J Mol Evol (2001) 52:40–50 DOI: 10.1007/s002390010132 © Springer-Verlag New York Inc. 2001 The Rates of Molecular Evolution in Rodent and Primate Mitochondrial DNA Daniel M. Weinreich* Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Received: 24 September 1999 / Accepted: 18 September 2000 Abstract. A higher rate of molecular evolution in ro- tioned and is found to be entirely the consequence of a dents than in primates at synonymous sites and, to a higher mutation rate in rodents. This conclusion is con- lesser extent, at amino acid replacement sites has been sistent with a replication-dependent model of mutation in reported previously for most nuclear genes examined. mtDNA. Thus in these genes the average ratio of amino acid re- placement to synonymous substitution rates in rodents is Key words: Molecular clock — Mitochondrial — lower than in primates, an observation at odds with the DNA — Mammals — Neutral theory — Mildly delete- neutral model of molecular evolution. Under Ohta’s rious theory — Maximum likelihood mildly deleterious model of molecular evolution, these observations are seen as the consequence of the com- bined effects of a shorter generation time (driving a Introduction higher mutation rate) and a larger effective population size (resulting in more effective selection against mildly The molecular clock (Zuckerkandl and Pauling 1965) deleterious mutations) in rodents. The present study re- was originally a phenomenological description of mo- ports the results of a maximum-likelihood analysis of the lecular evolution which noted that proteins (and later ratio of amino acid replacements to synonymous substi- their genes) fix substitutions at an approximately linear tutions for genes encoded in mitochondrial DNA rate with respect to time. Genes on mammalian single- (mtDNA) in these two lineages. A similar pattern is ob- copy nuclear DNA have been especially well-studied served: in rodents this ratio is significantly lower than in (Laird et al. 1969; Dickerson 1971; Easteal 1985; Wu primates, again consistent only with the mildly deleteri- and Li 1985; Li et al. 1987; Gu and Li 1992; Ohta 1993; ous model. Interestingly the lineage-specific difference is 1995; Easteal et al. 1995; Yang and Nielsen 1998) due to much more pronounced in mtDNA-encoded than in a wealth of data derived from mammalian model organ- nuclear-encoded proteins, an observation which is shown isms. The requirement to explain these observations has to run counter to expectation under Ohta’s model. Fi- contributed substantially to the development of the dom- nally, accepting certain fossil divergence dates, the inant theories of molecular evolution (Kimura 1968; lineage-specific difference in amino acid replacement-to- King and Jukes 1969; Ohta and Kimura 1971; Gillespie synonymous substitution ratio in mtDNA can be parti- 1989). In contrast, no comparison of rates of molecular evolution in the mitochondrial genomes among mam- mals has yet been made. Under the neutral theory (Kimura 1968) the rate of * Current address: Department of Biology, University of California at San Diego, Muir Biology Building, 9500 Gilman Drive, La Jolla, CA substitution of selectively equivalent alleles is propor- 92093-0116, USA tional to the mutation rate and independent of population Correspondence to: Daniel M. Weinreich; email: [email protected] size (King and Jukes 1969; Kimura and Ohta 1971). This 41 Table 1. GenBank accession numbers for complete mitochondrial Table 2. GenBank accession numbers for cytochrome b and cyto- sequences used chrome c oxidase subunit II sequences used Species Accession No. Accession No. Homo sapiens J01415 Species Cyt b CO II Pongo pygmaeus D38115 Mus musculus J01420 Rodents Rattus norvegicus X14848 Acomys wllsoni AJ010561 U18832 Apodemus sylvaticus AF160603 U18833 Cratogeomys castanops L11908 U18828 Geomys bursarius AF158693 U18829 model accords well with early measurements of amino Georychus capensis AF012243 U18837 Microtus pennsylvanicus AF119279 U62573 acid fixation rates (e.g., Dickerson 1971, Fig. 3) and an Tachyoryctes spendens AF160602 U62575 assumption of a temporally constant mutation rate. How- Primates ever, it cannot also account for estimates of nucleotide Daubentonia madagascarensis U53569 L22776 substitution rates, which were found to be inversely re- Eulemur fulvus collaris U53576 AF081041 lated to generation time (Laird et al. 1969). A constant Hapalemur griseus U53574 L22778 Hylobates syndactylus Y13303 M58007 mutation rate per organismal generation has some theo- Lemur catta U53575 L22780 retical appeal (Wu and Li 1985; Li 1993). If DNA rep- Pan paniscus D38116 D38116 lication is the primary source of mutations, then the per- Saimiri sciureus U53582 U36848 germline-cell-division mutation rate should be constant across lineages. A constant per-organismal generation divisions per organismal generation in rodents than pri- mutation rate follows if the number of germline cell di- mates (Vogel and Rathenberg 1975), replication-inde- visions per organismal generation is constant. However, pendent mutation, and more effective weak selection this reasoning leaves the chronologically constant amino against some synonymous substitutions (Akashi 1996) in acid substitution rate unexplained. rodents due to their larger N. Nor is the amino acid The mildly deleterious model (Ohta 1973) is intended substitution rate chronologically constant: putatively to account for both observations by considering weakly larger effective population size notwithstanding, mean deleterious amino acid replacement mutations with se- amino acid fixation rates are 1.7 (Ohta 1995; Yang and lection coefficients roughly in the range 0 Նs Ն−1/N, Nielsen 1998) to 1.9 (Li et al. 1987) times higher in where N is the effective population size. Such mutations rodents than other mammalian lineages. Nevertheless, in may reach fixation by genetic drift, negative selection comparisons of nuclear genes between rodents and other coefficients notwithstanding (Ohta and Kimura 1971), mammals, synonymous substitution rates appear more and under this model the rate of amino acid fixations is strongly correlated with the reciprocal of organismal inversely related to the population size. Ohta (1972, p. generation time than are amino acid replacement rates 151) cites as an “empirical fact” an inverse relationship [but see Easteal (1985) and Easteal et al. (1995) for an between generation time and effective population size alternative interpretation of these data]. (Chao and Carr 1984; but see Nei and Graur 1984). Thus Mitochondria are subcellular organelles common to under the mildly deleterious theory, organisms with most eukaryotes which possess their own genetic system shorter generation times experience a higher chronolog- (Gillham 1994). This consists of approximately 16,500 ical mutation rate. However, because they also have a bases of DNA encoding roughly 13 proteins and 22 RNA larger population size, natural selection is more effective genes in most metazoans (Wolstenholme 1992), together at eliminating mildly deleterious mutations, and the net with a distinct system of DNA replication, transcription, chronological fixation rate of amino acid replacement and translation. Mitochondria are maternally inherited, mutations will be roughly constant. and although as many as 10,000 copies of mitochondrial Owing to the redundancy of the genetic code we can DNA (mtDNA) have been reported in single cells (Gill- distinguish between two classes of mutation in protein- ham 1994), persistent mtDNA polymorphism within coding DNA sequence data: synonymous and amino acid pedigrees (heteroplasmy) has not been observed replacement. Surveys of published DNA sequences for (Hauswirth and Laipis 1982; Ivanov et al. 1996) and is nuclear-encoded genes in mammals have permitted a thought unlikely to occur on theoretical grounds (Clay- more careful examination of the neutral and mildly del- ton 1996; Jenuth et al. 1996). The absence of hetero- eterious models (Wu and Li 1985; Li et al. 1987; Ohta plasmy and their haploid maternal inheritance means that 1993; 1995; Yang and Nielsen 1998). The reality appears the mitochondrial effective population size (Nmt) is equal to be yet more complicated: the synonymous substitution to the effective population size of females (Nf) (Birky et rate is not constant in terms of organismal generation al. 1983). Thus assuming equal sex ratio and panmixia, ס time, nor is it as high in rodents as predicted by their Nmt ¼Nnuc (the diploid nuclear effective population generation time. This could be explained by one or more size). More generally, for any fixed mating structure, Nmt of the following (Wu and Li 1985): fewer germline cell may simply be regarded as a linear function of Nnuc.In 42 Fig. 1. The unrooted phylogenetic tree of Homo sapiens, Pongo pygmaeus, Mus musculus, and Rattus norvegicus. ␻ ס ( dN/dS) is the ratio of the nonsynonymous-to-synonymous substitution rates. Three evolutionary models were fit to the sequences shown in Table 1. A The value of ␻ is constrained to be constant among all branches. B ␻ ␻ Order-specific values of ( prı´mate and ␻ rodent) and a value for the common ␻ ancestor ( C.A.) are defined. C Branch-specific values of ␻ are defined. contrast to effective population size, mtDNA mutation is possible to estimate provisionally absolute mutation rates are decoupled from nuclear mutation rates (Vawter rates in the rodent and primate lineages. Although the and Brown 1986), and within mammals