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Timescale for the evolution of life on Earth: Molecular evolution approach (dm)

The major goal of our research is to develop reliable statistical methods for constructing phylogenetic trees and estimating divergence times for distantly related organisms, and to analyze protein or DNA sequence data to obtain some idea about the early stage of evolution of life. This year we investigated the efficiencies of various methods of phylogenetic reconstruction from molecular data and showed that the three most widely used methods, i.e., neighbor joining, maximum parsimony, and maximum likelihood methods, give essentially the same results as long as the reliability of branching patterns is tested by the bootstrap method and that there is no need to find the most parsimonious tree or the highest likelihood tree using extensive computer time. We also investigated the accuracies of various methods of estimating divergence times and showed that the most commonly used individual protein (IP) method generally gives overestimates. We then developed two concatenate distance (CD) methods to estimate divergence times. One was to compute average gamma distances for all proteins weighted with sequence length (dAG), and the other was to concatenate all protein sequences and then compute a single gamma distance (dMG). Theoretical and empirical studies have shown that the time estimates obtained by these methods are generally less biased than those obtained by the IP method. Using the new CD methods, we estimated that the times of divergence between eubacteria and eukaryotes, between protists (mostly Plasmodium genes) and other eukaryotes, and between plants, fungi, and animals were 3, 1.7, and 1.3 billion years ago, respectively.