Mexican DNA patterns reveal indigenous history and migrations

A major article in Science last week reveals the potential for modern DNA studies to reveal historic patterns of interaction and migration. It has implications for archaeology and especially for the use of ancient human DNA.

Moreno-Estrada, Andrés, et al. (2014). The Genetics of Mexico Recapitulates Native American Substructure and Affects Biomedical Traits. Science 344(6189): 1280-1285.

The authors sequenced large numbers (hundred of thousands) of SNPs (single nucleotide polymorphisms) from about 1000 individuals in Mexico, split between natives and mestizos (although I couldn't find in the article or the supplementary material how they determined who was which). In the data, you can see strong evidence for the genetic substructure of the population. That is, cultural, ethnic, and linguistic groups do have distinctive genetic signatures. For example, the Maya form a distinct group with additional internal structure. Within the Maya "clade" the Lacandon and Tojolobal form especially homogeneous subgroups that display little outside admixture. There's also a widespread "Central or Southern Mexican" clade (medium blue in Figure 2B and C) that impinges on the Maya. This clade is purest in southern Mexico (Oaxaca and environs), where it shows relatively little admixture. Maya genes also flowed into central Mexico (Figure 2B, bottom). In many cases, geography is a better predictor of genetics than language. Note, for example, how Nahua-speaking groups fall into more than one genetic group that is better defined spatially, which makes some sense when you think about actual mechanisms of gene flow. On the other hand, the data does contain genetic evidence of at least a couple of migrations. The most prominent one appears to go from the Yucatan Peninsula to what the authors call the Totonac region. If you plot the latitude and longitude of the sampling location given in the supplementary materials, it seems that it also close to the Huasteca. Whether this genetic contribution comes from the quite ancient Huastec migration or from a more recent Maya incursion, such as the Olmeca-Xicalanca conquest of Cacaxtla, is not addressed. I suspect, however, that the data could in theory be used as a molecular clock to date the migration, at least very roughly. Since the Huastec and Olmeca-Xicalanca migration are far apart in time, even a crude estimate would be sufficient to distinguish between them.

So, for archaeologists, there are a couple of significant facts. These kinds of studies can be used to understand prehistoric population dynamics. This is not news, perhaps. Genetic studies in Europe have been used for years to investigate the spread of agriculture and determine whether it was migration, diffusion, or both, and what the spatial dynamics were. It is interesting, however, to see it working in Mexico, which seems to me to be even more complex. Another important issue this study raises is the potential for ancient DNA to be matched to modern patterns. Presumably now we could take DNA from an archaeological individual and potentially match it preferentially to a "clade" defined by modern genetic distributions. That's an exciting possibility. It would provide far more information than the strontium isotope methods currently in use. Little ancient DNA has been sequenced in Mesoamerica, but now we have even more reason to do it.