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

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dc.contributor.authorChan, Eva K Fen_ZA
dc.contributor.authorHardie, Rae-Anneen_ZA
dc.contributor.authorPetersen, Desiree Cen_ZA
dc.contributor.authorBeeson, Karenen_ZA
dc.contributor.authorBornman, Riana M Sen_ZA
dc.contributor.authorSmith, Andrew Ben_ZA
dc.contributor.authorHayes, Vanessa Men_ZA
dc.date.accessioned2015-11-18T07:07:51Z
dc.date.available2015-11-18T07:07:51Z
dc.date.issued2015en_ZA
dc.description.abstractThe 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.en_ZA
dc.identifier.apacitationChan, E. K. F., Hardie, R., Petersen, D. C., Beeson, K., Bornman, R. M. S., Smith, A. B., & Hayes, V. M. (2015). Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. <i>PLoS One</i>, http://hdl.handle.net/11427/15129en_ZA
dc.identifier.chicagocitationChan, Eva K F, Rae-Anne Hardie, Desiree C Petersen, Karen Beeson, Riana M S Bornman, Andrew B Smith, and Vanessa M Hayes "Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa." <i>PLoS One</i> (2015) http://hdl.handle.net/11427/15129en_ZA
dc.identifier.citationChan, E. K., Hardie, R. A., Petersen, D. C., Beeson, K., Bornman, R. M., Smith, A. B., & Hayes, V. M. (2015). Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. PloS one, 10(3). doi:10.1371/journal.pone.0121223en_ZA
dc.identifier.ris TY - Journal Article AU - Chan, Eva K F AU - Hardie, Rae-Anne AU - Petersen, Desiree C AU - Beeson, Karen AU - Bornman, Riana M S AU - Smith, Andrew B AU - Hayes, Vanessa M AB - 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. DA - 2015 DB - OpenUCT DO - 10.1371/journal.pone.0121223 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2015 T1 - Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa TI - Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa UR - http://hdl.handle.net/11427/15129 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/15129
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0121223
dc.identifier.vancouvercitationChan EKF, Hardie R, Petersen DC, Beeson K, Bornman RMS, Smith AB, et al. Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. PLoS One. 2015; http://hdl.handle.net/11427/15129.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentDepartment of Archaeologyen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2015 Chan et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherHaplogroupsen_ZA
dc.subject.otherMitochondrial DNAen_ZA
dc.subject.otherPhylogeneticsen_ZA
dc.subject.otherMitochondriaen_ZA
dc.subject.otherAfricaen_ZA
dc.subject.otherNamibiaen_ZA
dc.subject.otherPhylogenetic analysisen_ZA
dc.subject.otherLanguageen_ZA
dc.titleRevised timeline and distribution of the earliest diverged human maternal lineages in southern Africaen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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