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Native American Ancestry in Modern US Population Helps Researchers Trace Early Migration Patterns

NEW YORK – Researchers at the Georgia Institute of Technology and the PanAmerican Bioinformatics Institute in Colombia have analyzed the admixture of Native Americans and the descendants of African, Western European, and Spanish migrants and settlers in the US, finding that the distinct Native American ancestry profiles in these three groups are indicative of their historical migration patterns.

In a paper published in PLOS Genetics, the researchers noted that Native American ancestry in the modern African descendant population didn't coincide with local geography. Instead, it formed a single group with origins in the southeastern US that was consistent with the Great Migration of the early 20th century.

The team also found what it called an "anomalous pattern" of Native American ancestry from the southwestern US, most likely corresponding to the Nuevomexicano descendants of early Spanish settlers to the region.

"As European and African descendants settled the continental US, they inevitably came into contact with established Native American populations resulting in admixture and the introduction of Native American genomic sequence into the expanding US population," the authors wrote. "A significant reservoir of Native American ancestry currently exists outside of recognized indigenous communities."

The researchers were aiming to characterize the major genetic ancestry groups for the continental US based on observable patterns of ancestry and admixture in the 15,620 individuals from the Health and Retirement Study (HRS), a project sponsored by the National Institute on Aging and conducted by the University of Michigan.

In analyzing the continental ancestry fractions in members of the three genetic groups the researchers studied, they found that the majority of Spanish descendant individuals showed substantially higher Native American ancestry compared to Western European descendants — median Native American ancestry for the Spanish descendant group was 38 percent, compared to 0.1 percent for the Western European descendant group. Further, individuals from the African descendant group show medians of 85 percent African ancestry, 14 percent European ancestry, and 1 percent Native American ancestry. In contrast, Western European descendants showed extremely low levels of admixture with non-European populations, with a median value of 99.8 percent European ancestry.

The team also analyzed sex-biased admixture among the three US genetic ancestry groups and found a relative excess of X chromosome ancestry, which indicated female-biased admixture. Spanish descendants showed the strongest pattern of sex-biased admixture, with female-biased Native American admixture and male-biased European admixture.

An analysis of the patterns of Native American allele frequencies across the continental US for individuals from the three ancestry groups showed ancestry patterns in the African descendant and Western European descendant groups that were intermediate to the Canadian and Northern Mexican Native American reference populations. The Spanish descendant group showed Native American ancestry patterns that were similar to the Mexican reference population, Mexican Native American populations, or the admixed Puerto Rican population, the researchers said.

Importantly, admixture analysis of the Spanish descendant group in the mountain region also pointed to two distinct subpopulations: one of Mexican descent and the other with a completely distinct pattern that was basal to the Mexican clade and intermediate between the Western US and Mexican clades.

"The results of the [analyses] are consistent with historical records indicating the presence of a unique group of Spanish descendants in the American Southwest, known as the 'Hispanos of New Mexico' or Nuevomexicanos," the authors wrote. "Members of the Nuevomexicano population have maintained a distinct cultural identity for centuries, and the ability to isolate individuals from this group based on analysis of their genotypes allowed us to address open questions related to their ancestry."

The researchers also compared the levels of Native American admixture between Nuevomexicanos and the other nearby Spanish descendant groups and found a Mexican pattern of Native American ancestry. The analysis also showed that Nuevomexicanos have significantly more European ancestry and less Native American ancestry than other Spanish descendant groups from the Western Census regions, and that they have significantly lower levels of African ancestry compared to the other Spanish descendant groups.

"Each of these different groups of people experienced distinct historical trajectories in the US, which we found to be manifested as group-specific patterns of Native American ancestry," the researchers wrote.

These results, they added, pointed to a scenario where African descendants admixed with local Native American groups in the antebellum South, followed by subsequent dispersal across the US during the Great Migration in the early- to mid-twentieth century. Further, individuals from the Western European descendant group showed more variant levels of Native American ancestry, along with substantially more region-specific patterns of Native American ancestry, pointing to a historical pattern of continuous, though infrequent, admixture between local Native American groups and European settlers as they moved westward across the US. And the more variable levels of Native American ancestry in the Spanish descendant group pointed to highly regional-specific patterns of Native American ancestry, consistent with known demographic trends.

"Much of the genetic legacy of the original inhabitants of the area that is now the continental US can be found in the genomes of the descendants of European and African immigrants to the region," the authors concluded. "Analysis of the Native American ancestry component for members of these groups allowed for the delineation of region-specific subpopulations, such as the Nuevomexicanos from the American southwest."