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Project Progress

The main goal of this research is to develop statistical methods for estimating the times of origin of major groups of organisms from molecular data as well as those of major groups of gene families and infer early evolutionary events on earth. The main results obtained during the last year are as follows: (1) Statistical methods of estimating divergence times — There are two different distance methods of estimating divergence times when sequence data from many genes are available: the individual gene and the concatenated distance methods. The first one is traditional and is used more frequently than the second. We have now investigated the statistical properties of the two methods and shown that the second method generally gives less biased and more reliable estimates (Nei and Glazko 2002). To test this theoretical prediction, we analyzed protein sequence data from several mammalian and primate species and showed that our prediction is indeed supported by empirical data (Nei and Glazko 2002; Glazko and Nei, submitted). (2) Rates of amino acid substitution for different categories of proteins — When many genes are used for time estimation, it is important to know the rate of amino acid substitution for different categories of proteins. We have therefore examined the rates for six different categories of proteins from human, mouse, Drosophila, nematode, and Arabidopsis and found that the rate varies substantially among different protein categories and the estimate of divergence time obtained varies at least two-fold among the protein categories. However, when we used all 81 proteins combined, the estimates of times of divergence of the human lineage from Drosophila, nematode, fungus, and plant lineages were about 808, 1024, 1450, and 1333 MY ago (G. V. Glazko, H. Piontkivska, and M. Nei, unpublished). (3) Evolution of histones — To investigate the evolutionary origin of histone genes, we compiled all prokaryotic genes that have similarity to eukaryotic genes. There were no homologous genes in eubacteria, but some species of archebacteria contained histone-like genes. We then constructed a phylogenetic tree for the four classes of histone genes (H2A, H2B, H3, and H4) from various organisms. This tree showed that these four classes of genes originated nearly at the same time from archebacteria (Rooney et al. 2002; Piontkivska et al. 2002).