Abstract
The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mitochondrial DNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveals a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era.
Introduction
The Austronesian dispersal eastward across the Pacific Ocean and westward across the Indian Ocean is increasingly well documented from historical, archaeological, and genetic perspectives (Beaujard 2012a, 2012b; Duggan et al. 2014; Brucato et al. 2016, 2018; Crowther et al. 2016; Skoglund et al. 2016; Bellwood 2017; Pierron et al. 2017). On the western edge of the Austronesian expansion, the Indian Ocean trading network during the last two millennia led to an exchange of ideas, goods, and also people among Africa, the Middle East, and Asia (Beaujard 2012a, 2012b). Recent studies have reconciled historical, linguistic, and genetic data to reconstruct this interaction network, identified the Asian population that is the source of the Austronesian dispersal (the Banjar from Southeast Borneo in Indonesia), and proposed a robust hypothesis for the timing (between the eighth and thirteenth centuries) and the nature of admixture processes in the East African offshore Islands of Madagascar and the Comoros (Pierron et al. 2014; Brucato et al. 2016, 2017, 2018).
Recent results based on genome-wide data from populations around the Indian Ocean rim support the scenario of a “direct route” from Southeast Borneo to the Comoros and Madagascar, as no significant Austronesian gene flow to other Western Indian Ocean populations was detected (Brucato et al. 2018). However, the global scale of these data might have prevented the tracking of minor genetic contributions from Austronesian migrants, potentially related to geographically and chronologically different events than the main early Austronesian dispersal. In this perspective, uniparental markers such as mitochondrial DNA (mtDNA) are an especially informative tool to identify traces of genetic inheritance, as minor genetic contributions with clear geographic provenance can become insignificant in the autosomal genome after a few generations due to recombination, but can still be maintained or even spread (by drift or sex-biased admixture) for uniparental markers that do not undergo recombination. This question is particularly interesting for the key genetic marker of the westward Austronesian expansion—the mtDNA haplogroup B4a1a1b (Malagasy motif; Razafindrazaka et al. 2010), the Indian Ocean variant of the Polynesian motif (B4a1a1 haplogroup; Soodyall et al. 1995), which has been previously identified in Madagascar and is likely present in the Comoros (Msaidie et al. 2011; Mazières et al. 2018). This lineage is the only Austronesian-specific marker that is both the main Asian maternal lineage found in Madagascar and the main lineage associated with the Austronesian expansion throughout the Indian Ocean and Oceania (Razafindrazaka et al. 2010; Cox et al. 2012; Tumonggor et al. 2013; Duggan et al. 2014; Kusuma et al. 2015).
The Malagasy motif (characterized by polymorphisms C1473T and T3423A) has only been found in Madagascar (ranging from 10% to 50% in frequency) (Tofanelli et al. 2009; Razafindrazaka et al. 2010; Cox et al. 2012; Pierron et al. 2014, 2017) and to date has not been found anywhere else, including within Indonesia and in other regions influenced by the Austronesian dispersal. Its direct precursor, the Polynesian motif (characterized by the polymorphisms A14022G, T16217C, A16247G, and C16261T) is largely restricted to the east of the Wallace’s line, from eastern Indonesia to the Pacific islands, with sporadic occurrences further west (e.g., Bali and Borneo; Cox et al. 2012; Tumonggor et al. 2013; Kusuma et al. 2015).
Here, we report the first mitogenomes and associated autosomal genome-wide data of individuals from East Africa and the Arabian Peninsula who have been identified to carry the Malagasy motif. To investigate broader questions about Austronesian gene flow within the Indian Ocean, we also present an analysis of the mitogenomes of the Banjar population of Southeast Borneo, who are considered to be descendants of the ancestral population that migrated to Madagascar and Comoros, and explore how this population connects with the newly discovered Malagasy motif lineages in Somalia and Yemen.