Patterns of admixture and population structure in native populations of Northwest North America

Abstract

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

Figure 1. Map of populations included in the combined dataset.

The Tlingit, Tsimshian, Nisga'a, Splatsin, Stswecem'c, and Haida populations, as well as the Northern Mexico Seri population indicated by a black diamond, were newly genotyped for this study. See Tables 1 and S1 for additional population information.

Figure 2. Genome-wide haplotype heterozygosities.

(A) Mean expected haplotype heterozygosity in each population, with standard deviations across the 22 autosomes. (B) The correlation between mean haplotype heterozygosity and geographic distance from Addis Ababa. Population colors and symbols follow Figure 1.

Figure 3. Population-level population structure for 71 populations.

Shown are a (A) multidimensional scaling (MDS) plot (Spearman ρ = 0.965; P<10⁻¹⁵, comparing population-pairwise Euclidean distances on the two-dimensional MDS plot to their population pairwise F _ST values), and (B) Neighbor-joining tree based on population pairwise F _ST. All the edges of the tree were supported by 100% of the 1,000 bootstrap replicates performed except for four edges corresponding respectively to the Kalash, Caucasian (CEU), Orcadian, and French populations (supported by 76%, 75%, 75%, and 74%, respectively, of the 1,000 bootstrap replicates). Population colors and symbols follow Figure 1.

Figure 4. Individual-level population structure.

(A) Multidimensional scaling plot of pairwise allele-sharing distance (ASD) among 2,140 individuals in the combined dataset. (B) Multidimensional scaling plot of pairwise ASD among 528 individuals from 63 worldwide populations, following the resampling of a maximum of 82 individuals each from 11 different population groups. Group choices for resampling were taken from Figure S6. Population colors and symbols follow Figure 1.

Figure 5. Procrustes-transformed multidimensional scaling plots of Eurasian and American individuals.

(A) 641 individuals from 53 populations after resampling of 82 individuals from each of 14 nonoverlapping groups of European, Central and South Asian, East Asian, and American populations (Figure S7). (B) 641 individuals from 41 populations after resampling of 82 individuals from each of 15 nonoverlapping groups of European, East Asian, and American populations (Figure S8). (C) 393 individuals from 22 populations after resampling of 82 individuals from each of 10 nonoverlapping groups of European and American populations (Figure S9). (D) 450 individuals from 34 populations after resampling of 82 individuals from each of 11 nonoverlapping groups of East Asian and American populations (Figure S10). Procrustes similarity statistics are t ₀ = 0.958 between Figures 4B and 5A, t ₀ = 0.999 between Figures 5A and 5B, t ₀ = 0.956 between Figures 5B and 5C, and t ₀ = 0.997 between Figures 5B and 5D. Population colors and symbols follow Figure 1.

Figure 6. Procrustes-transformed multidimensional scaling plot of Pacific Northwest individuals.

The plot is based on pairwise ASD among 82 individuals from six indigenous populations; t ₀ = 0.874 between overlapping individuals in Figures 5C and 6. Population colors and symbols follow Figure 1.

Figure 7. Worldwide Admixture structure.

Plotted are modes with clustering solutions obtained with 30 replicates at each value of K. Values of K and the number of runs in the mode shown appear on the left. In each plot, each cluster is represented by a different color, and each individual is represented by a vertical line divided into K colored segments with heights proportional to genotype memberships in the clusters. Thin black lines separate individuals from different populations. The same 528 individuals included in Figure 4B are considered in the Admixture analyses. Alternate clustering solutions for values of K from 2 to 12 appear in Figure S3.

Figure 8. Admixture structure in the Americas.

Plots are as described in Figure 7. The same 641 individuals from 41 European, East Asian, and American populations included in Figure 5B are considered in the Admixture analyses. Alternate clustering solutions for values of K from 2 to 12 appear in Figures S4.