The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Abstract

At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum. Limited gene flows from the Middle East can be seen in Swahili and Comorian populations at dates corresponding to historically documented contacts. However, the main admixture event in southern insular populations, particularly Comorian and Malagasy groups, occurred with individuals from Island Southeast Asia as early as the 8^th century, reflecting an earlier dispersal from this region. Remarkably, our results support recent archaeological and linguistic evidence-based suggestions that the Comoros archipelago was the earliest location of contact between Austronesian and African populations in the Swahili Corridor.

Keywords: Comoros; East Africa; Madagascar; admixture; migration; population genetics.

Figure 1

Genetic Diversity and Differentiation of Swahili and Comoros Populations Relative to Comparative Populations in the Low-SNP-Density Dataset (A) Principal-component analysis of the low-SNP-density dataset with EIGENSOFT. Swahili individuals are represented by squares, Comoros individuals are represented by diamonds, and all other individuals in the comparative dataset are represented by circles. (B) An EEMS gradient map is centered on populations along the East African coast (convergence of 3 × 10⁶ MCMC iterations). The color scale reveals low (blue) to high (orange) genetic barriers between populations localized on a grid of 500 demes. Each dot is proportional to the number of populations included. Red demes represent Swahili and Comoros populations; and green demes represent Middle Eastern, East African, and South African populations in the low SNP-density dataset.

Figure 2

ADMIXTURE Plot of the Low-SNP-Density Comparative Dataset for the Major Mode of K = 26, as Defined by CLUMPAK For clarity, only Near Eastern, Middle Eastern, East African, and South African populations as well as five representative populations from neighboring regions are represented (see Figure S9 for the full plot). Each colored line represents a sampled population whose genetic background can be decomposed into 26 genetic components.

Figure 3

Admixture Scenario for Populations along the Swahili Corridor as Estimated by GLOBETROTTER and ADMIXTURE Dark red arrows represent Swahili gene flow; light green arrows represent Island Southeast Asian Banjar or Malay; a yellow arrow represents Middle Eastern gene flow; and the purple arrow represents gene flow from the Horn of Africa. The pink arrow represents gene flow from central and southern Bantu speakers. Dates refer to the last detectable admixture event; dates below pie charts refer to the admixture event between the Swahili and Banjar or Malay; dates in italics represent secondary gene flow. Sex-biased gene flows are represented by male and female symbols in the tip of the arrows; note that they are not present in Malagasy Antemoro and Comorian Moheli.