Trans-specific Mhc polymorphism and the origin of species in primates

The major histocompatibility complex (Mhc) is a cluster of loci controlling the specific immune response in vertebrates. Mhc alleles often differ by a large number of nucleotide substitutions, some of which began to accumulate before the emergence of extant species. We have applied the theory of allelic genealogy to the primate Mhc genes with the aim of estimating the size of the founding populations. The calculations indicate that the long-term effective population size of the studied species was between 10⁴ and 10⁵ individuals and that it most likely never dropped below 10³ individuals.