virginia 26506, USA
2 Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA E-mail: mbatzer{at}lsu.edu (M.A.B.)
3 Department of Anatomy, Faculty of Medicine, Suez Canal University Ismailia, Egypt

Edited by Andrew Shedlock: Associate Editor


  Abstract

Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. However, issues regarding potential sources of homoplasy and other misleading events have been raised. We have collected available data for all phylogenetic and population level studies of primates utilizing Alu insertion data and examined them for potentially homoplasious and other misleading events. Very low levels of each potential confounding factor in a phylogenetic or population analysis (i.e., lineage sorting, parallel insertions, and precise excision) were found. Although taxa known to be subject to high levels of these types of events may indeed be subject to problems when using SINE analysis, we propose that most taxa will respond as the order Primates has—by the resolution of several long-standing problems observed using sequence-based methods.

Keywords: Alu; mobile element; phylogenetics; retrotransposon; SINE

Received November 4, 2005; Revised December 31, 2005; Accepted March 15, 2006
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