Insights into the Demographic History of African Pygmies from Complete Mitochondrial Genomes

C Batini,L Van Der Veen,D M Behar,G Spedini,G Destro-Bisol,J Lopes,D Comas,L Quintana-Murci,L B Jorde,F Calafell

doi:10.1093/molbev/msq294

Abstract

Pygmy populations are among the few hunter-gatherers currently living in sub-Saharan Africa and are mainly represented by two groups, Eastern and Western, according to their current geographical distribution. They are scattered across the Central African belt and surrounded by Bantu-speaking farmers, with whom they have complex social and economic interactions. To investigate the demographic history of Pygmy groups, a population approach was applied to the analysis of 205 complete mitochondrial DNA (mtDNA) sequences from ten central African populations. No sharing of maternal lineages was observed between the two Pygmy groups, with haplogroup L1c being characteristic of the Western group but most of Eastern Pygmy lineages falling into subclades of L0a, L2a, and L5. Demographic inferences based on Bayesian coalescent simulations point to an early split among the maternal ancestors of Pygmies and those of Bantu-speaking farmers (∼ 70,000 years ago [ya]). Evidence for population growth in the ancestors of Bantu-speaking farmers has been observed, starting ∼ 65,000 ya, well before the diffusion of Bantu languages. Subsequently, the effective population size of the ancestors of Pygmies remained constant over time and ∼ 27,000 ya, coincident with the Last Glacial Maximum, Eastern and Western Pygmies diverged, with evidence of subsequent migration only among the Western group and the Bantu-speaking farmers. Western Pygmies show signs of a recent bottleneck 4,000-650 ya, coincident with the diffusion of Bantu languages, whereas Eastern Pygmies seem to have experienced a more ancient decrease in population size (20,000-4,000 ya). In conclusion, the results of this first attempt at analyzing complete mtDNA sequences at the population level in sub-Saharan Africa not only support previous findings but also offer new insights into the demographic history of Pygmy populations, shedding new light on the ancient peopling of the African continent.

Highlights

African Pygmy populations are one of the few human groups identified by their physical appearance rather than ethnographic, cultural, geographical, or linguistic criteria
The whole mitochondrial genome was sequenced in a total of 205 individuals from ten Central African populations
A total of 121 different complete mitochondrial DNA (mtDNA) sequences were obtained from 205 individuals from ten Central African populations

Summary

Introduction

African Pygmy populations are one of the few human groups identified by their physical appearance rather than ethnographic, cultural, geographical, or linguistic criteria. Their height, among the smallest recorded for human populations (Cavalli-Sforza 1986a; Hitchcock 1999), has been interpreted as the consequence of different selective pressures (reviewed in Perry and Dominy 2009) These include thermoregulatory adaptation to the environment of the tropical forest (CavalliSforza, Menozzi, Piazza 1993), reduction of the total caloric intake in a food-limited environment (Hart and Hart 1986), improved mobility in the dense forest (Diamond 1991), or advantageous earlier reproductive age in short lifespan conditions (Migliano, Vinicius, Lahr 2007). Several studies have attempted to identify remnants of an ancient Pygmy language, which might have been lost after contact with farmers (Bahuchet 1993; Demolin 1996; Letouzey 1976)

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Conclusion