Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy

Abstract

The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma'anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genome-wide diversity in 211 individuals from the Ma'anyan and surrounding groups in southern Borneo. Surprisingly, the Ma'anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma'anyan despite the obvious linguistic association.

Figure 1. Map showing the location of each population group studied in this work.

The map is generated using Global Mapper v.15 software (http://www.bluemarblegeo.com/products/global-mapper.php).

Figure 2. ADMIXTURE plot using the low density database with K = 14 (the optimum determined by cross-validation).

Each component is identified by a specific color and a C label which corresponds to its order of appearance from K = 2 to K = 14.

Figure 3

(a) An f3 outgroup statistics analysis showing shared genetic history with Austronesian groups (represented by indigenous Formosan) compared to Mainland Southeast Asian groups (represented by the H’tin). (b) Genetic similarity between Ma’anyan and other Asian populations measured using f3 outgroup statistics. Error bars show the standard error of the f3 statistics. Red dots represent East Asian groups; blue dots represent Island Southeast Asian groups; green dots represent Mainland Southeast Asian groups.

Figure 4. Shared Identity-By-Descent fragments between pairs of individuals in Southeast Asia, filtering for shared IBD >20 cM, 40 cM and 60 cM.

Each individual is represented as a blue dot. Each individual is represented as a blue dot. Populations are represented by a circle of dots. Shared IBD fragments are represented by a black line. The maps were generated using Global Mapper v.15 software (http://www.bluemarblegeo.com/ products/global-mapper.php). The networks lines were generated using Cytoscape v.3.2.152 software (ref. 54).

Figure 5. Ancestry-specific Principal Component Analysis based on masked SNPs from the high density dataset obtained after PCAdmix analysis.