title: Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa.
abstract: 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.
authors: Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia.
authors: Eva K F
authors: EK
authors: Chan
authors: Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia.
authors: Rae-Anne
authors: RA
authors: Hardie
authors: Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia; J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America.
authors: Desiree C
authors: DC
authors: Petersen
authors: J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America.
authors: Karen
authors: K
authors: Beeson
authors: School of Health Systems and Public Health, University of Pretoria, Hatfield, South Africa.
authors: Riana M S
authors: RM
authors: Bornman
authors: Department of Archaeology, University of Cape Town, Rondebosch, South Africa.
authors: Andrew B
authors: AB
authors: Smith
authors: Laboratory for Human Comparative and Prostate Cancer Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales Australia, Randwick, NSW, Australia; J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California, 92037, United States of America; School of Health Systems and Public Health, University of Pretoria, Hatfield, South Africa; Central Clinical School, The University of Sydney, Camperdown, NSW, Australia.
authors: Vanessa M
authors: VM
authors: Hayes
mesh_terms: D000353:Africa, Southern; D005075:Biological Evolution; D044383:Black People / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D005828:Genetics, Population; D054629:Genome, Mitochondrial; D006239:Haplotypes; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial