There’s a new paper out on Amerindian genetic history in Science,mostly looking at 92 ancient mitochondrial genomes (500 to 8600 years old). Because mtDNA has a high mutation rate, it’s useful for seeing rapid changes in population size (Bayesian skyline analysis). It looks as if the Amerindian wave started about 16k years ago, first down the Pacific coast, since this was before the ice-free passage across the Rockies opened up.

There is that weird Andaman-like signature; which they say is compatible with a second migration. They also say that it might have come later, but looking at the distribution, that’s impossible. There’s no way to come in later and end up spread out at the 2% level all across the Amazon. More later.

They see clear evidence of a big population expansion after the move into the Americas – of course that makes sense.

People don’t seem to have moved around too much after the initial settlement. No big expansions like you see in the Old World.

Now for the weirdness. None of the ancient DNA samples have any descendants or close relatives today. Zip. “no ancient haplotype shares a common ancestor with a modern haplotype more recently than ~9,000 years ago. Their samples were mostly taken from large population centers along the western coast of South America: apparently those people went extinct after Columbus. The model that best fit their data was the following:

“Model C also assumes one panmictic population of constant size (2,000 females), and the same growth between 500–600 generations ago as in Model A. Following the massive increase in Ne we assumed a split into two demes (0 and 1) of equal size (50,000 females each with no migration between demes) around 360 generations ago (~9,000 years ago or the last time we observe an ancestor common to modern and ancient lineages in hg A2; black triangle in Fig. 3B), and a constant population size for both (‘geographically’) isolated demes. Ancient lineages were exclusively sampled from deme 1 by converting radiocarbon or archeological dates into number of generations. To account for an extinction of ancient lineages as a consequence of the contact with European colonizers, we modeled a drastic population decline from 50,000 to 1 female (virtually extinct) for deme 1 between 20 generations ago (~1500 AD) and to the present day (time 0). In contrast, we assumed an exponential growth for deme 0 to 100,000 females over the last 20 generations to account for the present-day mitochondrial diversity. ”

They posit two distinct kind of Indians: those that left fossil DNA, and those that left descendants. Good Indians, and bad Indians.

Now it makes sense that lowland types suffered more than people in the Andean or Mexican highlands: they faced African diseases like falciparum malaria and yellow fever as well as the huge array of Eurasian diseases. And the Spanish had their own problems with altitude in the Andean highlands.

But this is nuts! or at any rate amazing. It suggests that in large areas, Amerindians went extinct, and were later replaced by different Amerindians from other places (plus Spaniards and Portuguese), not too closely related. That’s not incredibly far from what happened in the Caribbean, maybe: we know the local Indians disappeared rapidly there (although even there, they are a significant maternal component in existing populations). And there are indications that at least some of the hunter-gatherer tribes of the Amazon might be new to the neighborhood.. And maybe densely populated areas were hit hardest by the new infectious diseases, with a few of the Amerindian equivalent of hillbillies surviving…

And maybe there is undersampling of existing populations. But it sure sounds weird.

“Our ancient samples were principally derived from large population centers along the western coast of South America, which experienced high extinction rates following European colonization. Historic accounts have reported that the population decline was more rapid and intense in the Gulf of Mexico and the Pacific coast of Peru than in other areas such as the Mesoamerican plateau or the Andean highlands (7).