Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan

Abstract

The area known today as Sudan may have been the scene of pivotal human evolutionary events, both as a corridor for ancient and modern migrations, as well as the venue of crucial past cultural evolution. Several questions pertaining to the pattern of succession of the different groups in early Sudan have been raised. To shed light on these aspects, ancient DNA (aDNA) and present DNA collection were made and studied using Y-chromosome markers for aDNA, and Y-chromosome and mtDNA markers for present DNA. Bone samples from different skeletal elements of burial sites from Neolithic, Meroitic, Post-Meroitic and Christian periods in Sudan were collected from Sudan National Museum. aDNA extraction was successful in 35 out of 76 samples, PCR was performed for sex determination using Amelogenin marker. Fourteen samples were females and 19 were males. To generate Y-chromosome specific haplogroups A-M13, BM60, F-M89 and Y Alu Polymorphism (YAP) markers, which define the deep ancestral haplotypes in the phylogenetic tree of Y-chromosome were used. Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post-Meroitic and Christian periods. Haplogroup B-M60 was not observed in the sample analyzed. For extant DNA, Y-chromosome and mtDNA haplogroup variations were studied in 15 Sudanese populations representing the three linguistic families in Sudan by typing the major Y haplogroups in 445 unrelated males, and 404 unrelated individuals were sequenced for the mitochondrial hypervariable region. Y-chromosome analysis shows Sudanese populations falling into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 8.1, 34.2, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur IX mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel test reveal a strong correlation between genetic and linguistic structures (r= 0.30, p= 0.007), and a similar correlation between genetic and geographic distances (r= 0.29, p= 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. For mtDNA analysis, a total of 56 haplotypes were observed, all belonging to the major sub-Saharan African and Eurasian mitochondrial macrohapolgroups L0, L1, L2, L4, L5, L3A, M and N in frequencies of 12.1, 11.9, 22, 4.2, 6.2, 29.5, 2, and 12.2% respectively. Haplogroups L6 was not observed in the sample analyzed. The considerable frequencies of macrohaplogroup L0 in Sudan is interesting given the fact that this macrohaplogroup occurs near the root of the mitochondrial DNA tree. Afro-Asiatic speaking groups appear to have sustained high gene flow form Nilo-Saharan speaking groups. Mantel test reveal no correlations between genetic, linguistic (r = 0.12, p = 0.14), and geographic distances (r = -0.07, p = 0.67). Accordingly, through limited on number of aDNA samples, there is enough data to suggest and to tally with the historical evidence of the dominance by Nilotic elements during the early state formation in the Nile Valley, and as the states thrived there was a dominance by other elements particularly Nuba/Nubians. In Y-chromosome terms this mean in simplest terms introgression of the YAP insertion (haplogroups E and D), and Eurasian Haplogroups which are defined by F-M89 against a background of haplogroup A-M13. The data analysis of the extant Y-chromosomes suggests that the bulk of genetic diversity appears to be a consequence of recent migrations and demographic events X