Alu insertion loci and platyrrhine primate phylogeny

David A. Ray, Jinchuan Xing, Dale J. Hedges, Michael A. Hall, Meredith E. Laborde, Bridget A. Anders, Brittany R. White, Nadica Stoilova, Justin D. Fowlkes, Kate E. Landry, Leona G. Chemnick, Oliver A. Ryder, Mark A. Batzer

Research output: Contribution to journalArticlepeer-review

102 Scopus citations


Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a cladogram that supports a sister relationship between Atelidae (spider, woolly, and howler monkeys) and Cebidae (marmosets, tamarins, and owl monkeys) and then the joining of this two family clade to Pitheciidae (titi and saki monkeys). The data support these relationships with a homoplasy index of 0.00. In this study, we report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates.

Original languageEnglish
Pages (from-to)117-126
Number of pages10
JournalMolecular Phylogenetics and Evolution
Issue number1
StatePublished - Apr 2005


  • Alu
  • Phylogeny
  • Platyrrhine
  • Primate


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