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, 21 (12), 1423-8

Determination of Population Origin: A Comparison of Autosomal SNPs, Y-chromosomal and mtDNA Haplogroups Using a Malagasy Population as Example

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Determination of Population Origin: A Comparison of Autosomal SNPs, Y-chromosomal and mtDNA Haplogroups Using a Malagasy Population as Example

Micaela Poetsch et al. Eur J Hum Genet.

Abstract

Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.

Figures

Figure 1
Figure 1
mtDNA haplogroup frequencies in HL (left) and CT (right) samples.
Figure 2
Figure 2
Y-chromosomal haplogroup frequencies in male HL (left) and CT (right) samples.
Figure 3
Figure 3
Comparison of maternal and paternal heritage in male HL (left) and CT (right) samples. The order is Y-chromosomal heritage – mtDNA origin. A, Africa; S, Asia; E, Eurasia. The full colour version of this figure is available at European Journal of Human Genetics online.
Figure 4
Figure 4
Comparison of maternal and paternal heritage with population affiliation by autosomal SNP analysis in male HL (left) and CT (right) samples. The order is autosomal SNPs – Y-chromosomal heritage – mtDNA origin. A, Africa; S, Asia; E, Eurasia. The full colour version of this figure is available at European Journal of Human Genetics online.
Figure 5
Figure 5
Median-joining network of paternal lineage. The structure is based on the Y-STR haplotypes, the colouring is based on the population affiliation according to autosomal SNPs results (grey: West Africa, white: Northern Africa, black: Asian, grey with a dot: no affiliation possible). Node sizes are proportional to frequencies of individuals. The full colour version of this figure is available at European Journal of Human Genetics online.

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