An investigation of the HLA class ii polymorphism in the Malagasy
Date
1999
Authors
Turner, Angela Anne
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Abstract
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.