HVR1-Derived Numts and the Reliability of Phylogenetic Studies in Chimpanzees (Pan troglodytes)

Sequences from the first hypervariable region (HVR1) of mitochondrial DNA (mtDNA) have been used extensively in chimpanzee phylogenetic studies. The transfer of mtDNA sequences into the nuclear genome results in numts (nuclear inserts of mtDNA), where then can persist 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 reference chimpanzee genome, identified and aligned numts, then inferred phylogenetic trees. True numts were distinguished from cloning or assembly artifacts by comparison to the HVR1 sequence of C0471 (the source of the chimpanzee genome). No difference was found in numt frequency from coding than non-coding regions. However, numts were more frequent from the nonoverlapping region between the two origins of replication. Numts were found on all chimpanzee chromosomes, in accordance with chromosome size. However, chromosome 2B had more numts than expected for its size, probably reflecting extensive rearrangement of 2B during hominoid evolution. Of 177 numts, 8 derived from HVR1. Potential phylogenetic problems posed by HVR1-derived numts were evaluated by comparing presumed HVR1 sequences obtained from African chimpanzees of known geographical provenance, to the 8 HVR1-derived numts. No numt contamination was found. The two potentially confounding numts showing high sequence homology to HVR1 are approximately half the length (173 bp and 203 bp) of true HVR1 sequences (374 bp) and can easily be distinguished by size. In contrast to the situation found in gorillas, HVR1-derived numts do not appear to present problems for chimpanzee phylogenetic studies.