The Analysis of Variation of mtDNA Hypervariable Region 1 Suggests That Eastern and Western Pygmies Diverged before the Bantu Expansion

Abstract

The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the "recent divergence" hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2-3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a "pre-Bantu divergence" hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region 1 of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre-Bantu divergence but failed to support the recent divergence hypothesis.

Addressing the wild yam question: how Baka hunter-gatherers acted and lived during two controlled foraging trips in the tropical rainforest of southeastern Cameroon

“…Furthermore resequencing 24 independent noncoding regions across the genome, Patin et al (2009) inferred the separation time between pygmy huntergatherers and African farmers to be 60000 years BP and the separation between the western and the eastern groups of pygmy as 20000 years BP. As for the latter, elsewhere, the separation time has been estimated at 18000 years BP based on mt-DNA analysis (Destro-Bisol et al, 2004). This genetic information indicates that the divergence between pygmy groups and other African groups was 70000-60000 years BP and the divergence of two Pygmy groups 20000-18000 years BP.…”

Working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history

“…The analysis also shows that the Mbuti pygmies cluster with the SAK at higher K values (K = 7), which could be due to either common ancestry or more recent gene flow. In addition, recent work on mtDNA, NRY, and autosomal data estimated the TMRCA of the pygmy and agricultural populations to be approximately 70-60 kya and the TMRCA of western and eastern pygmies to be approximately 20 kya (73,102,103). The findings of Tishkoff et al (1) raise the possibility that the pygmy populations, who have lost their indigenous language, once spoke some form of proto-Khoesan with click consonants.…”

Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers

“…However, peopling processes and migration dynamics remain poorly resolved in Africa, especially in CA. Patterns of mtDNA variation in AGR and PHG populations have been investigated in studies focusing on the control region [usually the hypervariable segment I (HVS-I)] and a few coding sites (14,(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35). A number of mtDNA haplogroups (Hgs) have been identified as possible genetic footprints of Bantu expansions.…”

“…These Hgs include L0a (21,24,29), L1c (23,32), L2a (29,30), L3b (26), and L3e (27,28). Studies of small numbers of eastern Mbuti PHG, in which only HVS-I was investigated (14), have suggested that the mtDNA gene pool of eastern Pygmies differs substantially from that of western PHG, who display genetic similarities to neighboring farming populations (30,33,34). However, the actual origins of the PHG and AGR populations and their interactions in space and time remain unclear because of the small samples sizes and limited number of directly sampled populations from CA and the low molecular resolution achieved with HVS-I and a few RFLP markers only.…”