near neutrality & compensatory evolution

Itoh T, Martin W & Nei M 2002 Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. PNAS 99:12944-12948.

• we are not considering the strict neutrality of alleles
• which would never exist in nature
• we are defining amino acid substitutions as neutral or nearly neutral as long as the gene function remains essentially the same
• under this definition, which was often used in the early days of study of molecular evolution (49–52), the compensatory mutations as formulated by Hartl and Taubes (53) belong to the realm of neutral mutations
• because they do not change the gene function in long-term evolution (no adaptation)
• if we consider short-term evolution and intraspecific polymorphism, there may be plenty of slightly deleterious mutations
• but they are not our concern