Molecular Genetic Variation in the Malagasy

Abstract

ABSTRACT The island of Madagascar has been separated from Africa for almost 70 million years and was the last of the major land masses to be colonised by humans. Several theories concerning Malagasy origins have been proposed, but the prehistory of the Malagasy is still unresolved. Historical, archaeological, linguistic and genetic data suggest two major contributors to the Malagasy, namely African and Indonesian populations, with additional contributions from Arab, Indian, Chinese and various other Asian sources. All the islanders speak a common language called Malagasy, and although there are dialectical differences, these are not sufficient to elucidate the geographic origins of the proto- Malagasy. Some studies have reported that differences in physical appearance and culture between populations occupying different regions of the island may suggest different ancestral histories. In this study, we made use of information from three different genetic systems, namely mitochondrial DNA (mtDNA), the Y chromosome and several autosomal DNA markers to trace the origins of the males and females who contributed to the gene pool of the present-day Malagasy. We found that the mtDNA 9-bp deletion was present, throughout the island, at a total frequency of 22.5%. The 1.1 kb mtDNA control region was sequenced from 228 Malagasy individuals from which one hundred and twenty four unique mtDNA types, defined by 151 nucleotide changes were derived. Studies have shown that when the 9-bp deletion is used in conjunction with mtDNA control region sequence variation, the 9-bp deletion is a useful marker to trace population affinities. We were able to demonstrate that an overall Asian to African contribution of approximately 2:1 is indicated in present-day Malagasy populations. We used the Y Ala polymorphism (YAP) in conjunction with M9 to distinguish between African and non-African Y chromosomes. Overall, an African contribution of 78.2% and a non-African contribution of 21.85% was calculated. To gain insight into the autosomal DNA found in the Malagasy, we made use of three loci with population specific alleles (Sbl9.3, AT3id and APO-4) and the human mannose binding protein. Again, we observed both African and Asian affinities in the various Malagasy ethnic groups. By jointly analysing all the marker systems that were used, we were able to demonstrate a close relationship between ethnic groups from the different geographic regions on the island, and found the Malagasy to be a relatively homogeneous population. To test the ethnic and geographical structure present on the island, we conducted an analysis of molecular variance (AMOVA). These tests showed little biological support in favour of such hierarchies. A correlation analysis showed that very weak correlations exist between the data generated by the different genetic systems. Furthermore, by vividly demonstrating the differential input from males and females to the present-day Malagasy, this study also illustrates the advantages of combining mtDNA data with Y chromosomal results from the same individuals.