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Genomic Analysis Sheds Light on Diversity of Malagasy People of Madagascar

NEW YORK (GenomeWeb) – The Malagasy people of Madagascar have recent African and Asian heritage, according to a new study.

Though Madagascar is about 250 miles off the coast of Africa, the origins of the Malagasy people have been a point of debate, though historical, linguistic, ethnographic, and other investigations have noted both African and Asian influences on the population.

In a new study, a University of Toulouse-led team of researchers collected genetic samples from more than 2,700 people living in nearly 260 different Madagascar villages. As the researchers reported yesterday in the Proceedings of the National Academy of Sciences, they uncovered recent Bantu and Indonesian ancestry among Malagasy individuals.

The proportion of African and Asian heritage individuals had varied with where they lived on Madagascar and suggested independent colonization of the island by African and Asian groups rather than by an already admixed population, the researchers added.

"The present Malagasy population shares recent common ancestors with Bantu and Austronesian populations now living [5,000 miles] apart," Toulouse's Thierry Letellier and his colleagues wrote in their paper.

The researchers conducted grid-based sampling of 257 villages across Madagascar to collect DNA for analysis. They analyzed the full mitochondrial genomes of 2,691 people, Y chromosomes from 1,554 male individuals, and the genome-wide SNP data of 700 people.

Phylogenetic analysis of the mitochondrial DNA data the researchers generated indicated that with the exception of a Madagascar-specific lineage all the other mtDNA lineages they found on the island were also present among Africans or East Asians. They noted that the frequency of East Asian and African mtDNA lineages was roughly equal. Additionally, they reported that the Madagascar-specific lineage M23 has a recent origin, dating back some 1,200 years.

The Y chromosome data, though, indicated that Y chromosomes of African origin were more common among the Malagasy people than those of East Asian origin, a split of 70 percent to 30 percent, they reported.

The genome-wide SNP data likewise indicated that Southeast Asian and East African Bantu groups contributed to the genetic makeup of the Malagasy people. On average, the researchers reported that the Malagasy population is about 60 percent African, 36 percent East Asian, and 4 percent West Eurasian.

Though an identical-by-descent analysis, Letellier and his colleagues found that Bantu and Indonesian populations — particularly Indonesian populations from south Borneo — shared many large fragments with Malagasy people.

Still, the genomic diversity of the Malagasy people varied by geography, as Asian ancestry was higher in the central highlands of the island and African ancestry was higher in the north and along the coast. In particular, maternal African lineages were more common in northern Madagascar, while maternal Asian lineages were more common in southern and central Madagascar. At the same time, paternal Asian lineages were less frequent than paternal African lineages, and paternal African lineages were present mainly on the coast and in the north.

Additional analyses indicated that each of the Malagasy genetic groups has the same origin and all diverge from southern Borneo and Bantu populations. The researchers dated the split between the Borneo and Malagasy populations to have occurred some 2,000 years to 3,000 years ago and the split between Bantu and Malagasy people took place about 1,500 years ago.

For all Malagasy genetic groups except one, the researchers found evidence of only one admixture event rather than several and they estimated that that admixture event occurred between 500 years and 900 years ago.

Based on their findings, the researchers envisioned a scenario in which the Indonesian population arrived on Madagascar before the African population did, and that a primarily male African population likely landed at the northern end of the island before spreading south.

"The hypothesis that Austronesians were the first to settle Madagascar before an African paternal wave is supported by the earlier split of Malagasy from Indonesian source populations and explains the predominance of both Austronesian maternal lineages and the Austronesian linguistic background," Letellier and colleagues added.