DOI: 10.1080/10635150600865419 SINEs of a Nearly Perfect Character

Abstract.—Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. How-ever, 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 phy-logenetic 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. [Alu; mobile element; phylogenetics; retrotransposon; SINE.] Although implemented previously in smaller stud-ies (Minghetti and Dugaiczyk, 1993; Murata et al., 1993, 1996, 1998; Ryan and Dugaiczyk, 1989), the SINE method of phylogenetic reconstruction began receiving increased attention when Norihiro Okada and colleagues pub-lished their investigation into the relationship between whales and artiodactyls (Nikaido et al., 1999; Shimamur