Abstract # 2277 Event # 112:

Scheduled for Friday, June 22, 2007 02:30 PM-02:45 PM: Session 12 (North Main Hall E) Oral Presentation

HVR1-Derived Numts Pose No Problems for Chimpanzee (Pan troglodytes) Phylogenetics

J. J. Ely1, B. Satpathy2 and D. R. Lee1
1Alamogordo Primate Facility, Bldg. 1303, PO Box 956, Holloman AFB, NM 88330-0956, USA, 2Hood College
     Sequences from the first hypervariable region (HVR1) of mitochondrial DNA (mtDNA) are used extensively in chimpanzee phylogenetic studies. Because mtDNA evolves more rapidly than nuclear DNA, numts (nuclear inserts of mtDNA) can appear as “molecular fossils” and cause problems in phylogenetic inference. To determine whether putative mtDNA sequences were contaminated by numts, we BLASTed the reference chimpanzee mtDNA sequence against the chimpanzee genome, aligned identified numts (Tcoffee) and inferred phylogenetic trees (MEGA2). Of 178 numts, 8 derived from HVR1. Numts were more frequent [F(1,21)=13.91, p=0.001] from genes than from non-coding sequences like HVR1. Chimpanzee chromosome 2B had more numts than expected based on size [Studentized residual=+2.88, p=0.008], probably reflecting extensive rearrangement of 2B during hominoid evolution. True numts were distinguished from cloning/assembly artifacts by comparison to the HVR1 sequence of C0471 (the source of the chimpanzee genome). Phylogenetic problems posed by HVR1-derived numts were evaluated by comparing presumed HVR1 sequences from African chimpanzees of known geographical provenance, to all 8 true HVR1-derived numts. No numt contamination was found. Although they are not artifacts, HVR1-derived numts do not pose problems for chimpanzee phylogenetics. The single problematical numt having sequence homology to HVR1 can be distinguished by size, since it is only half the length (172bp) of true HVR1 sequences (374bp). In contrast to gorillas and macaques, chimpanzee phylogenetics studies based on HVR1 are quite reliable.