Episodic adaptive evolution of primate lysozymes

ALTHOUGH the darwinian concept of adaptation was established nearly a century ago, it has been difficult to demonstrate rigorously that the amino-acid differences between homologous proteins from different species have adaptive significance. There are currently two major types of sequence tests for positive darwinian selection on proteins from different species: sequence convergence, and neutral rate violation (reviewed in ref. 1). Lysozymes from the stomachs of cows and langur monkeys, two mammalian species displaying fermentation in the foregut, are an example2,3 of amino-acid sequence convergence among homologous proteins4–6. Here we combine tests of neutral rate violation with reconstruction of ancestral sequences to document an episode of positive selection on the lineage leading to the common ancestor of the foregut-fermenting colobine monkeys. This analysis also detected a previously unsuspected adaptive episode on the lineage leading to the common ancestor of the modern hominoid lysozymes. Both adaptive episodes were followed by episodes of negative selection. Thus this approach can detect adaptive and purifying episodes, and localize them to specific lineages during protein evolution.

[1]  M. Nei Molecular Evolutionary Genetics , 1987 .

[2]  A. Wilson,et al.  Stomach lysozymes of ruminants. I. Distribution and catalytic properties. , 1984, The Journal of biological chemistry.

[3]  W. Swanson,et al.  Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[4]  D. Chivers,et al.  Morphology of the gastrointestinal tract in primates: Comparisons with other mammals in relation to diet , 1980, Journal of morphology.

[5]  J. Gillespie The causes of molecular evolution , 1991 .

[6]  D. Irwin,et al.  Evolution of stomach lysozyme: the pig lysozyme gene. , 1996, Molecular phylogenetics and evolution.

[7]  M. Nei,et al.  A new method of inference of ancestral nucleotide and amino acid sequences. , 1995, Genetics.

[8]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[9]  Hiroshi Akashi,et al.  Molecular Evidence for Natural Selection , 1995 .

[10]  T Gojobori,et al.  Large-scale search for genes on which positive selection may operate. , 1996, Molecular biology and evolution.

[11]  Wen-Hsiung Li,et al.  Fundamentals of molecular evolution , 1990 .

[12]  Allan C. Wilson,et al.  Adaptive evolution in the stomach lysozymes of foregut fermenters , 1987, Nature.

[13]  A. Wilson,et al.  Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters. , 1987, Cold Spring Harbor symposia on quantitative biology.

[14]  J. Oates,et al.  Colobine Monkeys: Their Ecology, Behaviour and Evolution , 1995 .

[15]  C. Luo,et al.  A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. , 1985, Molecular biology and evolution.

[16]  A. Wilson,et al.  Concerted evolution of ruminant stomach lysozymes. Characterization of lysozyme cDNA clones from sheep and deer. , 1990, The Journal of biological chemistry.

[17]  L. Jin,et al.  Variances of the average numbers of nucleotide substitutions within and between populations. , 1989, Molecular biology and evolution.

[18]  M. Nei,et al.  Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection , 1988, Nature.

[19]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[20]  V. Vacquier,et al.  The Divergence of Species-Specific Abalone Sperm Lysins is Promoted by Positive Darwinian Selection. , 1992, The Biological bulletin.