The spatial distribution of fixed mutations within genes coding for proteins
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We have examined the extensive amino acid sequence data now available for five protein families — the α crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromesc — with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10−44. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.
Key wordsBase substitution patterns Mutability Poisson density Geometric density Negative binomial density Natural selection Amino acids Proteins Genes Nucleotides
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- De Jong WW, Goodman M (1982) Mammalian phylogeny studied by sequence analysis of the eye lens protein α-crystallin. Z Säugetierkunde 47:257–276Google Scholar
- Goodman M (1981) Decoding the pattern of protein evolution. Progr Biophys Mol Biol 38:105–164Google Scholar
- Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool 28:132–163Google Scholar
- Goodman M, Romero-Herrera AE, Dene H, Czelusniak J, Tashian RE (1982) Amino acid sequence evidence on the phylogeny of primates and other eutherians. In: Goodman M (ed) Macromolecular sequences in systematic and evolutionary biology. Plenum Press, New York, pp 115–191Google Scholar
- Hoel PG (1954) Testing goodness of fit. In: Introduction to Mathematical Statistics, Chapter 9, Chapman and Hall, Ltd. (London), John Wiley & Sons (New York)Google Scholar
- Holmquist R (1980) The method of parsimony: an experimental test and theoretical analysis of the adequacy of molecular restoration studies. J Mol Biol 135:939–958Google Scholar
- Holmquist R, Pearl D, Jukes TH (1982) Nonuniform molecular divergence. In: Goodman M (ed) Macromolecular sequences in systematic and evolutionary biology. Plenum Press, New York, pp 281–315Google Scholar