Communicated by Motoo Kimura, National Institute of Genetics, Shizuoka-ken, Japan, September 9, 1994 ABSTRACT We analyzed the complete mitochondrial DNA (mtDNA) sequences of three humans (African, European, and Japanese), three African apes (common and pygmy chimpanzees, and gorilla), and one orangutan in an attempt to estimate most accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated with an approximately clock-like regularity. From these substitutions and under the assumption that the orangutan and African apes diverged 13 million years ago, we obtained a divergence time for humans and chimpanzees of 4.9 million years. This divergence time permitted calibration of the synonymous substitution rate (3.89 x 10-8/site per year). To obtain the substitution rate in the displacement (D)-loop region, we compared the three human mtDNAs and measured the relative abundance of substitutions in the D-loop region and at synonymous sites. The estimated substitution rate in the D-loop region was 7.00 x 10-8/site per year. Using both synonymous and D-loop substitutions, we inferred the age of the last common ancestor of the human mtDNAs as 143,000 ± 18,000 years. The shallow ancestry of human mtDNAs, together with the observation that the African sequence is the most diverged among humans, strongly supports the recent African origin of modern humans, Homo sapiens sapiens.Light will be thrown on the origin of man and his history (1).

We have determined and compared the promoter, coding, and intronic sequences of the urate oxidase (Uox) gene of various primate species. Although we confirm the previous observation that the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2, we find that the inactivation in the gibbon lineage results from an independent nonsense mutation at a different CGA codon in exon 2 or from either one-base deletion in exon 3 or one-base insertion in exon 5, contrary to the previous claim that the cause is a 13-bp deletion in exon 2. We also find that compared with other organisms, the primate functional Uox gene is exceptional in terms of usage of CGA codons which are prone to TGA nonsense mutations. Nevertheless, we demonstrate rather strong selective constraint against nonsynonymous sites of the functional Uox gene and argue that this observation is consistent with the fact that the Uox gene is unique in the genome and evolutionarily conserved not only among animals but also among eukaryotes. Another finding that there are a few substitutions in the cis-acting element or CAAT-box (or both) of primate functional Uox genes may explain the lowered transcriptional activity. We suggest that although the inactivation of the hominoid Uox gene was caused by independent nonsense or frameshift mutations, the gene has taken a two-step deterioration process, first in the promoter and second in the coding region during primate evolution. It is also argued that the high concentration of uric acid in the blood of humans and nonhuman primates has developed molecular coevolution with the xanthine oxidoreductase in purine metabolism. However, it remains to be answered whether loss of Uox activity in hominoids is related to protection from oxidative damage and the prolonged life span.

Different alleles undergoing strong symmetric balancing selection show a simple genealogical structure (allelic genealogy), similar to the gene genealogy described by the coalescence process for a sample of neutral genes randomly drawn from a panmictic population at equilibrium. The only difference between the two genealogies lies in the different time scales. An approximate scaling factor for allelic genealogy relative to that of neutral gene genealogy is {fV/(2M)} [In{S/(16frM2)}13 2, where M = Nu and S = 2Ns (N, effective population size; u, mutation rate to selected alleles per locus per generation; s, selection coefficient). The larger the value of \/S/M (.100), the larger the scaling factor. These rindings, supported by simulation results, allow one to apply the theoretical results of the coalescence process directly to the allelic genealogy. Combined with the trans-species evolution of the major histocompatibility complex polymorphism for which balancing selection is believed to be responsible, allelic genealogy predicts that the number of breeding individuals in the human population could not be as small as 50-100 at any time of its evolutionary history. The analysis appears to contradict the founder principle as being important in recent mammalian evolution. It differs from the genealogy described by the linesof-descent process (5) in which coalescences of genes occurring within each line and the age of each line are the main interest, but the allelic genealogy are not taken into account. GeneAlthough allelic genealogy was developed to examine quantitatively the extraordinary polymorphism of the major histocompatibility complex (MHC) molecules (6-10), the study was largely based on computer simulation (4). In this paper, I show that there exists a simple mathematical structure of allelic genealogy under strong symmetric balancing selection and use this theory to discuss the evolutionary implication of transspecies mode of MHC polymorphisms (7).By balancing selection (one of the most efficient mechanisms to maintain polymorphism), I mean a collection of different selection schemes, all of which lead to the mean gene-frequency change given below. It has been shown that for this equation of the gene-frequency change, there can exist two fundamentally different selection models (4). In fact for any allele-frequency equation there are many alternative fitness models (11). This is unfortunate for the study of population genetics because simply observing a genefrequency change cannot identify the underlying mechanism. However, this is not the concern here (see ref. 4).Under balancing selection, alleles (allelic lines) can persist for a much longer time than neutral alleles, even in a relatively small population (12,13). Those selected alleles may therefore differ from each other by more than one nucleotide change. When new alleles are produced each with an initial frequency of 1/(2N), where N is the effective population size, they differ from their parental ones by single changes. If new alleles happen...

Humans are genetically deficient in the common mammalian sialic acid N-glycolylneuraminic acid (Neu5Gc) because of an Alu-mediated inactivating mutation of the gene encoding the enzyme CMP-N-acetylneuraminic acid (CMP-Neu5Ac) hydroxylase (CMAH). This mutation occurred after our last common ancestor with bonobos and chimpanzees, and before the origin of present-day humans. Here, we take multiple approaches to estimate the timing of this mutation in relationship to human evolutionary history. First, we have developed a method to extract and identify sialic acids from bones and bony fossils. Two Neandertal fossils studied had clearly detectable Neu5Ac but no Neu5Gc, indicating that the CMAH mutation predated the common ancestor of humans and Neandertals, Ϸ0.5-0.6 million years ago (mya). Second, we date the insertion event of the inactivating human-specific sahAluY element that replaced the ancestral AluSq element found adjacent to exon 6 of the CMAH gene in the chimpanzee genome. Assuming Alu source genes based on a phylogenetic tree of human-specific Alu elements, we estimate the sahAluY insertion time at Ϸ2.7 mya. Third, we apply molecular clock analysis to chimpanzee and other great ape CMAH genes and the corresponding human pseudogene to estimate an inactivation time of Ϸ2.8 mya. Taken together, these studies indicate that the CMAH gene was inactivated shortly before the time when brain expansion began in humankind's ancestry, Ϸ2.1-2.2 mya. In this regard, it is of interest that although Neu5Gc is the major sialic acid in most organs of the chimpanzee, its expression is selectively down-regulated in the brain, for as yet unknown reasons. hominid evolution ͉ sialic acids ͉ Alu sequences