60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Abstract

Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70–50 ka into Eastern or Southern Africa, (2) postglacial movements (15–10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.

Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns

“…Genetic variants in the nuclear and mitochondrial genomes have been traditionally used to trace the ancient global migration paths of different human populations [1, 2]. Such studies assumed most variants to be neutral and hence merely reflective of the age of the populations studied.…”

Mitochondrial haplogroup influences motor function in long-term HIV-1 infected individuals

“…The L3 lineage is thought to have arisen in the eastern African mitochondrial gene pool approximately 60-70 ka and subsequently diverged into multiple sub-clades including the N and M lineages, which gave rise to all non-L haplogroups outside of Africa. The L3e lineage arose in central African (Sudan region) 35-60 ka and has further diverged into a number of sub-clades L3e1'2'3'4 which have spread across sub-Saharan Africa and now constitute roughly one third of all L3 lineages [33][34][35]39].…”

Mosaic maternal ancestry in the Great Lakes region of East Africa

“…We note that although L2a dispersed from West-Central Africa with the Bantu, it is also thought to have dispersed earlier from the same region, in the early to mid-Holocene, via the "Green Sahara" into Sudan and, to a lesser extent, the Horn of Africa (Kuper and Kröpelin 2006;Silva et al 2015) (see also the PCA results, above).…”

“…Most of the Ugandan L2a variation is concentrated within a single subclade, L2a2'3'4, which dates to ~30 ka (Silva et al 2015) and is much more prevalent in Central and East 14 Africa than other L2 subclades. Intriguingly, many of the Ugandan Eastern and Western Nilotic L2a lineages within the subclade L2a2'3 either match or are closely related to Sudanese -and indeed many of the Ugandan Bantu lineages, too.…”

“…Whether this might be an indication of a Sudanese source for a fraction of Ugandan diversity merits further investigation, but a source somewhere in Eastern Africa seems likely. L2a4, dating to ~24 ka (Silva et al 2015) appears likely indigenous to East Africa itself, and L2a5, which dates to ~46 ka, is also Eastern African and includes several Ugandan Bantu and Nilotic speaking individuals, including one lineage that has also reached Southern Nilotic speakers of Tanzania. Corroborating this interpretation, most of the few sampled Central Sudanic speakers from Uganda, whose languages are assumed to predate the appearance of Nilotic and Bantu languages in the region, also fall within these L2a subclades, again suggesting an earlier expansion.…”