The effects of variable mutation rates across sites on the phylogenetic estimation of effective population size or mutation rate of DNA sequences.

Multiple hits at some sites of human mitochondrial DNA sequences suggest that the commonly assumed infinite-sites model can be violated. Under the neutral Wright-Fisher model without recombination and population subdivision, we investigated, by computer simulations, the effect of multiple hits on the estimation of the essential parameter theta = 4Nmu by FU's UPBLUE procedure. We found that with moderate mutation rate heterogeneity, UPBLUE performs very well in terms of unbiasness and efficiency. Under extreme mutation rate heterogeneity, if sample size is reasonably large (e.g., > 60), UPBLUE is still very satisfactory; otherwise we developed a new correction equation. Given knowledge of the degree of mutation rate heterogeneity, the performance of UPBLUE with the new correction equation was tested to be fairly satisfactory: there is almost no bias and the sampling variance is only slightly higher than the theoretical minimum variance. Thus, with an appropriate correction, UPBL.UE is relatively robust to the multiple hits. In genealogies reconstructed by UPGMA, we found that the total length of branches directly linked to the tips is underestimated, and those far away tend to be overestimated, while the total length of all branches is not biased.