Table 1.
Hominoid-Rate Slowdown Tested Using Genomic Sequence Data from Human, Baboon, and Marmoset
Figure 1.
A Neighbor-Joining Tree of Five Primate Species, Generated Using High-Quality Data from the Encode Region ENm001
The numbers of substitutions per 100 sites in each branch, using the two-parameter correction [58], are shown.
Figure 2.
Phylogeny of the Four Taxa Analyzed in This Study
TO denotes the time since the split between the two Old World monkey species, and TH denotes the time since the split between the two hominoids. Fossil records suggest that TO and TH are very close to each other. X and Y denote the common ancestors of human-chimpanzee and of macaque-baboon, respectively. The genetic divergence between the two hominoid species (KH) is the sum of KHX and KCX. Likewise, KO is the sum of KMY and KBY.
Figure 3.
Contrasting Molecular Clocks of Transitions at CpG Sites versus Those at Non-CpG Sites
The y-axis shows the rate difference in the baboon-macaque pair to that in the human-chimpanzee pair. The Old World monkey pair has accumulated significantly more transitions in non-CpG sites, as expected by the generation time effect. In contrast, transitions at CpG sites, which are primarily of methylation origin, show no difference between the two pairs. Data are shown for all sites, repetitive sites (as identified from the RepeatMasker program [57]), and nonrepetitive sites (after removing repetitive sites). Confidence intervals are generated by bootstrapping 10,000 times.
Table 2.
The Ratio of the Pairwise Divergence between Macaque and Baboon (KO) to the Pairwise Divergence between Human and Chimpanzee (KH), Using All Substitutions
Table 3.
Rate Differences between Lineages from Various Data Sources
Figure 4.
The Proportion of CpG Sites in Data Affects the Degree of Hominoid-Rate Slowdown
We considered a simple model in which all sites can be classified into either CpG sites or non-CpG sites and estimated evolutionary rates in hominoids from the human-chimpanzee comparison. The x-axis is the proportion of CpG sites in the data. The y-axis is the observed degree of hominoid rate slowdown, shown as the ratio of the substitution rate in Old World monkeys to the rate in hominoids, given the “true” ratio (determined by the generation-time effect), depicted as r. While regions relatively devoid of CpG sites will reflect the true generation-time effect, the observed ratio approaches 1 as the data include more CpG sites (i.e., the substitution rate in hominoids and Old World monkeys will be similar). Data points for when data consists of 2.5% and 12% CpG sites for r = 1.3 and 1.4 are shown for convenience.