The geographical analysis of the mitochondrial DNA control region found in southern African population's by using a bioinformatics approach

Abstract

South Africa’s demographic complexity has been historically shaped by interethnic admixture between the native KhoiSan inhabitants and the Bantu expansion that started 3000 - 5000 YBP and reached South Africa about 1000 years ago. This, followed by the arrival of the European settlers in the 16th century who brought in slaves from their Asian colonies, mainly from Malaysia and the east- and western Africa. By the late 19th- and early 20th century colonial India (South Asia) also migrated to South Africa. It has been hypothesized that the history of South African has influence ethnic group distribution in South African, to the degree that it is not homogeneous. This study further theorized that the history contributed to the gene flow at a regional level and not restricted to the ethnic distribution of genetic variation. Therefore, this study focuses on the geographical and ethnic dispersal of maternal lineages by investigating the mitochondrial DNA (mtDNA). It is predicted that the maternal lineages could be limited or appear in high frequencies in specific ethnic and/or geographical region in South Africa. This, in turn, can aid mitochondrial DNA forensic human identification applications when a specific haplotype is questioned. This study produced a complete mitochondrial DNA control region (nucleotide position 16 024-576) sequences generated with Sanger and next-generation sequencing for 246 individuals residing in the Western Cape, Northern Cape and KwaZulu-Natal provinces of South Africa. The control region is of particular interest due to the vast majority of rapidly evolving sites that are of relevance in both forensic genetics and population studies. The haplotypes were inferred against the revised Cambridge Reference Sequences and haplogroups were determined by online tool HaploGrep 2.