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Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in post-Roman Periods

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Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in post-Roman Periods

Verena J Schuenemann et al. Nat Commun.

Abstract

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level.

Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Geographic context, of the samples used in this study.
Map of Egypt depicting the location of the archaeological site Abusir-el Meleq (orange X) and the location of the modern Egyptian samples (orange circles) (design of the graphic by Annette Günzel).
Figure 2
Figure 2. DNA preservation and DNA damage of the samples used in this study.
(a) coverage boxplots separated by tissue type (bone, mummified tissue, teeth), (b) boxplots showing damage of first base at the 3′ end separated by tissue type according to a, (c) damage on first base at the 5′ end of mapped reads separated by tissue type according to a and b.
Figure 3
Figure 3. Analysis of 90 ancient Egyptian mitochondrial genomes.
(a) Mitochondrial DNA haplogroup frequencies of three ancient and two modern-day populations, (b) Principal Component Analysis based on haplogroup frequencies: (sub-Saharan Africa (green), North Africa (light green), Near East (orange), Europe (yellow), ancient (blue), (c) MDS of HVR-I sequence data: colour scheme as above; note that ancient groups were pooled, (d) Skygrid plot depicting effective population size estimates over the last 5,000 years in Egypt. Vertical bars indicate the ages of the analysed 90 mitochondrial genomes (three samples with genome-wide data highlighted in red). Note that the values on y axis are given in female effective population size times generation time and were rescaled by 1:14.5 for the estimation of the studied population size (assuming 29-year generation time and equal male and female effective population sizes) (images by Kerttu Majander).
Figure 4
Figure 4. Principal component analysis and genetic clustering of genome-wide DNA from three ancient Egyptians.
(a) Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes, (b) subset of the full ADMIXTURE analysis (Supplementary Fig. 4).
Figure 5
Figure 5. Shared drift and mixture analysis of three ancient Egyptians with other modern and ancient populations.
(a) Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations, (b) The data shown in a, compared with the same estimates for modern Egyptians, ordered by shared drift with modern Egyptians, (c) Admixture f3-statistics, testing whether modern Egyptians are mixed from ancient Egyptians and some other source. The most negative Z-scores indicate the most likely source populations.

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