Abstract
A simple neutral model predicts that the ratio of non-synonymous to synonymous fixed differences between species will be the same as the ratio of non-synonymous to synonymous polymorphisms within species. This prediction is tested with existing mitochondrial datasets from 25 animal species. In slightly over half of the studies, the ratio of replacement to silent polymorphisms within species is significantly greater than the ratio of replacement to silent fixed differences between species. These observations are best explained by a substantial number of mildly deleterious amino acid mutations that contribute to heterozygosity but rarely become fixed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Akashi, H., 1995. Inferring weak selection from patterns of polymorphism and divergence at’ silent’ sites in Drosophila DNA. Genetics 139: 1067–1076.
Ballard, J.W.O. & M. Kreitman, 1994. Unraveling selection in the mitochondrial genome of Drosophila. Genetics 138: 757–772.
Baker, R.J., R.A. Van Den Bussche, A.J. Wright, L.E. Wiggins, M.J. Hamilton, E.P. Reat, M.H. Smith, M.D. Lomakin & R.K. Chesser, 1996. High levels of genetic change on rodents of Chernobyl. Nature 380: 707–708.
Brookfield, J.F.Y. & P.M. Sharp, 1994. Neutralism and selection face up to DNA data. Trends Genet. 10: 109–111.
Brower, A.V.Z., 1994. Rapid morphological radiation and conver gence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc. Nat. Acad. Sci. USA 91: 6491–6495.
Bruna, E.M., R.N. Fisher & T.J. Case, 1996. Morphological and genetic evolution appear decoupled in Pacific skinks (Squamata: Scincidae: Emoia). Proc. R. Soc. Lond. B 263: 681–688.
Carr, S.M., A.J. Snellen, K.A. Howse & J.S. Wroblewski, 1995. Mitochondrial DNA sequence variation and genetic stock struc ture of Atlantic cod (Gadus morhua) from bay and offshore loca tions on the Newfoundland continental shelf. Mol. Ecology 4: 79–88.
Charlesworth, B., 1994. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. Camb. 63: 213–227.
Charlesworth, B., M.T. Morgan & D. Charlesworth, 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289–1303.
Charlesworth, D., B. Charlesworth & M.T. Morgan, 1995. The pat tern of neutral molecular variation under the background selection model. Genetics 141: 1619–1632.
Clark, A.J., 1984. Natural selection with nuclear and cytoplasmic transmission. I. A deterministic model. Genetics 107: 679–701.
DaSilva, M.N.F. & J.L. Patton, 1993. Amazonian phylogeogra-phy: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha). Mol. Phylogenet. Evol. 2: 243–255.
Edwards, S.V. & A.C. Wilson, 1990. Phylogenetically informative length polymorphism and sequence variability in mitochondri al DNA of Australian songbirds (Pomatostomus). Genetics 126: 695–711.
Fisher, R.A., 1958. The Genetical Theory of Natural Selection, 2nd ed. Dover Publications, Inc., New York.
Fu, Y.X. & W.H. Li, 1993. Statistical tests of neutrality of mutations. Genetics 133: 693–709.
Gaut, B.S. & M.T. Clegg, 1993a. Nucleotide polymorphism in theAdhl locus of pearl millet (Pennisetum glaucum)(Poaceae). Genetics 135: 1091–1097.
Gaut, B.S. & M.T. Clegg, 1993b. Molecular evolution of the Adhl locus in the genus Zea. Proc. Nat. Acad. Sci. 90: 5095–5099.
Gillespie, J.H., 1991. The Causes of Molecular Evolution. Oxford University Press, Oxford.
Gillespie, J.H., 1994. Substitution processes in molecular evolution. III. Deleterious alleles. Genetics 138: 943–952.
Gillespie, J.H., 1994. Alternatives to the neutral theory, pp. 1–17 in Non-neutral Evolution. Theories and Molecular Data, edited by B. Golding. Chapman and Hall, New York.
Gillespie, J.H., 1995. On Ohta’s hypothesis: most amino acid sub stitutions are deleterious. J. Mol. Evol. 40: 64–69.
Guttman, D.S. & D.E. Dykhuizen, 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138: 993–1003.
Hammer, M., 1995. A recent common ancestry for human Y Chromosomes. Nature 378: 376–378.
Hedges, S.B., J.P. Bogart & L.R. Maxson, 1992. Ancestry of uni sexual salamanders. Nature 356: 708–710.
Hey, J., 1997. Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol. Biol. Evol. 14: 166–172.
Hudson, R.R., M. Kreitman & M. Aguade, 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153–159.
Hutter, C.M. & D.M. Rand, 1995. Competition between mitochondr ial haplotypes in distinct nuclear genetic environments: Drosophila pseudoobscura vs. D. persimilis. Genetics 140: 537–548.
Jukes, T.H. & C.R. Cantor, 1969. Evolution of protein molecules, pp. 21–132 in Mammalian Protein Metabolism, edited by H.N. Munro, Academic Press, New York.
Kaneko, M., Y Satta, E. T. Matsura & S. Chigusa, 1993. Evolution of the mitochondrial ATPase 6 gene in Drosophila: unusually high level of polymorphism in D. melanogaster. Genet. Res. 61: 195–204.
Kelly, J.K., 1997. A test of neutrality based on interlocus associa tions. Genetics 146: 1197–1206.
Kilpatrick, S.T. & D.M. Rand, 1995. Conditional hitchhik ing of mitochondrial DNA: frequency shifts of Drosophila melanogaster mtDNA variants depend on nuclear genetic back ground. Genetics 141: 1113–1124.
Kimura, M., 1968. Evolutionary rate at the molecular level. Nature 217: 624–626.
Kimura, M., 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
Kreitman, M. & H. Akashi, 1995. Molecular evidence for natural selection. Ann. Rev. Ecol. Syst. 26: 403–422.
Li, W.-H. & L. A. Sadler, 1991. Low nucleotide diversity in man. Genetics 129: 513–523.
MacRae, A.F. & W.W. Anderson, 1988. Evidence for non-neutrality of mitochondrial DNA haplotypes in Drosophila pseudoobscura. Genetics 120: 485–494.
McDonald, J.H., 1996. Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to diver gence. Mol. Biol. Evol. 13: 253–260.
McDonald, J. H. & M. Kreitman, 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652–654.
Moritz, C., C.J. Schneider & D.B. Wake, 1992. Evolutionary rela tionships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41: 273–291.
Nachman, M.W. & C.F. Aquadro, 1994. Polymorphism and diver gence at the 5′ flanking region of the sex determining locus, Sry, in mice. Mol. Biol. Evol. 11: 539–547.
Nachman, M.W., S.N. Boyer & C.F. Aquadro, 1994. Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Nat. Acad. Sci. USA 91: 6364–6368.
Nachman, M.W., W.M. Brown, M. Stoneking & C.F. Aquadro, 1996. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142: 953–963.
Ohta, T., 1972. Population size and rate of evolution. J. Mol. Evol. 1: 305–314.
Ohta, T. & J.H. Gillespie, 1996. Development of neutral and nearly neutral theories. Theoret. Pop. Biol. 49: 128–142.
Ohta, T. & M. Kimura, 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1: 18–25.
Rand, D.M. & L.M. Kann, 1996. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 13: 735–748.
Rand, D.M. & L.M. Kann, 1998. Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica 102/103: 393–407.
Rand, D.M., M. Dorfsman & L.M Kann, 1994. Neutral and nonneutral evolution of Drosophila mitochondrial DNA. Genetics 138: 741–756.
Sawyer, S.A. & D.L. Hartl, 1992. Population genetics of polymor phism and divergence. Genetics 132: 1161–1176.
Sawyer, S.A., D.E. Dykhuizen & D.L. Hartl, 1987. Confidence interval for the number of selectively neutral amino acid poly morphisms. Proc. Nat. Acad. Sci. USA 84: 6225–6228.
Sokal, R.R. & F.J. Rohlf, 1995. Biometry, 3rd edition. W.H. Freeman and Co., New York.
Summers, K., E. Bermingham, L. Weigt, S. McCafferty & L. Dahlstrom, 1997. Phenotypic and genetic divergence in three species of dart-poison frogs with contrasting parental behavior. J. Hered. 88: 8–13.
Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
Takahata, N., 1993. Relaxed natural selection in human populations during the Pleistocene. Jpn. J. Genet. 68: 539–547.
Talbot, S.L. & G.F. Shields, 1996. Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Mol. Phylogenet. Evol. 5: 477–494.
Templeton, A.R., 1996. Contingency tests of neutrality using intra/ interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263–1270.
Watterson, G.A., 1978. The homozygosity test of neutrality. Genetics 88: 405–417.
Watterson, G.A., 1975. On the number of segregating sites in genetic models without recombination. Theoret. Pop. Biol. 7: 256–276.
Wood, T.C. & C. Krajewski, 1996. Mitochondrial DNA sequence variation among the subspecies of Sarus Crane (Grus antigone). Auk 113: 655–663.
Zink, R.M. & R.C. Blackwell, 1996. Patterns of allozyme, mitochon drial DNA, and morphometric variation in four sparrow genera. Auk 113: 59–67.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1998 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Nachman, M.W. (1998). Deleterious mutations in animal mitochondrial DNA. In: Woodruff, R.C., Thompson, J.N. (eds) Mutation and Evolution. Contemporary Issues in Genetics and Evolution, vol 7. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-5210-5_6
Download citation
DOI: https://doi.org/10.1007/978-94-011-5210-5_6
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-010-6193-3
Online ISBN: 978-94-011-5210-5
eBook Packages: Springer Book Archive