title: SINEs of a nearly perfect character.
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.
authors.affiliation: Department of Biology, West Virginia University, PO Box 6057, Morgantown, West Virginia 26506, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.forename: Abdel-Halim
authors.initials: AH
authors.lastname: Salem
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements; D000818:Animals; D010802:Phylogeny; D011323:Primates / Q000235:genetics*