Reconstructing Native American population history

Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Figure 1. Geographic, linguistic and genetic overview of 52 Native American populations

(A) Sampling locations of the populations, with colors corresponding to linguistic groups. (B) Cluster-based analysis (k=4) using ADMIXTURE shows evidence of some West Eurasian-related and sub-Saharan-African-related ancestry in many Native Americans prior to masking (top), but little afterward (bottom). Thick vertical lines denote major linguistic groupings, and thin vertical lines separate individual populations. (C) Neighbor-Joining tree based on F_ST distances relating Native American to selected non-American populations (sample sizes in parentheses). Native American and Siberian data were analyzed after masking but consistent trees were obtained on a subset of completely unadmixed samples (Figure S3). Some populations have evidence for substructure, and we represent these as two different groups (e.g. Maya1 and Maya2).

Figure 2. Distinct streams of gene flow from Asia into America

We present an Admixture Graph (AG) that gives no evidence of being a poor fit to the data and is consistent with three streams of Asian gene flow into America. Solid points indicate inferred ancestral populations; drift on each lineage is given in units proportional to 1000×F_ST; and mixture events (dotted lines) are denoted by the percentage of ancestry. The Asian lineage leading to First Americans is the most deeply diverged, while the Asian lineages leading to Eskimo-Aleut speakers and the Na-Dene speaking Chipewyan are more closely related and descend from a common Siberian ancestral population that is a sister group to the Han. The inferred ancestral populations are indicated by filled circles and the lineages descending from them are colored: First American (blue), ancestors of the Na-Dene speaking Chipewyan (green) and Eskimo-Aleut (red). The model also infers a migration of people related to Eskimo-Aleut speakers across the Bering Strait, thus bringing First American genes to Asia (the Naukan are shown, but the Chukchi show a similar pattern; Note S7). Estimated admixture proportions are shown along the dotted lines, and lineage-specific drift estimates are in units proportional to 1000×F_ST

Figure 3. A model fitting populations of entirely First American ancestry

We show an Admixture Graph (AG) depicting the relationships among 16 selected Native American populations with entirely First American ancestry along with 2 outgroups (Yoruba and Han). The Colombian Inga are modeled as a mixture of Andean and Amazonian ancestry. The Paraguayan Guarani are fit as a mixture of separate strands of ancestry from eastern South America. The Central American Cabecar are modeled as a mixture of strands of ancestry related to South Americans and to North Americans, supporting back-migration from South into Central America. The coloring of edges indicates alternative insertion points for the admixing lineages leading to the Cabecar that produce a similar fit to the data in the sense that the χ² statistic is within 3.84 of the AG shown. The red coloring shows that the South American lineage contributing to the Cabecar split off after the divergence of the Andean populations, and the blue coloring shows that the other lineage present in the Cabecar diverged before the separation of Andeans.