Haplotype Diversity

Haplotype Diversity

Haplotype Diversity and Structure of Y Chromosome STR and SNPs of East Africans: further evidence to the antiquity of its populations

Abstract

East Africa has been in the spotlight of palaeoanthropological investigation for its role as a potential cradle of humanity and as a gateway out of Africa Since the discovery of the first hominin fossils. A Y chromosome SNP and mitochondrial genotyping on east African populations complement this notion and demonstrated the high effective population size and diversity of its populations attesting to the antiquity of the populations of the region. As Y chromosome STRs analysis has become increasingly important for forensic and human population genetics study; in this study Y-chromosome specific STRs (Y-STRs) and SNPs genotyping are used to study the recent population histories and their role in paternity testing and forensic applications in east African populations. To answer these pertinent questions a total of 562 unrelated male samples (94 from this study) from different east African populations were analysed for their 17- loci Y-STR distribution. Moreover, a Phylogenetic and population differentiation analysis of 17-loci Y-STR were carried out on the east African and global samples to see the contribution of east Africans to the global genetic landscape.

The 17 loci Y-STR loci analysis allowed a total of 451 (395 unique and 56 shared) haplotypes to be defined.  SNP defined haplogroups identified and subsequent phylogenetic and population differentiation analyses done in the studied populations once more attesting to the long existence of the east African populations and their contribution to the out-of-Africa scenario. Haplotypes differences between individuals from east Africa also conforms to the relatively larger male effective size and emphasize the necessity of including Ne measures in population and forensic studies. Joint Y-SNP and Y-STR data on more individuals and populations will help to clarify the association between the two Y-chromosome markers and their implication to forensics and better understanding of human evolutionary history in the region.

Key words: Y chromosome, Short tandem repeats, Y-STR, SNPs, East Africa

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