Distribution of the number of fourfold-degenerate sites in the human-mouse orthologous genes. The average number of fourfold-degenerate sites from 3,722 genes of human-mouse comparison is 245, which is 15.7% of the average cDNA length (1,568).

(a) A histogram of the neutral evolutionary distances estimated by using fourfold-degenerate sites of 2,019 human and mouse genes (mean = 0.466 and variance = 0.035; two outliers were removed from each tail). The normal distribution curve is drawn by using the observed mean and the expected variance under the null hypothesis of uniform neutral mutation rate among genes. (b) The distribution of evolutionary distances estimated from genes of varying sequence lengths.

Average differences in neutral evolutionary distances using human-mouse comparison (Δd₄) were plotted for gene pairs located within 0.5 (a) and 0.1 Mbp (b). (c) Average neutral evolutionary distances (d₄) from the genes located within a human-mouse conserved segment were plotted corresponding to their position on the human chromosomes. The x axis refers to the starting location of the conserved segments in a super chromosome where all 22 autosomes were concatenated in order from head to tail. A total of 108 conserved segments, each containing a minimum of five genes, were used. The horizontal line indicates the average d₄ computed by using all 1,901 genes.

Relative evolutionary rate among different mammalian lineages. The relative evolutionary rate differences (Δr) in a gene for two lineages (say, A and B) were computed as Δr = [l_A − ½(l_A + l_B)]/½(l_A + l_B), where l_A and l_B are the least-squares estimates of the branch lengths leading to the two lineages using the average distances between species/groups A and B and their distances with the outgroup(s). Δr was computed for each gene, and the mean value taken over all genes for groups A and B. Negative values indicate that group B is evolving faster than group A. Only the genes passing the disparity index test were used in this analysis.

(a) Proportion of genes rejected for 15 mammalian pairs using the disparity index test in testing the null hypothesis of homogeneity of substitution patterns in fourfold-degenerate sites at a 5% significance level (26). The total number of genes examined is shown in parentheses next to the name of the species pair; the number of genes rejected is shown next to the corresponding bar. (b) Scatter plot showing the relationship of ΔGC₄ (GC content difference at fourfold-degenerate sites in orthologous sequences) with p₄ (proportion of fourfold-degenerate sites with A/T ↔ G/C difference) for genes passing (black) and failing (red) the disparity index test. Green markers show the expected relationship of ΔGC₄ calculated from sequence length and p₄ for each gene by using equation 10 in ref. 26. (c) Overestimation of evolutionary distance caused by genes evolving with heterogeneous patterns of evolution for seven representative mammalian pairs. Open bars show the estimate of average distance from all genes passing the homogeneity test (26, 27). Dark bars show the average distance for the rejected genes (heterogeneous).

Accumulation of neutral substitutions over time (million years) in diverse mammalian species. The average distance per lineage is plotted for inter- and intraordinal comparisons by using, respectievely, molecular data-based (a) and fossil-based (b) time estimates reported previously. Linear regression produced a rate of 2.22 × 10⁻⁹ substitutions per site per year million years ago (r = 0.97, n = 43) for the molecular data and 2.61 × 10⁻⁹ substitutions per site per year (r = 0.92, n = 33) for the fossil data. The divergence time estimates (million years ago, Mya) from molecular data (30, 35, 40–43)/fossil records (44–46), and the number of fourfold sites/genes used were: human-chimpanzee (5.5/5.5, 6,302/33), human-gorilla (7/–, 3,605/23), human-orangutan (8/–, 4,329/30), chimpanzee-gorilla (7/–, 1,674/13), chimpanzee-orangutan (8/–, 1,497/10), gorilla-orangutan (8/–, 1,936/15), cercopithecidae-hylobatidae (23/20, 1,290/10), hominidae-hylobatidae (15/–, 2,321/19), cercopithecidae-hominidae (23/20, 38,128/231), catarrhini-platyrrhini (47/37, 8,194/54), cetacea-ruminantia (60/53, 955/8), cetacea-suina (60/53, 682/10), ruminantia-tylopoda (67/53, 736/5), ruminantia-suina (65/53, 30,063/204), bovinae-caprinae (20/20, 24,474/158), bovoidea-cervoidea (23/20, 1,765/16), canidae-felidae (46/37, 5,651/41), gerbillinae-cricetinae (66/–, 1,172/11), gerbillinae-murinae (66/–, 2,605/24), murinae-cricetinae (66/–, 52,043/264), mus-rattus (41/–, 486,306/2,139), primates-carnivora (95/–, 49,267/266), primates-cetartiodactyla (95/–, 179,032/985), primates-perissodactyla (95/–, 11,593/75), primates-lagomorpha (91/–, 54,670/260), primates-hystricognath rodents (109/–, 18,292/110), primates-sciurognath rodents (115/–, 543,962/2,708), cetartiodactyla-carnivora (83/–, 24,086/160), cetartiodactyla-perissodactyla (83/–, 9,188/75), cetartiodactyla-lagomorpha (92/–, 30,465/175), cetartiodactyla-hystricognath rodents (109/–, 10,227/72), cetartiodactyla-sciurognath rodents (115/–, 119,345/756), carnivora-perissodactyla (74/–, 5,364/44), carnivora-lagomorpha (92/–, 9,498/58), carnivora-hystricognath rodents (109/–, 4,986/31), carnivora-sciurognath rodents (115/–, 28,644/191), perissodactyla-lagomorpha (92/–, 4,131/34), perissodactyla-hystricognath rodents (109/–, 1,779/18), perissodactyla-sciurognath rodents (115/–, 7,843/60), hystricognath rodents-lagomorpha (109/–, 5,447/36), hystricognath-sciurognath rodents (115/–, 19,930/123), sciurognath rodents-lagomorpha (112/–, 36,672/219). In the above, a dash indicates the absence of information.