Molecular Evolution Activities

This is a comprehensive bibliography (under construction) of primary and secondary sources on the neutral theory of molecular evolution. It currently covers the period 1973-2001.

Author :

Nei, M.;Xu, P.;Glazko, G.

Year :


Title :

Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms

Journal :

Proceedings of the National Academy of Sciences of the United States of America

Volume :


Issue :


Pages :


Short Title :

Estimation of divergence times from multiprotein sequences for a few mammalian species and several d

Custom 3 :


Abstract :

When many protein sequences are available for estimating the time of divergence between two species, it is customary to estimate the time for each protein separately and then use the average for all proteins as the final estimate. However, it can be shown that this estimate generally has an upward bias, and that an unbiased estimate is obtained by using distances based on concatenated sequences. We have shown that two concatenation-based distances, i.e., average gamma distance weighted with sequence length (d(2)) and multiprotein gamma distance (d(3)), generally give more satisfactory results than other concatenation-based distances. Using these two distance measures for 104 protein sequences, we estimated the time of divergence between mice and rats to be approximately 33 million years ago. Similarly, the time of divergence between humans and rodents was estimated to be approximately 96 million years ago. We also investigated the dependency of time estimates on statistical methods and various assumptions made by using sequence data from eubacteria, protists, plants, fungi, and animals. Our best estimates of the times of divergence between eubacteria and eukaryotes, between protists and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc.
 -- contributed by John Beatty, March 29, 2002