MALAGASY GENETIC ANCESTRY

By : Rebenjamina Francis

Melanesian Austronesian/Malayo-Polynesian Solidarity

20 June 2024

Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo

Nicolas Brucato,†,1 Pradiptajati Kusuma,†,1,2 Murray P. Cox,3 Denis Pierron,1 Gludhug A. Purnomo,2 Alexander Adelaar,4 Toomas Kivisild,5,6 Thierry Letellier,1 Herawati Sudoyo,2,7 and Franc¸ois-Xavier Ricaut*,1

1 Evolutionary Medicine Group, Laboratoire d’Anthropologie Mole´culaire et Imagerie de Synthe`se UMR 5288 CNRS, Universite´ Toulouse III, Universite´ de Toulouse, Toulouse, France

2 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia

3 Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

4 Asia Institute, University of Melbourne, Melbourne, Australia

5 Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom

6 Estonian Biocentre, Tartu, Estonia

7 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia

† These authors contributed equally to this work.

*Corresponding author: E-mail: francois-xavier.ricaut@univ-tlse3.fr. Associate editor: Connie Mulligan

Abstract

Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. 

Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favored admixture between the Malay and an autochthonous Borneo group, the Ma’anyan. Reconciling genetic, historical, and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analyzed groups in the founding of the Malagasy gene pool.

Key words: Madagascar, Austronesian, Borneo, Banjar, genome-wide

The Malagasy Asian Ancestry Derives from Southeast Borneo To identify the most probable Asian parental groups of the Malagasy, we adopted a two-stage approach: first, we identified the most likely proxy populations using a data set with wide geographical coverage but relatively low density of single nucleotide polymorphism (SNP), then followed by a higher density SNP data set that gives increased statistical power. This allows us to reconstruct the admixture processes that led to the emergence of modern Malagasy. 

The admixture profile of our data set (2,183 individuals from 61 populations genotyped for 40,272 SNPs; supplemen tary figs. S2 and S3, Supplementary Material online), based on ADMIXTURE analyses (Alexander et al. 2009), shows that the Malagasy genetic diversity is best described as a mixture of 68% African genomic components and 32% Asian components, corresponding well with the results of previous studies (Capredon et al. 2013; Pierron et al. 2014). While the African ancestry component in Malagasy appears to be broadly similar to that still present today in South African Bantu, the Asian ancestry presents a more complex pattern. This complexity is the key reason why previous studies have been unable to point firmly to a unique Asian source, making any subsequent anthropological inferences debatable (Pierron et al. 2014). 

This problem arose with a study of the Ma’anyan population of Borneo, whose language has long been identified as the closest to the Malagasy language (Dahl 1951), but who surprisingly exhibit no clear genetic connection to Malagasy (Kusuma et al. 2016). 

Instead, the higher genetic complexity of the Asian ancestry component in Malagasy likely reflects the fact that more than a single source population was involved in its formation. Affinities to the Malagasy Asian components are found at high frequency across several Island Southeast Asian groups, but notably in Malay, a dominant group of ancient seafaring traders (first millennium CE), and admixed groups from Borneo (i.e., Banjar, Ngaju, South Kalimantan Dayak, Lebbo, Murut, Dusun, and Bidayuh; supplementary fig. S2, Supplementary Material online). 

The connection between Malagasy, and the Borneo and Malay populations, is supported by f3-statistics (z-scores<2; supplementary ta ble S2, Supplementary Material online) (Patterson et al. 2012) and TreeMix analyses (35% of Malay/Borneo gene flow to Malagasy; supplementary fig. S4, Supplementary Material online) (Pickrell and Pritchard 2012). 

However, to more specifically identify the Asian ancestry of the Malagasy genome, we performed a Local Ancestry analysis with PCAdmix (Brisbin et al. 2012) using two proxy parental meta-populations comprising 100 individuals with African ancestry (randomly selected from Yoruba, South African Bantu, Kenyan Luhya, and Somali groups) and Asian ancestry (randomly selected from Chinese, Philippine Igorot, Bornean Ma’anyan, and Malay groups). Masking the haplotypes inferred to derive from Africa, we performed an ancestry-specific Principal Components Analysis (PCA) (Patterson et al. 2006) and TreeMix analysis (Pickrell and Pritchard 2012). Both show that the Asian genomic components of Malagasy cluster tightly with Southeast Borneo groups (Banjar, South Kalimantan Dayak, Ngaju, and Ma’anyan) (1,664 SNPs; fig. 1A and supplementary fig. S5, Supplementary Material online). This connection is supported by the highest f 3-statistics and the lowest FST genetic distances also being observed between Asian ancestry of the Malagasy and these same Southeast Borneo groups (f3> 0. 12; FST<0.02; fig. 1B; supplementary tables S3 and S4, Supplementary Material online). To explore this connection in more detail, we turned to the high density SNP data set (551 individuals from 24 populations genotyped for 374,189 SNPs; supplementary table S1, Supplementary Material online). This allows more statistically powerful analyses based on haplotypes. 

We confirmed the earlier result that Malagasy have the highest values of cumulative shared identity-by-descent fragments with Southeast Borneo populations (fig. 1C; supplementary fig. S6, Supplementary Material online). To expand on this, however, we inferred the population sources of the Malagasy, their relative ratios and the dates of potential admixture events with GLOBETROTTER (Hellenthal et al. 2014), defining each population in our data set as a donor/ surrogate group and the Malagasy as the recipient, using the haplotype “painting” data obtained with Chromopainter (Lawson et al. 2012). 

The best fit outcome for the Malagasy was obtained under a model of a single admixture event between two sources: the Banjar representing 37% of modern Malagasy and the South African Bantu population representing the other 63% (r 2 ¼0.99, P < 0.01; fig. 2 and supplementary table S5, Supplementary Material online). The admixture event was dated to 675 years BP (95% CI: 625–725 years BP, supplementary table S5, Supplementary Material online), which is similar to the dates of admixture estimated by ALDER (550–750 years BP) using Banjar population in combination with the South African Bantu (sup plementary table S6, Supplementary Material online) (Loh et al. 2013). 

When each Malagasy ethnic group is analyzed separately, similar parental populations, admixture proportions, and dates are obtained with the noticeable older estimated dates toward the east coast of Madagascar (supplementary table S5, Supplementary Material online). Crucially, these dates of genetic admixture, in agreement with a previous study (Pierron et al. 2014), reflect the midpoint or end of noticeable admixture between groups of Asian and African ancestry in Madagascar, rather than the start of this contact. 

Therefore, they could correspond to the end of the period of the main Austronesian presence in Madagascar that started around the first millennium CE (Dahl 1951, 1991; Dewar and Wright 1993; Adelaar 1995; Cox et al. 2012; Adelaar forthcoming). On the other hand, around 1100–700 years BP, climatic changes in the South of Genetic Ancestry of the Malagasy in Southeast Borneo . doi:10.1093/molbev/msw117 MBE 2397.

Copy and paste:

11 July 2024 : 5 Muharram 1446H: 11.37 a.m