A trans-species polymorphism. Some genetic polymorphisms are found in distantly related species, having persisted across multiple speciation events. (source)
It is widely known that considerable genetic overlap exists between human populations, even those that are geographically distant from each other and quite different physically. You probably learned in BIO101 that genetic variation is much greater within than between human populations.
It is less widely known that this high degree of genetic overlap also exists between many species that are nonetheless distinct morphologically, physiologically, and behaviorally (Frost, 2011). This is especially so with young sibling species. Such species differ only over a small fraction of the genome—at those genes where a certain variant is adaptive in one species but not in the other. Elsewhere, over most of the genome, the same variant works just fine in both species, either because the gene itself is of little or no value or because certain body functions are pretty much the same in a wide range of organisms.
With time, and reproductive isolation, two sibling species will gradually lose this genetic overlap, as a result of random mutations here and there over the entire genome. The two species will be less and less alike even at “junk genes” of little value.
Even so, some overlap will remain. It’s not just that we see the same gene in distantly related species. We also see the same gene with the same set of alleles—a trans-species polymorphism (Klein et al., 1998). A good example is the ABO blood group system. On the basis of that gene marker, I probably have more in common with certain apes than I do with some of my readers. Such polymorphisms have in fact persisted for millions of years across multiple speciation events.
Until recently, it was believed that trans-species polymorphisms were no more than an oddity. Now, it looks like they may be more common than previously thought:
[…] we searched for trans-species polymorphisms between humans and chimpanzees using genome-wide resequencing data for 10 western chimpanzees from the PanMap project and 179 humans from the 1000 Genomes Pilot 1 data. […] In addition to the MHC region, we identified over 100 cases, a set significantly enriched for transmembrane glycoproteins, which are often involved in interactions with pathogens. To further rule out the possibility of deep coalescent events by chance, we examined patterns of variation in seven samples of Gorilla gorilla. We discovered 25 cases shared among all three species, which we verified by Sanger sequencing. In a subset, within species diversity levels were unusually high and the tree of haplotypes clustered by allelic type rather than by species, providing definitive evidence for trans-species polymorphisms. (Segurel et al, 2012)
At such genes, variation within species exceeds variation between species … and even between genera.
So just what, then, makes a species a species? The traditional answer is reproductive isolation, and the resulting accumulation of genetic differences over time. Yet this answer seems increasingly problematic. On the one hand, we have cases of living fossils that remain essentially the same over eons of time. Analysis of “junk DNA” would show a steady accumulation of genetic change over those eons, although nothing has changed in appearance or behavior. A coelacanth today is still a coelacanth after millions and millions of years.
On the other hand, we have cases of sibling species that have emerged in recent times and have become quite different from each other both anatomically and behaviorally. Yet genetic analysis of such species often shows considerable genetic overlap. If we use any of the usual genetic markers (blood groups, enzymes, etc), individuals may not be assignable to a single species with reasonable certainty.
So if genes in general don’t matter, what exactly does? What matters is what matters. Genes for highly adaptive traits matter. Differences you can see matter. Therefore, reproductive isolation in itself is not what makes two populations different; it’s the different ways in which they adapt to different environments.
If a population splits in two with one group moving into one environment and the other moving into another, the two groups will nonetheless continue to look and act similarly as long as their respective environments remain similar (of course, if the two groups are human societies, one of them might create a radically different cultural environment). It is the difference in selection pressures, as a result of differing environments, that will drive them apart … and such differentiation will proceed even if reproductive isolation is still incomplete:
Judging from the number of studies devoted to it, the nature of a reproductive barrier is currently central to the interests of researchers working on speciation. It seems to us, however, that the process of adaptation to the environment is a much more important and interesting part of speciation. The erection of the reproductive barrier may mark the end of speciation, but it tells us little about the process that makes the species differ from one to another, the process that creates biological diversity. (Klein et al., 2007)
Frost, P. (2011). Human nature or human natures? Futures, 43, 740–748. http://dx.doi.org/10.1016/j.futures.2011.05.017
Klein, J., A. Sato, S. Nagl, and C. O’hUigin. (1998). Molecular trans-species polymorphism, Annual Review of Ecology and Systematics, 29, 1-21.
Klein, J., A. Sato, and N. Nikolaidis. (2007). MHC, TSP, and the origin of species: From immunogenetics to evolutionary genetics, Annual Review of Genetics, 41, 281-304http://e-groups.unb.br/fm/lmpdc/arquivos/artigos/MARILEN%20QUEIROZ%20MHC%20evolutionary%20genetics.pdf
Segurel, L., E. Leffler, Z. Gao, S. Pfeifer, A. Auton, O. Venn, L. Stevison, A. Venkat, J. L. Kelley, J. Kidd, C. Bustamante, R. Bontrop, M. Hammer, J. Wall, P. Donnelly, G. McVean, & M. Przeworski. (2012). When ancestry runs deep: Trans-species polymorphisms in apes, Annual Meeting of the American Society of Human Genetics, November 6-10http://www.ashg.org/2012meeting/abstracts/fulltext/f120121882.htm