It is common for strong results from population genetics to be confused when it is translated for public consumption. The best example is that of “mtDNA Eve.” Despite the big warning label that mtDNA Eve is one of many female ancestors, the public has gained the impression that she is the female ancestor. A similar problem is cropping up with the Khoisan paper which reports that they went through a relatively mild bottleneck in comparison to other modern human populations. There’s a reason I titled the post The Least Bottlenecked Humans of All. It’s a defensible reduction of the results. In contrast many popular treatments are translating the results into the conclusion that “the Khoisan had the largest population of all human groups at some point in the past.” The reason I avoided this formulation is that plainly stated I doubt that at any time the Khoisan as we understand them, a genetically-culturally coherent group in southern Africa, had the largest population of all. Humans of various sorts have been common across Afro-Eurasia for over a million years. Is it plausible that ancestors of the Khoisan had the largest populations of all? Anne Gibbon’s somewhat cautiously stated piece in Science, Dwindling African tribe may have been most populous group on planet, relays the sentiment which I share:

Other researchers agree that it’s likely that the Khoisan descend from a large population. But because sampling of African genomes is still so spotty, not everyone is yet convinced that the Khoisan “was the largest population on Earth at some point,” says evolutionary geneticist Pontus Skoglund of Harvard University. “Many African populations are not included for comparison,” he says, so it is possible that some of the diversity seen in the Khoisan was inherited from recent interbreeding that cannot yet be detected. Either way, the study makes it clear that even though the Khoisan are genetically diverse by today’s standards, even they carry just a fraction of our ancestors’ genetic legacy over the past 120,000 years. “It is quite staggering how much extraordinary genetic variation and ethnic diversity was present but is now lost,” Skoglund says. The Khoisan, retaining more than the rest of us, offer a rare window to look back in time at some of that diversity.

The biggest gap in the current study is that many extinct lineages were not included. Obviously they couldn’t be included, because they’re extinct, though at some point in the future ancient DNA or (more likely in the African context) reconstruction of ancient genomes from extant populations which have absorbed them, might allow for a better understanding of Pleistocene human population sizes. Population genomics is powerful, but it has limits. We need to be cautious about assuming that what we can illuminate with current methods is all that can be conceived in our natural philosophy.