title: Tracking Alu evolution in New World primates.
abstract: BACKGROUND
  Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates.
  
  
  RESULTS
  Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies.
  
  
  CONCLUSIONS
  The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA 70803, USA. david.ray@mail.wvu.edu
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements; D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D005075:Biological Evolution; D018899:CpG Islands; D019143:Evolution, Molecular; D017353:Gene Deletion; D005819:Genetic Markers; D016678:Genome; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation; D002679:Pan troglodytes; D010802:Phylogeny; D051078:Platyrrhini; D011110:Polymorphism, Genetic; D011323:Primates; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements
chemical_list: D005819:Genetic Markers