More On Madagascar's Genetic Origins

The biggest surprises of a new paper on the genetic origins of the people of Madagascar are the roughly 2/3rds African origin demonstrated when some previous estimates had been closer to 35%-50%, and more surprisingly, that the affinity of that African component to Southern African Bantu, when previous data had rejected that hypothesis in favor of an affinity to East African Bantu populations (less some recent Nilo-Saharan admixture).

Southern African Bantu have a substrate of pre-Bantu Mozambique people which is very distinctive from any extant African population to the extent that it basically constitutes a "lost race" of Africans that coincides with linguistic substrates of Bantu languages in that region indicating that the pre-Bantu people of Mozambique spoke a click language.  There are also uniparental markers private to Mozambique that are largely absent from Madagascar.  So, there are strong reasons to be skeptical of a Southern African as opposed to East African source for the African genetic contribution to Madagascar.

The lack of a strong historical connection between Mozambique across the strait from Madagascar and that island is likewise demonstrated by a lack of archaeological support for those kinds of trade ties and a lack of Southeast Asian genetic traces in mainland Africa (anywhere).

The conclusions on the Asian genetic origins side of the analysis, on the other hand, are plausible and very consistent with previous research on the topic, although the analysis does not identify indications from previous studies that the migration was probably along the Indian Ocean's coast with stops in South Asia and East Africa, rather than directly across the Indian Ocean as a graphic in the new paper misleadingly suggests.

I'll need to look more closely at the various papers involved to see if these new results can be reconciled with the prior research, and if not, to determine the likely source of the disparity.  The two-thirds percentage is probably right, but the South African Bantu affinity seems suspect. The fact that only the Asian conclusions and not the controversial African ones end up in the abstract of the paper is also notable.

The pertinent portion of the paper addressing this point states:

The admixture profile of our dataset (2183 individuals from 61 populations genotyped for 40,272 SNPs; Supplementary figures 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. . . . 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). . . . 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 dataset 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% (r2 =0.99, P<0.01; Figure 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 (Supplementary table S6, Supplementary Material online)(Loh, et al. 2013). When each Malagasy ethnic group is analysed separately, similar parental populations, admixture proportions and dates are obtained with the noticeable older by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from estimated dates towards 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 Africa forced Bantu populations to move to more hospitable places (Huffman 2000). This South Bantu migration has previously been suggested as an explanation for the higher density of populations observed in the South of Madagascar (Beaujard 2012a). As all of our sampled groups live in the South of Madagascar, and considering that the estimated dates of admixture are more recent on the west coast (Supplementary tables S5 and S6, Supplementary Material online), it is tempting to interpret our admixture date as marking the last significant Bantu migration to Madagascar, perhaps initiated by climatic changes in Africa.

Suffice it to say that the analysis of the African side of the genetic contribution is shallow and does not rigorously compare competing hypotheses of African contributions.

The Supplemental Materials indicate that the African samples other than South African Bantu come from International HapMap, et al. (2010) (i.e. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58. doi: 10.1038/nature09298) and Pagani, et al. (2012) (i.e. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet 91: 83-96. doi: 10.1016/j.ajhg.2012.05.015). The South African Bantu sample comes from May, et al. (2013) (Genetic diversity in black South Africans from Soweto. BMC Genomics 14: 644. doi: 10.1186/1471-2164-14-644).

Another data set of Southeastern Bantu speakers referenced in May, et al. (2013) seems to overlap with the Soweto sample and derives from Schlebusch, et al., "Genomic variation in seven Khoe-San groups reveals adaptation and complex African history." Science. 2012, 338: 374-379.

It is also possible that Soweto Bantus are very genetically distinct from Mozambique Bantus and may be more similar to ancestral East African Bantus than modern East African Bantus, because they may lack subsequent Nilo-Saharan Ancestry and may, in general have less of a substrate influence.

The abstract of the paper and its citation data are as follows:

Malagasy genetic diversity results from an exceptional proto-globalisation 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 favoured 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 analysed groups in the founding of the Malagasy gene pool.

Brucatol, et al., "Malagasy genetic ancestry comes from an historical Malay trading post in Southeast Borneo." 33 (7) Molecular Biology and Evolution (July 5, 2016).

The literature cited is as follows (and admittedly includes some other papers I haven't yet seen):

* Adelaar A. 2009a. Towards an Integrated Theory about the lndonesian Migrations to Madagascar. In. Ancient human migrations: a multidisciplinary approach.: University of Utah Press

* Adelaar KA. 1995. Borneo as a cross-roads for comparative Austronesian linguistics. In: Canberra AAEP, editor. The Austronesians: historical and comparative perspectives. p. 81–102.

* Adelaar KA. 2009b. Loanwords in Malagasy. In: Haspelmath M, Tadmor U, editors. Loanwords in the world’s languages: a comparative handbook. Berlin, Germany: De Gruyter Mouton. p. 717-746.

* Adelaar KA 1989. Malay influence on Malagasy: linguistic and culture-historical implications. Oceanic Linguistics 28: 1-46. doi: 10.2307/3622973

* Adelaar KA. forthcoming. Who were the first Malagasy, and what did they speak? In: Acri A, Landmann A, editors. Cultural Transfer in Early Monsoon Asia. Singapore: Institute of Southeast Asian Studies.

* Alexander DH, Novembre J, Lange K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19: 1655-1664. doi: 10.1101/gr.094052.109 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Beaujard P. 2012a. Les mondes de l’ocean indien. Vol. 2 : L’océan Indien, au cœur des globalisations de l'Ancien Monde (7e-15e siècles). Paris, France: Armand Collin. Beaujard P. 2012b. Les mondes de l’océan Indien. Vol. 1 : De la formation de l’État au premier système-monde afro-eurasien (4e millénaire av. J.-C.-6e siècle apr. J.-C.). Paris, France:

* Armand Collin. Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD 2012. PCAdmix: Principal componentsbased assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Human Biology 84: 343-364. doi: 10.3378/027.084.0401

* Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut F-X, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza L-P, Champion B, Dugoujon J-M 2013. Tracing arab-islamic inheritance in Madagascar: Study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 8: e80932. doi: 10.1371/journal.pone.0080932

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* Dahl OC 1991. Migration from Kalimantan to Madagascar. Oslo, Norway: Norwegian University Press : Institute for Comparative Research in Human Culture.

* Dewar RE, Wright HT 1993. The culture history of Madagascar. Journal of World Prehistory 7: 417-466. doi: 10.1007/BF00997802 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Fourquet R, Sarthou J, Roux J, Aori K 1974. Hemoglobine S et origines du peuplement de Madagascar: nouvelle hypothese sur son introduction en Afrique [Hemoglobin S and origins for the settlement of Madagascar: new hypothesis on its introduction to Africa]. Arch. Inst. Pasteur Madagascar 43: 185–220.

* Fuller DQ, Boivin N, Hoogervorst T, Allaby R 2011. Across the Indian Ocean: the prehistoric movement of plants and animals. Antiquity 85: 544-558.

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* Hewitt R, Krause A, Goldman A, Campbell G, Jenkins T 1996. beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids. Am. J. Hum. Genet. 58: 1303–1308.

* Huffman TN. 2000. Mapungubwe and the origins of the Zimbabwe culture. In: Leslie M, Maggs T, editors. African naissance: The Limpopo valley 1000 years ago. Cape Town, South Africa: South African Archaeological Society. p. 14-29.

* Hurles ME, Sykes BC, Jobling MA, Forster P 2005. The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet 76: 894-901.

* Kusuma P, Brucato N, Cox MP, Pierron D, Razafindrazaka H, Adelaar A, Sudoyo H, Letellier T, Ricaut F-X 2016. Contrasting Linguistic and Genetic Influences during the Austronesian Settlement of Madagascar. Scientific Reports 6:26066. doi: doi: 10.1038/srep26066

* Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut F-X 2015. Mitochondrial DNA and the Y by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 16: 191. doi: 10.1186/s12864-015-1394-7

* Lawler A 2014. Sailing Sinbad's seas. Science 344: 1440-1445. doi: 10.1126/science.344.6191.1440

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* Pickrell JK, Pritchard JK 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967. doi: 10.1371/journal.pgen.1002967

* Pierron D, Razafindrazaka H, Pagani L, Ricaut F-X, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa J-A, Blench RM, Letellier T, Kivisild T 2014. Genome-wide evidence of Austronesian–Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proceedings of the National Academy of Sciences 111: 936-941. doi: 10.1073/pnas.1321860111

* Ras JJ. 1968. Hikajat Banjar: a study in Malay historiography. The Hague: Martinus Nijhoff. by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Serva M, Petroni F, Volchenkov D, Wichmann Sr 2012. Malagasy dialects and the peopling of Madagascar. Journal of the Royal Society Interface 9: 54-67. doi: 10.1098/rsif.2011.0228

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* Tofanelli S, Bertoncini S, Castri L, Luiselli D, Calafell F, Donati G, Paoli G 2009. On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol 26: 2109-2124.