Ethnic variation in Hpa 1 endonuclease cleavage patterns of human mitochondrial DNA

The mtDNAs of 235 individuals from five ethnic groups were analyzed for restriction site variation by digestion with restriction endonuclease Hpa I, Southern transfer, and hybridization with 32P-labeled human mtDNA. Six different cleavage patterns (morphs) were found, all of which could be related to each other by single nucleotide substitutions. Differences were found in the frequency of these morphs among the populations. The largest difference observed was in the frequency of the morph most common in Caucasians and Orientals compared to the frequency of that found in Africans. This difference apparently originated by the sequence change G-T-C-A-A-C to G-T-T-A-A-C. This alteration permitted recognition by Hpa I but did not alter the amino acid sequence. Two other observed differences were due to separate substitutions occurring in the ribosomal RNA genes. Comparison with primate data shows that the morph with two fragments, found in 12.5% of Oriental and 4% of Bantu samples, might be the ancestral type common to all hominoids. These two conserved sites were localized in tRNA genes in the anticodon loop. Assuming that the two-fragment morph is ancestral, this finding is consistent with previous data suggesting that Asia is genetically central to the radiations that are thought to have given rise to the human ethnic groups.