Little is known regarding the rates at which natural selection can mod
ify or retain antigen presenting alleles at the major histocompatibili
ty complex (MHC). Discovery of identical [1101 base pairs (bp)] coding
regions at the MWC class I C locus in Pan troglodytes and Pan paniscu
s, chimpanzee species that diverged similar to 2.3 million years ago,
now indicates that a class I allotype can survive for at least this pe
riod. Remarkable conservation was also reflected in the (1799 bp) intr
ons where a maximum of only six substitutions distinguished live allel
es (three from P. troglodytes and two from P., paniscus) that encoded
the identical heavy chain allotype. Analysis of a more distantly relat
ed human allele, HLA-Cw0702, corroborated that intron variation was n
on-uniform along the gene, Thus we provide a clear reference frame for
the lifetime of an MHC class I allotype, a direct estimate of allelic
substitution rates, and evidence for an unusual evolution of MH(I cla
ss I introns.