Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific

Length changes in human mitochondrial DNA (mtDNA) are potentially usefulmarkers for inferring the evolutionary history of populations. One suchlength change is a nine base pair (9-bp) deletion that is located in theintergenic region between the COII gene and the Lysine tRNA gene(COII/tRNALys intergenic region). This deletion has been used as a geneticmarker to trace descent from peoples of East Asian origin. A geographiccline of the deletion frequency across modern Pacific Islander populationssuggests that the deletion may be useful for tracing prehistoric Polynesianorigins and affinities. Mitochondrial DNA sequence variation within twovariable segments of the control region (CR) permits a number of inferencesregarding the evolutionary history of the 9-bp deletion that cannot bedetermined from frequency data alone. We obtained CR sequences from 74mtDNAs with the 9-bp deletion from Indonesia, coastal Papua New Guinea(PNG), and American Samoa. Phylogenetic and pairwise distribution analysisof these CR sequences pooled with previously published CR sequences revealsthat the deletion arose independently in Africa and Asia and suggestspossible multiple origins of the deletion in Asia. A clinal increase of thefrequency of the 9-bp deletion across the three Pacific populations isassociated with a decrease in CR sequence diversity, consistent withfounder events. Furthermore, analysis of pairwise difference distributionsindicates an expansion time of proto-Polynesians that began 5,500 yr agofrom Southeast Asia. These results are consistent with the express trainmodel of Polynesian origins.