Suppose I sequence one of your genes, and then I sequence the same gene from me, and from a chimpanzee. Are you going to be more genetically similar to me or to the chimp? Obviously, assuming you are a human, you’ll be more similar to me at most genes. But not necessarily every gene. If I pick the right spot in the genome, the chimp might look like a close cousin compared to a distant relative such as myself. Even though the ancestors of chimps and humans parted ways millions of years ago, we still haven’t finished sorting out all of our genetic material into two independent branches of the evolutionary tree. Behold the bizarre phenomenon of trans-species polymorphism.
As any good investor knows, a diversified portfolio can reduce risk. The same is true for certain immunity genes. Genes of the major histocompatibility complex (MHC) help vertebrates to recognize invading germs and parasites so the immune system can start fighting back. At any given MHC genetic locus, just like for every gene, you have two variants (alleles): one from your mother and one from your father. Organisms with two very different MHC alleles can recognize more pathogens than organisms with two identical alleles, so they survive better. There’s even some evidence that animals (including humans) prefer mates who smell like they have different MHC genotypes, so their offspring will have two different alleles (yes, they’ve actually done these studies in humans by having people smell sweaty t-shirts worn by someone of the opposite sex. In theory, if you know the MHC genotype of that special someone, you could douse yourself with sweat from someone of a really different MHC genotype, and get lucky this Valentine’s Day. In theory.).
Anyway, as a result, natural selection has favored a vast diversity of MHC alleles in the gene pool of most vertebrate species. At most “normal” genes, new variants occasionally appear and replace the older variants, whether by natural selection or by random chance (genetic drift). Not so with MHC, because no one allele is as good as two different alleles. So different allelic lineages hang around a very long time, even through speciation events. The MHC diversity that existed in the most common ancestor of human and chimps is still with us, floating around the gene pools of both species.
And not it’s just us. Trans-species polymorphism has been documented in several different vertebrate groups. MHC genes are not the only genes showing trans-species polymorphism, either. One way of defining “species” is that a species is a group of organisms who are all each other’s closest relatives throughout their genomes (the so-called “phylogenetic species concept”). Trans-species polymorphism shows that this in not an entirely accurate to define species, since humans and chimps are clearly distinct species. We’re just maybe not as distinct as you might assume.