The mitochondrial DNA heritage of the Baganda, Lugbara and Acholi from Uganda

Abstract

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations.