Kinetics and free energy in human mitochondrial D-loop DNA base substitutions

Essential to the application of mtDNA diversity as a measure of time elapsed from a common ancestor, is the rate at expressed as base substitution per unit time. Substitutions do not occur randomly. In the human mtDNA control region, three segments have substitution rates that are ‘abnormally’ high: the ‘hypervariable segments (HVS). One can infer a rate averaged over the HVS as an estimate of a constant rate. Horai et al (1995) calculated for HVSI and HVSII rates of 1.0×10−7 and 0.74×10−7 [site-year]−1 based on the split in human and chimpanzee lineages of 4–6 Mya. Tamura and Nei (1993) used 95 sequences for HVSI and HVSII comprising 625 base sites and calculated the rate to be 0.25–1.5×10−7 [site-year]−1 based on the same split in lineages. Howell et al. (1996) and Parsons et al. (1997) made direct measurements of the base substitution rate which yielded values of 2.6×10−6 and 2.5×10−6 [site-year]−1, respectively. The difference between these rates could be reconciled by taking the rate of ca. 1×10−7 as the steady state rate, being the difference between rapid forward and reverse rates, and 2.6×10−6 as the forward rate. The steady state rate is 4% of the forward rate and so is close enough to equilibrium that one may utilize the Boltzmann equation to obtain the Gibbs free energy values, ΔAG′, for base substitutions. This was done for the base substitutions averaged over a 625 base sequence, comprising most of the D-loop of human mt-DNA, from the data presented by Tamura and Nei (1993). ΔG′ values ranged between 0.2 and 0.7 kcal./mol for the four transitions and 2.3 and 3.1 kcal./mol for the eight transversions. Base substitution ΔG′ distribution plots were obtained for base changes within a 200 base sequence of HSVII of human mtDNA, reported by Jorde et al. (1995), relative to a modified Cambridge Reference Sequence (mCRS) standard for 241 individuals representing European, Asian and African populations. The ΔG′ distribution plot provides a novel way of comparing base changes between populations using a single biochemical parameter. The plots show similarity in mtDNA between European and Asian populations and wider distribution od ΔG′ values in African populations, indicating differences from the European/Asian group and within the African populations. The steady state model underlying the ΔG′ free energy distribution analysis precludes its use in estimating population age. Consideration of the biochemical reactions controlling mtDNA base sequence strongly imply that mtDNA sequence analysis should not be used for such estimations. A key factors controlling mtDna sequence is the steric requirement that D-loop control region mtDNA accommodate the transcription factors polymerases and primers that mediate the transcription and replication of mtDNA, providing selection at the level of these biochemical reactions. This selection is more likely to have induced particular base changes in isolated populations in adaptation to their geographical environments. Considered in this manner, greater mtDNA diversity represents isolation of a given population after the evolution ofHomo Sapiens, while lesser mtDNA diversity represents the older human mainstream population.