So, a paper published in Science yesterday describes the analysis of the skull and mitochondrial DNA of a skeleton discovered in Hoyo Negro, a water-filled cave beneath the surface of the Yucatán Peninsula.  In addition to the human skeleton (whom the scientists named “Naia” before removing her head for further study), the cave contains the remains of 26 other large mammals, including a saber-tooth tiger and some sort of a mammoth-type thing.

Check out the story over at National Geographic for some cool underwater pictures.

There are a couple of things that make this an interesting story. First of all, it’s a freaking underwater cave with a 12,000-year-old human skeleton and a saber-tooth tiger. Second, it adds an interesting piece of data to our understanding of how people first came to America. (Spoiler: the answer is not “Jesus brought them on the Ark”.)

The standard story of the colonization of the Americas goes something like this. Back during the last ice age(s), maybe 15,000 to 25,000 years ago, the sea levels were lower, and there was a land bridge connecting Siberia to Alaska. During that period, people from Northeastern Asia crossed over and spread throughout North and South America. Thousands of years later, their descendants had the misfortune of being discovered by the Europeans.

The dates of archaeological sites throughout the hemisphere generally fit with this story, as do genetic data collected from contemporary Native Americans and from skeletal remains. Native Americans, both past and present, are genetically most closely related to the peoples of Siberia, and the genetic divergence between the two groups is consistent with the populations having separated around the time when the land bridge existed.

The problem is that when you look at skull shapes (“cranio-facial morphology”), they seem to tell a different story.  Contemporary Native Americans have facial features similar to those found in Northeastern Asia. But “Paleoamericans” (dating from more than about 9,000 years ago) have features more closely resembling those found in African and Southeast Asian populations.

Those features suggest a different story, one where humans arrived in America in two waves. In this scenario, the humans who crossed the Bering land bridge would be the second wave, perhaps displacing the original, first-wave settlers. This is a story that entered the public consciousness more than fifteen years ago, following the discovery of “Kennewick Man”, who was described as possessing “caucasoid” features by James Chatters, who is also the first author on this paper. A certain strain of “thinker” took this to mean that the White people who came to America were not colonizers, but liberators, having been the continent’s original inhabitants.

The single-wave model suggests the possibility that the difference in skull morphology observed between earlier and later Paleoamericans represents evolutionary change that occurred after the migration across the land bridge. At first blush, this seems a bit questionable, since it would have the American population evolving to more closely resemble their genetic relatives in Asia, but only after having become geographically separated from those relatives.

The persistence of this controversy is due, in part, to the fact that the genetic data has generally come from different sources than the morphological data. This is where Naia comes in. Naia has the longer, more slender, Africa-esque cranium found in other early sites, but her mitochondrial DNA haplotype is a typical Native American one. This seems to support the idea that the people who left these narrow skulls all over America and the people who left their descendants all over America were the same people.

The biggest caveat, of course, is that this is a single skeleton. It is exciting and informative, since very few samples of this age have been discovered, and none of them have been of this quality. But those small numbers also mean that anything we discover about this skeleton is bound to be consistent with multiple stories, and things are unlikely to be resolved without a lot more data.

The other caveat is that the mitochondrial DNA is only one piece of the genetic history. It is possible that these really were two separate populations, and that Naia just happened to have some second-wave ancestors on her mother’s side. If we were to examine the rest of her genome, we might find some or all of it to be more similar to some other population (like the lost thirteenth tribe, who immigrated to America from Israel and/or Kobol).

Will we get the rest of Naia’s genome? I hope so, but we’ll see. It is relatively easy to collect mitochondrial DNA from archaeological samples, since there are hundreds of copies of the small, circular mitochondrial chromosome in each cell. There are only two copies per cell of the rest of the genes, which reside in the cell’s nucleus. So, it is possible that the sample was sufficiently well preserved that mitochondrial DNA could be extracted, but degraded enough that the nuclear DNA is not recoverable.

Whatever the eventual conclusion, the story will be interesting. Either the peopling of America involved a mixture of multiple populations that will be fun to unravel, or it involved some interesting, almost convergent, morphological evolution. Stay tuned!