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In this paper, a simple distance measure was used to estimate the age (T) of the common ancestor of eukaryotes and prokaryotes which takes the rate variation among sites and the pattern of amino acid substitutions into account. Our new estimate of T based on Doolittle et al.'s data is about 2.5 billion years ago (Ga), with 95% confidence interval from 2.1 to 2.9 Ga. This result indicates (1) that Doolittle et al.'s estimate (approximately 2.0 Ga) seems too recent, and (2) that the traditional view about the divergence time between eukaryotes and prokaryotes (T0 = 3.5 Ga) can be rejected at the 0.1% significance level.
Xun Gu (Fri,) studied this question.