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. Lysozymes from the stomachs
of cows and langur monkeys, two mammalian species displaying fermentation
in the foregut, are an example of amino-acid sequence convergence among
homologous proteins. 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.