Neanderthals and Amerindians: Intragroup Genetic Diversity and Population Size

John Hawks writes:

“Neandertals have strikingly limited genetic variation. They once lived across a range from Spain to Siberia. Yet when we compare    sequences across their whole genomes, we find them to be much less different across this geographic range than people living in the same regions today. I think this is one of the most fascinating findings of ancient genomics. It may tell us something about Neandertal populations that we did not begin to suspect without their DNA. But there is one explanation for this fact that I and others pointed out long before DNA evidence: The Neandertal population was surely much, much smaller than Holocene population of Europe. Small population size over a long time can restrict genetic diversity. So maybe the Neandertals preserved little genetic variation simply because there were so few of them.”

The same thing – word by word – can be said about American Indians. Neandertals are obviously older than African humans, as archaeological dates abundantly testify. Then what makes African populations older than Amerindians if Amerindians show the same pattern of genetic variation – low diversity, same alleles showing up from Alaska to Tierra del Fuego – and low population size, as Neandertals?

Hawks goes on to quote from the seminal paper by Reich et al. (2003):

“Using the 56 Mb of autosomal DNA sequences determined from [the Mezmaiskaya specimen], we estimate that the DNA sequence divergence between the Vindija and Mezmaiskaya Neanderthals corresponds to a date of 140,000 +/- 33,000 years ago… This remarkably low divergence—which is about one-third of the closest pair of present-day humans that we analysed—is in agreement with the observation that diversity among Neanderthal mtDNAs is low relative to present-day humans and indicates that the Vindija and Mezmaiskaya Neanderthals descend from a common ancestral population that experienced a drastic bottleneck since separating from the ancestors of the Denisova individual.”

In modern human origins research, the argument of greater diversity in Africa has been a cornerstone of the out-of-Africa thinking but in reality greater diversity is not an indication of population antiquity, but of long-term population size. Correspondingly, lower diversity of Amerindians has been interpreted as an indication of their recency compared to other continental groups – and this argument walks hand-in-hand with the argument for the antiquity of Africans, but, again, ancient Neandertal DNA has falsified it.