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Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

View ORCID ProfileKendra A. Sirak, Daniel M. Fernandes, Mark Lipson, Swapan Mallick, Matthew Mah, Iñigo Olalde, Harald Ringbauer, Nadin Rohland, Carla S. Hadden, View ORCID ProfileÉadaoin Harney, Nicole Adamski, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kimberly Callan, Matthew Ferry, Ann Marie Lawson, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Nick Patterson, Ron Pinhasi, Jessica C. Thompson, Dennis Van Gerven, David Reich
doi: https://doi.org/10.1101/2021.02.17.431423
Kendra A. Sirak
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
3Department of Anthropology, Emory University, Atlanta, GA 30322, USA
5Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
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  • ORCID record for Kendra A. Sirak
  • For correspondence: kendra_sirak@hms.harvard.edu
Daniel M. Fernandes
4Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
5Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
6CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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Mark Lipson
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Swapan Mallick
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Matthew Mah
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Iñigo Olalde
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
9Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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Harald Ringbauer
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Nadin Rohland
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Carla S. Hadden
10Center for Applied Isotope Studies, University of Georgia, Athens GA 30602, USA
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Éadaoin Harney
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
11Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Nicole Adamski
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Rebecca Bernardos
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Nasreen Broomandkhoshbacht
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kimberly Callan
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Matthew Ferry
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Ann Marie Lawson
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Megan Michel
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Jonas Oppenheimer
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kristin Stewardson
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Fatma Zalzala
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Nick Patterson
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Ron Pinhasi
4Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
5Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
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Jessica C. Thompson
3Department of Anthropology, Emory University, Atlanta, GA 30322, USA
12Department of Anthropology, Yale University, New Haven, CT 06511, USA
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Dennis Van Gerven
13Department of Anthropology, University of Colorado at Boulder, Boulder, CO 80309, USA
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David Reich
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Abstract

Nubia has been a corridor for the movement of goods, culture, and people between sub-Saharan Africa, Egypt, and West Eurasia since prehistory, but little is known about the genetic landscape of the region prior to the influence of the Islamic migrations that began in the late 1st millennium CE. We report genome-wide data for 66 individuals from the site of Kulubnarti (∼650–1000 CE), increasing the number of ancient individuals with genome-level data from the Nile Valley from three to 69. Our results shed light on the genetic ancestry of a Christian Period group and help to address a long-standing question about the relationships among people buried in two neighboring cemeteries who show skeletal evidence of differences in morbidity and mortality that are broadly suggestive of differences in social status. We find that the Kulubnarti Nubians were admixed with ∼43% Nilotic-related ancestry on average (individual proportions varied between ∼36-54%) and the remaining ancestry reflecting a West Eurasian-related gene pool likely introduced into Nubia through Egypt, but ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The admixed ancestry at Kulubnarti reflects interactions between genetically-distinct people in northeast Africa spanning almost a millennium, with West Eurasian ancestry disproportionately associated with females, highlighting the impact of female mobility in this region. We find no significant differences in ancestry among individuals from the two plausibly socially-stratified cemeteries at Kulubnarti, supporting hypotheses that the groups may have been socially divided but were not genetically distinct. We identify seven pairs of inter-cemetery relatives as close as second-degree, suggesting that any social divisions at Kulubnarti did not prevent mixing between groups. Present-day Nubians are not directly descended from the Christian Period people from Kulubnarti without additional admixture, attesting to the dynamic history of interaction that continues to shape the cultural and genetic landscape of Nubia.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia
Kendra A. Sirak, Daniel M. Fernandes, Mark Lipson, Swapan Mallick, Matthew Mah, Iñigo Olalde, Harald Ringbauer, Nadin Rohland, Carla S. Hadden, Éadaoin Harney, Nicole Adamski, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kimberly Callan, Matthew Ferry, Ann Marie Lawson, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Nick Patterson, Ron Pinhasi, Jessica C. Thompson, Dennis Van Gerven, David Reich
bioRxiv 2021.02.17.431423; doi: https://doi.org/10.1101/2021.02.17.431423
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Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia
Kendra A. Sirak, Daniel M. Fernandes, Mark Lipson, Swapan Mallick, Matthew Mah, Iñigo Olalde, Harald Ringbauer, Nadin Rohland, Carla S. Hadden, Éadaoin Harney, Nicole Adamski, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kimberly Callan, Matthew Ferry, Ann Marie Lawson, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Nick Patterson, Ron Pinhasi, Jessica C. Thompson, Dennis Van Gerven, David Reich
bioRxiv 2021.02.17.431423; doi: https://doi.org/10.1101/2021.02.17.431423

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