Nature 2020 01 30 Part.01

(Ann) #1

670 | Nature | Vol 577 | 30 January 2020


Article



  1. de Maret, P. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.)
    627–643 (Oxford Univ. Press, 2013).

  2. Cornelissen, E. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane,
    P.) 403–417 (Oxford Univ. Press, 2013).

  3. Vansina, J. New linguistic evidence and ‘the Bantu expansion’. J. Afr. Hist. 36 , 173–195
    (1995).

  4. Tishkoff, S. A. et al. The genetic structure and history of Africans and African Americans.
    Science 324 , 1035–1044 (2009).

  5. Berniell-Lee, G. et al. Genetic and demographic implications of the Bantu expansion:
    insights from human paternal lineages. Mol. Biol. Evol. 26 , 1581–1589 (2009).

  6. Bostoen, K. et al. Middle to late Holocene Paleoclimatic change and the early Bantu
    expansion in the rain forests of Western Central Africa. Curr. Anthropol. 56 , 354–384
    (2015).

  7. Patin, E. et al. Dispersals and genetic adaptation of Bantu-speaking populations in Africa
    and North America. Science 356 , 543–546 (2017).

  8. Bostoen, K. in Oxford Research Encyclopedia of African History (ed. Spear, T.) https://
    oxfordre.com/africanhistory/view/10.1093/acrefore/9780190277734.001.0001/acrefore-
    9780190277734-e-191 (Oxford Univ. Press, 2018).

  9. Mendez, F. L. et al. An African American paternal lineage adds an extremely ancient root
    to the human Y chromosome phylogenetic tree. Am. J. Hum. Genet. 92 , 454–459 (2013).

  10. Krahn, T., Schrack, B., Fomine, F. L. M. & Krahn, A.-M. Searching for our most distant
    (paternal) cousins in Cameroon. Institute for Genetic Genealogy 2016 Conference, San
    Diego (2016).

  11. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-
    glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370 ,
    20130624 (2015).

  12. Gonder, M. K., Mortensen, H. M., Reed, F. A., de Sousa, A. & Tishkoff, S. A. Whole-mtDNA
    genome sequence analysis of ancient African lineages. Mol. Biol. Evol. 24 , 757–768
    (2007).

  13. Batini, C. et al. Phylogeography of the human mitochondrial L1c haplogroup: genetic
    signatures of the prehistory of Central Africa. Mol. Phylogenet. Evol. 43 , 635–644 (2007).

  14. Wood, E. T. et al. Contrasting patterns of Y chromosome and mtDNA variation in Africa:
    evidence for sex-biased demographic processes. Eur. J. Hum. Genet. 13 , 867–876 (2005).

  15. Karmin, M. et al. A recent bottleneck of Y chromosome diversity coincides with a global
    change in culture. Genome Res. 25 , 459–466 (2015).

  16. Mendez, F. L., Poznik, G. D., Castellano, S. & Bustamante, C. D. The divergence of
    Neandertal and modern human Y chromosomes. Am. J. Hum. Genet. 98 , 728–734 (2016).

  17. Fan, S. et al. African evolutionary history inferred from whole genome sequence data of
    44 indigenous African populations. Genome Biol. 20 , 82 (2019).

  18. Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human
    divergence to 350,000 to 260,000 years ago. Science 358 , 652–655 (2017).

  19. Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171 , 59–71
    (2017).

  20. Gallego Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian
    admixture in Eastern Africa. Science 350 , 820–822 (2015).

  21. Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G. & Siepel, A. Bayesian inference of ancient
    human demography from individual genome sequences. Nat. Genet. 43 , 1031–1034
    (2011).

  22. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse
    populations. Nature 538 , 201–206 (2016).
    26. van de Loosdrecht, M. et al. Pleistocene North African genomes link Near Eastern and
    sub-Saharan African human populations. Science 360 , 548–552 (2018).
    27. Plagnol, V. & Wall, J. D. Possible ancestral structure in human populations. PLoS Genet. 2 ,
    e105 (2006).
    28. Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C. & Wall, J. D. Genetic evidence
    for archaic admixture in Africa. Proc. Natl Acad. Sci. USA 108 , 15123–15128 (2011).
    29. Durvasula, A. & Sankararaman, S. Recovering signals of ghost archaic admixture in the
    genomes of present-day Africans. Preprint at bioRxiv https://doi.org/10.1101/285734
    (2018).
    30. Hey, J. et al. Phylogeny estimation by integration over isolation with migration models.
    Mol. Biol. Evol. 35 , 2805–2818 (2018).
    31. Ragsdale, A. P. & Gravel, S. Models of archaic admixture and recent history from two-
    locus statistics. PLoS Genet. 15 , e1008204 (2019).
    32. Huysecom, E. et al. The emergence of pottery in Africa during the 10th millennium calBC:
    new evidence from Ounjougou (Mali). Antiquity 83 , 905–917 (2009).
    33. Gasse, F. Hydrological changes in the African tropics since the Last Glacial Maximum.
    Quat. Sci. Rev. 19 , 189–211 (2000).
    34. Triska, P. et al. Extensive admixture and selective pressure across the Sahel belt. Genome
    Biol. Evol. 7 , 3484–3495 (2015).
    35. Laval, G., Patin, E., Barreiro, L. B. & Quintana-Murci, L. Formulating a historical and
    demographic model of recent human evolution based on resequencing data from
    noncoding regions. PLoS ONE 5 , e10284 (2010).
    36. Soares, P. et al. The expansion of mtDNA haplogroup L3 within and out of Africa. Mol.
    Biol. Evol. 29 , 915–927 (2012).
    37. Behar, D. M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree
    from its root. Am. J. Hum. Genet. 90 , 675–684 (2012).
    38. Poznik, G. D. et al. Punctuated bursts in human male demography inferred from 1,244
    worldwide Y-chromosome sequences. Nat. Genet. 48 , 593–599 (2016).
    39. Pickrell, J. et al. The genetic prehistory of southern Africa. Nat. Commun. 3 , 1143 (2012).
    40. Scerri, E. in Oxford Research Encyclopedia of African History (ed. Spear, T.) https://
    oxfordre.com/africanhistory/view/10.1093/acrefore/9780190277734.001.0001/acrefore-
    9780190277734-e-137 (Oxford University Press, 2017).
    41. Hublin, J.-J. et al. New fossils from Jebel Irhoud, Morocco and the pan-African origin of
    Homo sapiens. Nature 546 , 289–292 (2017).
    42. Harvati, K. et al. The later Stone Age calvaria from Iwo Eleru, Nigeria: morphology and
    chronology. PLoS ONE 6 , e24024 (2011).
    43. Scerri, E. M., Blinkhorn, J., Niang, K., Bateman, M. D. & Groucutt, H. S. Persistence of
    Middle Stone Age technology to the Pleistocene/Holocene transition supports a
    complex hominin evolutionary scenario in West Africa. J Archaeol. Sci. Rep. 11 , 639–646
    (2017).
    44. Scerri, E. M. L. et al. Did our species evolve in subdivided populations across Africa, and
    why does it matter? Trends Ecol. Evol. 33 , 582–594 (2018).
    45. Henn, B. M., Steele, T. E. & Weaver, T. D. Clarifying distinct models of modern human
    origins in Africa. Curr. Opin. Genet. Dev. 53 , 148–156 (2018).
    Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in
    published maps and institutional affiliations.


© The Author(s), under exclusive licence to Springer Nature Limited 2020
Free download pdf