Reconstructing the prehistory of the malagasy

Abstract

The origins of the Malagasy have been reasonably well documented using historical, cultural and linguistic data. Genetic studies, albeit few, have made use of different types of markers [autosomal DNA, Y chromosome DNA and mitochondrial DNA (mtDNA)], to shed light on the peopling of Madagascar. In this study mtDNA was used to trace the maternal ancestry of 981 Malagasy from different regions in Madagascar. All individuals were screened for the intergenic COII/tRNALys 9-bp deletion followed by hypervariable region DNA sequencing in conjunction with phylogenetically informative single nucleotide polymorphism (SNP) typing. The 9-bp deletion occurred at a frequency of 22.73% (223/981) of which 17.04% (38/223) was traced to an African origin, 82.96% (185/223) to Asian origins. Individuals with the Asian form of the deletion who harboured the substitution that defined the “Polynesian motif” were also screened for two additional substitutions at positions 1473(C→T) and 3423(T→A) that define the “Malagasy motif”. The Malagasy motif was found in 61.43% (137/223) of individuals with the deletion. Overall, SNP data in conjunction with hypervariable region sequence data delineated 295 unique mtDNA sequences in the sample of which 41.28% (405/981) were traced to African ancestry and 58.71% (576/981) to non-African origins. In addition to the mtDNA haploid marker system, this study has for the first time made use of a 96 SNP ancestry informative marker panel to further shed light on the autosomal contributions to the Malagasy. This study corroborates the findings from other lines of evidence like historical, linguistic and archaeological data concerning the primary/parental origins of the Malagasy. However, these findings have provided a refinement in the data showing that the female gene pool has an appreciably higher contribution from non-African sources of origin compared with African origins. This is in contrast to what is observed using Y chromosome data.