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Mosaic maternal ancestry in the Great Lakes region of East Africa

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Abstract

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

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Acknowledgments

This study was supported by Fundação para a Ciência e Tecnologia (FCT) and co-financed by the European Social Fund (Human Potential Thematic Operational Programme) through grants SFRH/BPD/76207/2011 (VG) and SFRH/BPD/81986/2011 (RP). PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013) and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)—PEst-OE/BIA/UI4050/2014. AS is supported by “Ministerio de Ciencia e Innovación” (SAF2011-26983), the Plan Galego IDT (EM 2012/045) and the grant from the Sistema Universitario Gallego-Modalidad REDES (2012-PG226) from the Xunta de Galicia. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT, the Portuguese Foundation for Science and Technology. This work is funded by FEDER funds through the Operational Programme for Competitiveness Factors—COMPETE and National Funds through the FCT—Foundation for Science and Technology, under the project “PEst-C/SAU/LA0003/2013”. NORTE-07-0162-FEDER-00018—Contributos para o reforço da capacidade do IPATIMUP enquanto actor do sistema regional de inovação and NORTE-07-0162-FEDER-000067—Reforço e consolidação da capacidade infraestrutural do IPATIMUP para o sistema regional de inovação, both supported by Programa Operacional Regional do Norte (ON.2—O Novo Norte), through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN). We would like to acknowledge the contribution of Magdalen Awor, Fr. Germano Serra and Iva Gomes for collecting the Karamoja samples. We thank Eric Bridgeland for collecting the Kabale samples, Dr Narcis Kabatereine (Vector Control Division, Uganda Ministry of Health) for the Piida samples, and Abigail Enaburekhan, Sadie Anderson-Mann, Rebecca Cole and Steven Groom for preliminary work on the Kabale and Piida sequences.

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    Authors and Affiliations

    1. Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal

      Verónica Gomes, António Amorim, Rui Pereira, Maria João Prata & Leonor Gusmão

    2. Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal

      Verónica Gomes, António Amorim, Rui Pereira, Maria João Prata & Leonor Gusmão

    3. Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK

      Maria Pala, Douglas J. Clarke, Catherine Hill & Martin B. Richards

    4. Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CIBERER, Galicia, Spain

      Antonio Salas, Vanesa Álvarez-Iglesias, Alberto Gómez-Carballa, Ángel Carracedo & Paula Sánchez-Diz

    5. Faculty of Sciences, University of Porto, Porto, Portugal

      António Amorim & Maria João Prata

    6. Faculty of Biological Sciences, University of Leeds, Leeds, UK

      Maru Mormina, Marie-Anne Shaw & Martin B. Richards

    7. Department of Applied Social Studies, University of Winchester, Winchester, UK

      Maru Mormina

    8. Leeds Institute of Molecular Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK

      Marie-Anne Shaw

    9. Department of Pathology, University of Cambridge, Cambridge, UK

      David W. Dunne

    10. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

      Vânia Pereira

    11. Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal

      Teresa Rito

    12. ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal

      Teresa Rito

    13. Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal

      Pedro Soares

    14. DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil

      Leonor Gusmão

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    Corresponding author

    Correspondence to Martin B. Richards.

    Ethics declarations

    Conflict of interest

    The authors declare that they have no conflict of interest.

    Research involving human participants

    All procedures performed in studies involving human participants were approved by the University of Leeds, Faculty of Biological Sciences Ethics Committee, and that of the University of Huddersfield, School of Applied Sciences.

    Informed consent

    Informed consent was obtained from all individuals participants included in the study.

    Additional information

    Maria Pala, Antonio Salas & Pedro Soares, and Leonor Gusmão & Martin B. Richards have contributed equally to this work.

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    Cite this article

    Gomes, V., Pala, M., Salas, A. et al. Mosaic maternal ancestry in the Great Lakes region of East Africa. Hum Genet 134, 1013–1027 (2015). https://doi.org/10.1007/s00439-015-1583-0

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