View Full Version : Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

10-19-2021, 12:11 AM
Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

Juan Esteban Rodriguez-Rodriguez, Alexander G Ioannidis, Erika Landa-Chavarria, Javier Blanco-Portillo, Consuelo D. Quinto-Cortes, Rosenda I Penaloza-Espinosa, Karla Sandoval, Andres Moreno-Estrada

doi: https://doi.org/10.1101/2021.10.09.463780
(This article is a preprint and has not been certified by peer review)



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.

Screenshots from preprint:


Figure 1. Admixture timings across cosmopolitan populations by Mexican state.
A ) The density map shows the inferred date of the first admixture event predicted by Tracts for each sampling location. Intermediate space between data points is filled with interpolated values in MapViewer according to the observed adjacent estimates. Values indicate how many generations in the past the admixture event between Native Americans and Europeans resulted in the initial admixed population. Crosses represent the sampling locations within the state, namely Hermosillo (Sonora), Ciudad Victoria (Tamaulipas), Zacatecas City (Zacatecas), Guanajuato City (Guanajuato), Acapulco (Guerrero), Xalapa (Veracruz), Oaxaca City (Oaxaca), Campeche City (Campeche) and Merida (Yucatan). The Baja California Peninsula has been excluded as no sampling location were present on the peninsula. Caution should be used to draw conclusions from areas with no data, as well as intermediate locations between sampling points.
B ) The bar plot shows the demographic model that best fits the data per state, including the inferred timing of migration pulses (indicated by number of generations in the past) and the type of each model. Older timings are shown on the left while recent events are on the right side. The solid section of the bars represents the initial admixture event between Native Americans and Europeans, while theremainder of the bars with patterned lines represent the occurrence of further incoming migration pulses into the already admixed population. In most cases these represent a dual pulse of Native American and European ancestry into an already admixed population. Only Durango and Yucatan show a second pulse of solely European ancestry. Oaxaca and Campeche did not exhibit second pulses after the initial admixture event.


Figure 2. Native American substructure in cosmopolitan Mexican states.
A ) Native American individuals are shown with empty figures, and cosmopolitan Mexican populations are shown as an average per state with filled shapes. Both Native Americans and cosmopolitan Mexicans have their non-native ancestries masked. Individuals with <10% of Native American ancestry were not included.
B ) Populations exhibiting western, central, eastern and southern native affinities were included in the inset figure as shown with the rectangle. MDS 1 corresponds to the x-axis in the density kernel plot. Native American populations were grouped into geographic and genetic categories and plotted as densities, while cosmopolitan Mexican averages were plotted as single points on the x-axis according to their MDS 1 projection.


Figure 3. East and Southeast Asian substructure in cosmopolitan Mexican individuals.
A ) Map shows the sampling locations from East and Southeast Asian populations included in the Asian MDS. Sampling locations shown in the map as circles represent isolated populations with contrasting genetic profiles. Cosmopolitan Mexican populations with individuals exhibiting >5% Asian ancestry are shown in the map with black points, most individuals were sampled in Guerrero. The Manila Galleon passage from the Philippines to Acapulco, Guerrero is shown approximately on the map with a black dashed arrow. Blue arrows show ocean currents exploited for this eastward trip. The Pacific Ocean extent is not shown to scale.
B ) An MDS shows the East and Southeast Asian reference individuals with filled circles, while cosmopolitan Mexican individuals are plotted with rectangular labels. The color code in the reference panel coincides with the sampling location on the map, while cosmopolitan Mexican label colors approximately match the native population with which they have the most affinity.