Molecular Biology and Evolution, Vol 16, 1357-1368, Copyright © 1999 by Society for Molecular Biology and Evolution
L Excoffier and Z Yang
Mitochondrial D-loop hypervariable region I (HVI) sequences are widely used
in human molecular evolutionary studies, and therefore accurate assessment
of rate heterogeneity among sites is essential. We used the
maximum-likelihood method to estimate the gamma shape parameter alpha for
variable substitution rates among sites for HVI from humans and chimpanzees
to provide estimates for future studies. The complete data of 839 humans
and 224 chimpanzees, as well as many subsets of these data, were analyzed
to examine the effect of sequence sampling. The effects of the genealogical
tree and the nucleotide substitution model were also examined. The
transition/transversion rate ratio (kappa) is estimated to be about 25,
although much larger and biased estimates were also obtained from small
data sets at low divergences. Estimates of alpha were 0.28-0.39 for human
data sets of different sizes and 0.20- 0.39 for data sets including
different chimpanzee subspecies. The combined data set of both species gave
estimates of 0.42-0.45. While all those estimates suggest highly variable
substitution rates among sites, smaller samples tend to give smaller
estimates of alpha. Possible causes for this pattern were examined, such as
biases in the estimation procedure and shifts in the rate distribution
along certain lineages. Computer simulations suggest that the estimation
procedure is quite reliable for large trees but can be biased for small
samples at low divergences. Thus, an alpha of 0.4 appears suitable for both
humans and chimpanzees. Estimates of alpha can be affected by the
nucleotide sites included in the data, the overall tree length (the amount
of sequence divergence), the number of rate classes used for the
estimation, and to a lesser extent, the included sequences. The
genealogical tree, the substitution model, and demographic processes such
as population expansion do not have much effect.
ORIGINAL ARTICLE
Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees
Department of Anthropology, University of Geneva, Switzerland.
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