An investigation of the HLA class ii polymorphism in the Malagasy

Turner, Angela Anne
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Madagascar, the last large landmass to be colonized, has been described as a laboratory of evolution, but due to the partially restricted entry of Western scientists in the past, little is known about the natural history of the island. A major aim of the Human Genetics Department at the SAIMR, is to determine who the forerunners of the Malagasy were. Linguistic, cultural, physical and some genetic evidence suggests that Indonesians and Africans are likely to have been the two main population groups who contributed to the Malagasy. The present study sought to make the genetic characterization of the Malagasy more complete and to further explore their origins. This was done by typing the alleles present at two major histocompatibility complex gene loci and analysing data gathered on several serogenetic systems. Alleles present at the DQA1 locus were typed with the aid of a commercially available DQA1 typing kit and DPB1 alleles were typed by DNA sequencing and comparison to sequences reported in the literature. Three possibly novel DPB1 alleles were found in this study. DQA1 andDPBl allele frequencies, DQA1-DPB1 estimated haplotype frequencies, as well as some non-HLA serogenetic loci allele frequencies were used in various statistical calculations. Global linkage equilibrium was found between the DQA1 and DPB1 loci of Indonesians and the Tsonga; while global linkage disequilibrium was found amongst the three Malagasy groups studied (the Merina, Antemoro and Tsimihety). This is an indication of a recent admixture in the Malagasy. Admixture estimations revealed that Africans, represented here by the Tsonga, were the major contributors to the weighted average of the three Malagasy groups, followed by an Indonesian and a small Arab contribution. Principal coordinate analysis, as well as the phylogenetic trees constructed using Ds genetic distance matrices, showed the highland group, the Merina, to be closest to the Indonesians. The two lowland groups, the Antemoro and Tsimihety, were closest to the Tsonga. Arabs fell approximately midway between the Indonesians and Tsonga and were quite close to the three Malagasy groups studied. Although the Merina appeared closest to the Indonesians, the DPB 1*0501 allele which occurred at a frequency of 0.1809 in Indonesians was absent from the Merina sample and suggests that Indonesians may not be as important a contributor to the Merina as once thought. Other allele frequencies indicate the possible existence of additional “parental” groups. A substantial African contribution to the Tsimihety was evident from this study.