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

Thijessen Naidoo,Rajeshree Mahabeer,Johannes C Erasmus,Carina M Schlebusch,Himla Soodyall,Heeran Makkan,Pareen Patel

doi:10.1186/2041-2223-1-6

Thijessen Naidoo, Rajeshree Mahabeer + Show 5 more

Open Access

https://doi.org/10.1186/2041-2223-1-6

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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.

Highlights

The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology
We report on the development of single base extension (SBE) assays used to refine the resolution of Y chromosome haplogroups commonly found in Africa, having incorporated a few single nucleotide polymorphism (SNP) to delineate the common non-African Y chromosomes following a hierarchical screening process
SNP selection and screening strategy Seven multiplex SBE assays, which incorporated Y chromosome markers described in the YCC Phylogeny 2003 [10], were developed which resolved Y chromosome haplogroups

Summary

Introduction

The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. Given that human genome variation evolves over time due to several factors - among them mutation, genetic drift, migration and selection - the genome has retained some of the record of these historical and evolutionary events. A standard nomenclature established by the Y Chromosome Consortium [1] resolved the global pattern of Y chromosome variation into 18 major haplogroups that were classified using capital letters A through to R This has recently been revised by Karafet et al [2] to a Y chromosome haplogroup phylogeny that contains 311 branches delineated by approximately 600 markers (primarily bi-allelic) and includes an additional two haplogroups (S and T), increasing the major haplogroup number to 20. This, together with high levels of population differentiation, [3] have added value to the Y chromosome as a tool for reconstructing the history and migrations of humans over time

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