Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

Abstract

BackgroundThe ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa.ResultsSeven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.ConclusionsThe use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.

Complex Patterns of Genomic Admixture within Southern Africa

“…Encounters with the Khoesan led not only to the incorporation of ‘click’ sounds in the isiXhosa non-Khoesan language [64], but also genetic contributions. Previous studies have reported mtDNA [14] and Y-chromosome [15] Khoesan contributing haplogroups within Southern Bantu speakers (specifically the amaXhosa, amaZulu, Basotho and Batswana). All study subjects (n = 15) self-identified via their maternal and paternal ethnic classification and all identified with ancestral roots within the Eastern Cape region of South Africa.…”

“…The 103 individuals in this study represent five southern African populations defined as Khoesan, specifically Ju/'hoan and !Xun, Southern Bantu, specifically amaXhosa, and European-initiated admixed populations, specifically Coloured and the newly described Baster population (Figure 1). At the time of submission there had been limited largely gender-specific analyses performed for pooled subsets of Southern Bantu [14], [15], while gender-specific [14], [16] and more extensive analysis for the Coloured had focused on non-regional sub-structure [17], [18]. While we previously considered the extent of whole exome diversity between two Ju/'hoan and a single !Xun, providing limited genome-wide analysis using the smaller 500 K Illumina arrays [5], no study had determined possible admixture contributions to these foraging-based populations.…”

Extensive Population Structure in San, Khoe, and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes

“…In both Y-chromosome and mitochondrial DNA studies, these hunter-gatherer populations tend to carry unique and older lineages than the lineages associated with the Bantu-speaking people. Some of the most divergent haplogroups known among modern humans, for mitochondrial DNA and the Ychromosome, are found commonly and at their highest frequencies in the Khoe-San people (Behar et al, 2008, Chen et al, 2000, Karafet et al, 2008, Knight et al, 2003, Naidoo et al, 2010, Schlebusch et al, 2009, Scozzari et al, 1999, Tishkoff et al, 2007, Underhill et al, 2001, Batini et al, 2011, Schlebusch et al, 2011. Additionally, in autosomal studies, San people group in a distinct cluster from that of Bantuspeakers (Cavalli-Sforza et al, 1994, Tishkoff et al, 2009, Li et al, 2008, Schlebusch et al, 2012, Pickrell et al, 2012.…”

Pharmacogenomic Research in South Africa: Lessons Learned and Future Opportunities in the Rainbow Nation

“…Although the Bantu and Khoisan are discernable from one another, over time, admixture has occurred between these two groups [25, 30, 31], which is reflected in the clicks present in some of the Bantu languages spoken in South Africa (see Table 1 for the official South African languages). Almost a quarter (23.8%) of the population indicated isiZulu as their home language in the 2001 Census [32].…”