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Comparative Study
. 2003 Jun 10;100(12):7181-8.
doi: 10.1073/pnas.1232172100. Epub 2003 May 23.

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo

Derek E Wildman  1 , Monica Uddin, Guozhen Liu, Lawrence I Grossman, Morris Goodman
Affiliations
Comparative Study

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo

Derek E Wildman et al. Proc Natl Acad Sci U S A. .

Abstract

What do functionally important DNA sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? Here we compare approximately 90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. On a time scale, the coding DNA divergencies separate the human-chimpanzee clade from the gorilla clade at between 6 and 7 million years ago and place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago. The evolutionary rate of coding DNA in the catarrhine clade (Old World monkey and ape, including human) is much slower than in the lineage to mouse. Among the genes examined, 30 show evidence of positive selection during descent of catarrhines. Nonsynonymous substitutions by themselves, in this subset of positively selected genes, group humans and chimpanzees closest to each other and have chimpanzees diverge about as much from the common human-chimpanzee ancestor as humans do. This functional DNA evidence supports two previously offered taxonomic proposals: family Hominidae should include all extant apes; and genus Homo should include three extant species and two subgenera, Homo (Homo) sapiens (humankind), Homo (Pan) troglodytes (common chimpanzee), and Homo (Pan) paniscus (bonobo chimpanzee).

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Figures

Fig. 1.
Fig. 1.
The optimal MP and ML tree topology when all sites are included. Additionally, this topology represents the most parsimonious tree under a variety of data partitions including only first, second, and third positions. Branch lengths for branches A–J are in percent value and are Ka, Ks, and ML 1 and 2 distances. ML 1 distances are from the six datasets (Materials and Methods). Model parameters varied for different branches; however, the HKY+Γ model was always chosen as described in the text. ML 2 branch lengths are from the 90-kb dataset (Table 2) and were obtained by using the HKY+Γ model; α shape parameter = 0.3508. The names for the branches are: A, human terminal; B, chimpanzee terminal; C, gorilla terminal; D, orangutan terminal; E, OWM terminal; F, mouse terminal; G, human–chimpanzee stem; H, African ape stem; I, ape stem; and J, catarrhine stem extended to the primate–rodent mrca. Branches are not drawn to scale. Dates for the catarrhine mrca, African ape mrca, and human–chimpanzee mrca are averages and standard deviations of estimates obtained by global and local molecular clock models (see text and Table 4). Tree scores, bootstrap support values, and data partitions are shown in Table 2. *, Equally partitioned ML distances on branches F and J.
Fig. 2.
Fig. 2.
Rates of nucleotide substitution from the catarrhine mrca to present day OWMs, the catarrhine mrca to the ape mrca, the ape mrca to each of the four present day apes, and the catarrhine mrca to mouse. Rates, as number of substitution per site per year × 10-9, are for nonsynonymous sites, all sites (ML 1), and synonymous sites. Rates were calculated by using the branch lengths and dates shown in Fig. 1, and assigning the date of 80 Ma to the rodent–primate mrca.
Fig. 3.
Fig. 3.
Variability at first, second, and third codon position sites showing nucleotide changes on the human–chimpanzee stem, the chimpanzee-terminal branch, and the human-terminal branch. Such variability is estimated for each of the three branches by the ratio: number of changes throughout the full tree at those sites showing nucleotide changes on that branch/number of nucleotide changes on that branch. The dataset used to construct the MP tree for the six extant taxa consisted of concatenated coding sequences from 45 genes. Chimpanzee- and human-terminal branches were represented by all 45 genes. Each of the remaining taxa had a minimum of missing sequence data.
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References

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