Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa

• Published in: PloS one Vol. 10; no. 3; p. e0121223
• Main Authors: Chan, Eva K F, Hardie, Rae-Anne, Petersen, Desiree C, Beeson, Karen, Bornman, Riana M S, Smith, Andrew B, Hayes, Vanessa M
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.03.2015; Public Library of Science (PLoS)
• Subjects: Africa, Southern; African Continental Ancestry Group - genetics; Archaeology; Biological Evolution; Coalescence; Coalescing; Demography; Divergence; DNA, Mitochondrial - genetics; Evolution; Female; Genetics, Population; Genome, Mitochondrial; Genomes; Genomics; Haplotypes; Humans; Hunter-gatherers; Laboratories; Last Glacial Maximum; Medical research; Medicine; Migration; Mitochondria; Mitochondrial DNA; Molecular Sequence Data; Phylogenetics; Phylogeny; Populations; Prostate cancer; Public health; Venter, J Craig; Africa, Southern; La Jolla California; Austria; United States > US; Southern Africa; Namibia; Africa; Zimbabwe; South Africa; California; Australia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0121223

The oldest extant human maternal lineages include mitochondrial haplogroups L0d and L0k found in the southern African click-speaking forager peoples broadly classified as Khoesan. Profiling these early mitochondrial lineages allows for better understanding of modern human evolution. In this study, we profile 77 new early-diverged complete mitochondrial genomes and sub-classify another 105 L0d/L0k individuals from southern Africa. We use this data to refine basal phylogenetic divergence, coalescence times and Khoesan prehistory. Our results confirm L0d as the earliest diverged lineage (∼172 kya, 95%CI: 149-199 kya), followed by L0k (∼159 kya, 95%CI: 136-183 kya) and a new lineage we name L0g (∼94 kya, 95%CI: 72-116 kya). We identify two new L0d1 subclades we name L0d1d and L0d1c4/L0d1e, and estimate L0d2 and L0d1 divergence at ∼93 kya (95%CI:76-112 kya). We concur the earliest emerging L0d1'2 sublineage L0d1b (∼49 kya, 95%CI:37-58 kya) is widely distributed across southern Africa. Concomitantly, we find the most recent sublineage L0d2a (∼17 kya, 95%CI:10-27 kya) to be equally common. While we agree that lineages L0d1c and L0k1a are restricted to contemporary inland Khoesan populations, our observed predominance of L0d2a and L0d1a in non-Khoesan populations suggests a once independent coastal Khoesan prehistory. The distribution of early-diverged human maternal lineages within contemporary southern Africans suggests a rich history of human existence prior to any archaeological evidence of migration into the region. For the first time, we provide a genetic-based evidence for significant modern human evolution in southern Africa at the time of the Last Glacial Maximum at between ∼21-17 kya, coinciding with the emergence of major lineages L0d1a, L0d2b, L0d2d and L0d2a.