Native American genetic ancestry in Mexico is derived from three known ancestral genetic populations (west-central, Nahua, and Mayan) and a fourth "ghost population" originating in Sonora.
Researchers were also able to characterize a Filipino ancestry component derived from the historically attested 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico which has not previously been identified as a contributor to Mexican ancestry. The body text notes that:
In order to pinpoint the origin of the Asian component in Mexico, a MAAS-MDS was performed with a reference panel of East Asian, Southeast Asian and Oceanian populations. Cosmopolitan Mexicans having more than 5% combined East Asian and Melanesian ancestry were included, resulting in one individual from Sonora, one from Oaxaca, one from Yucatan and twelve from Guerrero.
Sonora and Yucatan grouped near Chinese reference populations; Oaxaca clustered broadly with maritime Southeast Asia; while Guerrero showed a heterogeneous profile. No cosmopolitan Mexican sample showed Melanesian variation; therefore, the MAAS-MDS plot was zoomed into, excluding populations with Melanesian contributions, for visibility. Most individuals from Guerrero clustered with maritime Southeast Asia, except for one individual positioned near southern China. Individuals from Guerrero resemble western Indonesian and non-Negrito Filipino populations, specifically those from Sumatra, Mindanao, Visayas and Luzon. Admixture dating of these Asian haplotypes in Guerrero using Tracts fit a single pulse admixture model at 13 generations ago, or in 1620 CE using 30 years per generation. . . .
This coincides with the Manila Galleon slave trade during the colony, which had a period of activity from 1565 to 1679 CE. This slave trade route originated after the need for additional labor arose due to the demographic collapse of the native populations, and ended when these Asian slaves, mostly residing in Spanish colonial Asia, were actively declared indigenous vassals of the crown and thus free. At that time the Atlantic slave trade from Africa became predominant over the Pacific route. This Southeast Asian component from the Manila Galleon trade could have extended to neighboring coastal Pacific areas of southern Mexico, as could be the case of the individual from Oaxaca.
Moreover, although historical records report the residence of “Chinos” predominantly in Guerrero, smaller numbers are also recorded in places such as Colima, Guadalajara, Zacatecas, San Luis Potosi, Veracruz, Puebla, Toluca and, in particular, Mexico City. Thus, we do not rule out the presence of this component in the other populations from the study due to insufficient sampling or statistical power, as well as locations not considered in this study.On the other hand, East Asian ancestry in Sonora and Yucatan, both distant locations from Guerrero, could possibly represent post-colonial migration events, such as Chinese immigration, mainly from the Guangdong Province, into northern Mexico and the immigration of Korean henequen workers into the Yucatan Peninsula, both occurring during and after the Porfiriato Period (between 1880 and 1910 CE). However, more extensive sampling across the country is needed to shed light on these genetic signals in order to associate them with these post-colonial historical events.
The discussion section of the paper is unusually multidisciplinary and thoughtful. Reads the whole thing.
The paper and its abstract are as follows:
Mexico has considerable population substructure due to pre-Columbian diversity and subsequent variation in admixture levels from trans-oceanic migrations, primarily from Europe and Africa, but also, to a lesser extent, from Asia. Detailed analyses exploring sub-continental structure remain limited and post-Columbian demographic dynamics within Mexico have not been inferred with genomic data. We analyze the distribution of ancestry tracts to infer the timing and number of pulses of admixture in ten regions across Mexico, observing older admixture timings in the first colonial cities and more recent timings moving outward into southern and southeastern Mexico.
We characterize the specific origin of the heterogeneous Native American ancestry in Mexico: a widespread western-central Native Mesoamerican component in northern Aridoamerican states and a central-eastern Nahua contribution in Guerrero (southern Mexico) and Veracruz to its north. Yucatan shows lowland Mayan ancestry, while Sonora exhibits a unique northwestern native Mexican ancestry matching no sampled reference, each consistent with localized indigenous cultures.
Finally, in Acapulco, Guerrero a notable proportion of East Asian ancestry was observed, an understudied heritage in Mexico. We identified the source of this ancestry within Southeast Asia—specifically western Indonesian and non-Negrito Filipino—and dated its arrival to approximately thirteen generations ago (1620 CE). This points to a genetic legacy from the 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico. Although this piece of the colonial Spanish trade route from China to Europe appears in historical records, it has been largely ignored as a source of genetic ancestry in Mexico, neglected due to slavery, assimilation as “Indios” and incomplete historical records.
Juan Esteban Rodríguez-Rodríguez, "Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon" bioRxiv (October 16, 2021) (open access).