
…This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.
First, I think the sequencing of the Clovis child actually clinched the model that the Paleo-Indians are the ancestors of modern native people. Instead of one mitochondrial lineage, they had reasonable depth on the whole genome. This paper is really more interesting for the archaeological component. The question to me is why people seem to think that populations couldn’t have evolved in situ over ~10,000 years? This is a matter of priors, how common is morphological transformation, and how fast can it occur?
As it is I think the question in regards to the Paleo-Indians was more straightforward than people wanted to accept. The Ainu of Japan exhibited the same morphological differentiation from other Northeast Asians as the Paleo-Indians, to the point where many posited that they were more closely related to Europeans. Nevertheless even early blood group analysis pinpointed that their nearest relations were other Siberian groups. Morphological patterns are obviously informative. But one reason that they’re interesting is that they vary between populations, and that variation suggests a certain level of evolutionary pliability. One of the ironies of traits which we use to differentiate populations, such as skin color and facial features, is that these might actually have relatively shallow time depth within a given lineage.

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