Tracing pastoralist migrations to southern Africa with lactase persistence alleles.
Although southern African Khoisan populations are often assumed to have remained largely isolated during prehistory, there is growing evidence for a migration of pastoralists from eastern Africa some 2,000 years ago, prior to the arrival of Bantu-speaking populations in southern Africa. Eastern Africa harbors distinctive lactase persistence (LP) alleles, and therefore LP alleles in southern African populations may be derived from this eastern African pastoralist migration. We sequenced the lactase enhancer region in 457 individuals from 18 Khoisan and seven Bantu-speaking groups from Botswana, Namibia, and Zambia and additionally genotyped four short tandem repeat (STR) loci that flank the lactase enhancer region. We found nine single-nucleotide polymorphisms, of which the most frequent is -14010(∗)C, which was previously found to be associated with LP in Kenya and Tanzania and to exhibit a strong signal of positive selection. This allele occurs in significantly higher frequency in pastoralist groups and in Khoe-speaking groups in our study, supporting the hypothesis of a migration of eastern African pastoralists that was primarily associated with Khoe speakers. Moreover, we find a signal of ongoing positive selection in all three pastoralist groups in our study, as well as (surprisingly) in two foraging groups.
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
Enrico
E
Macholdt
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
Vera
V
Lede
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
Chiara
C
Barbieri
Department of Biological Sciences, University of Botswana, Gaborone, Botswana.
Sununguko W
SW
Mpoloka
Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Hua
H
Chen
Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Montgomery
M
Slatkin
Laboratoire Dynamique du Langage, UMR5596, CNRS and Université Lyon Lumière 2, 69007 Lyon, France. Electronic address: brigitte.pakendorf@cnrs.fr.
Brigitte
B
Pakendorf
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. Electronic address: stoneking@eva.mpg.de.
Mark
M
Stoneking
D000353:Africa, Southern; D044383:Black People / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics*; D005787:Gene Frequency; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D049690:History, Ancient; D063426:Human Migration / Q000266:history*; D006801:Humans; D043322:Lactase / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic
D043322:Lactase