Aridoamerica and Mesoamerica are two distinct cultural areas that hosted numerous pre-Hispanic civilizations between 2,500 BCE and 1,521 CE. The division between these regions shifted southward due to severe droughts ca. 1,100 years ago, allegedly driving demographic changes and population replacement in some sites in central Mexico.
Here, we present shotgun genome-wide data from 12 individuals and 26 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica.
We find population continuity spanning the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the last 2,300 years.
Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from an ancient unsampled ′ghost′ population.
Ghost population contribution to pre-Hispanic MexicoEarlier reports have demonstrated the detection of ancestry from an unsampled group, designated UpopA, among the present-day Mixe from Mexico and Lagoa Santa from Brazil populations.We tested the presence of UpopA in the pre-Hispanic individuals, using an admixture graph model with the same topological framework but some modifications. We used Mbuti as an outgroup, Ami as the East Asian, MA1 as the ancient north Eurasian, USR1 as the ancient Beringian, Anzick-1 and Spirit Cave as the NNA, and Athabascan as the SNA.Interestingly, the Mummy F9_ST_a from the north and the individuals from CdV from central Mexico have ancestry from a ‘ghost’ population, at 28% and 17%, respectively (|Z-score|: 2.142 434 and 1.655, respectively), consistent with the “ghost” UpopA ancestry reported in Mixe.We repeated this test with the Mixe population to verify the contribution of the ghost population in our tested admixture graph structures, and found Mixe to have an ancestry coming from an unsampled UpopA population at 13% (|Z-score|: 2.34), which is similar to previous estimates of 11%. Models including individuals from other archaeological sites had |Z-score| values over 3 and branches with inner zeros, thus we rejected them. . . .
Furthermore, the qpGraph admixture models explored for the pre-Hispanic populations showed F9_ST_a and the ancient individuals from CdV have ancestry from an unsampled population that we hypothesize is the ghost population previously found named UpopA.
The contribution from UpopA was identified in present-day Mixe from Mexico and Lagoa Santa, Brazil, through qpGraph models and estimated to have diverged ~24,700 years ago from Native Americans.
Also, a more recent study through D statistics analysis has suggested that UpopA contributed to present day populations from north Mexico as Akimel O’odham, Guarijo, Rarámuri, Cora, Mexicanero, and Tepehuano, as well as in present-day populations from central and south Mexico as Mixe, Totonac, Nahuas from Puebla, Otomi from Hidalgo, Chocholteco and, Mocho.
Our study is the first to identify this UpopA ancestry in admixture models involving pre-Hispanic individuals from Mexico. Further aDNA studies from the Americas could help better characterize the source of this UpopA ghost population contributing to many present-day Indigenous populations from Mexico.
If true, the existence of such a ghost population would call for a dramatic paradigm change regarding the founding of the Americas and might also shed insight into the Paleo-Asian ancestry seen in South America although the UpopA ghost population is not described in this paper as having a Paleo-Asian character and this may be entirely separate population for the source of the Paleo-Asian DNA.
Even though we identified previously unreported variants in the ancient mitogenomes, the spatial distribution of the haplogroups found, namely A, B, C and D, closely resembles that of present-day Mexico.
The information on the paternal lineage was limited, since, despite confirming the presence of the Native American chromosomal haplogroup Q in the pre-Hispanic males, there was no clear differential spatial distribution of the two identified sub-haplogroups, Q1a2a1-L54 and Q1a2a1a1a1-M3, in both Aridoamerica and Mesoamerica. Few studies have recovered information of ancient Y chromosome haplogroups across the Americas and, given the sex-biased admixture events after European colonization, the frequency of haplogroup Q in the present-day population is low.
The Supplemental Materials note that:
In the Sierra Tarahumara, we found two sub-linages of the mitochondrial haplogroup C (C 100%), as previously reported. In contrast, Central Mexico shows a higher diversity of mitochondrial haplogroups. Cañada de la Virgen was the site with the highest number of sub-haplogroups, 5 distributed in B 50%, A 25%, C 12%, and D 12%. Michoacán presented four different subhaplogroups (A 40%, D 40%, and C 20%). Sierra Gorda also presented four different subhaplogroups but corresponding to major lineages A 50%, B 43%, and D 7%, respectively.