Reconstruction of Phylogenetic Trees and Estimation of Divergence Times Under Nonconstant Rates of Evolution

The rate-constancy or “molecular clock” hypothesis has often been taken as a basis for reconstructing phylogenetic relationships among organisms or genes and for dating evolutionary events (see, e.g., Dayhoff 1972; Wilson et al. 1977). However, there is now strong evidence that the rate-constancy assumption is often seriously violated (see, e.g., Britten 1986). For example, among different mammalian orders, the rate of nucleotide substitution may vary by a factor of two or three, and within primates, there is a well-documented slowdown in the lineage leading to man (Wu and Li 1985; Britten 1986; Koop et al. 1986; Li and Tanimura 1987). It is therefore important to take into consideration the possibility of unequal rates among lineages when reconstructing phylogenetic trees and when dating divergence events.