Paleogenetic Investigation of Medieval Nubian Population from

El-Kurru, Sudan
Abagail Breidenstein1, Ainash Chidebayeva1, Ella Reiter2,3, Giada Ferarri2, Geoff Emberling1, Abigail Bouwman2, Frank Ruehli2, Verena
Schuenemann2 and Abigail W. Bigham1
1 University of Michigan, Ann Arbor, Michigan, 2 Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland, 3 Institute for
Archaeological Sciences, University of Tübingen, Tübingen, Germany

INTRODUCTION R E S U LT S
• Northeast Africa is an important region – host to various civilizations, gateway for trade and migration to • Capture methods were more successful than amplification (previous pilot work by authors)
Europe, Middle East, Asia; Ancient Nubia has been occupied since 7,000 BCE and spans from modern day • Remains from latest excavation were more successful than earlier field seasons
Aswan in southern Egypt to Khartoum in Northern Sudan
• 2014/2015 – avg 1109 mapped reads (N=6)
• Populations in this region of the Nile Valley were mobile with broad trade contacts since prehistoric times,
• 2016 – avg 2006 mapped reads (N=14)
through the empire of Kush, the Medieval Christian kingdoms, and the arrival of Islam in the 14th century CE;
trade, conquest, colonialism – all of which contributed to their genetic ancestry (Krings et al. 1999, Lalueza • Results of capture yielded generally low coverage of Mt Genome – Avg range from 0.0290 to 1.8275 (Table 2,
Fox 1997) some Ind. not listed, Supplementary Table)
• Using up to 3 polymorphic sites in the Hypervariable Region I, 5 individuals had sufficient coverage for
• New focus on African material for paleogenetic work due to advancing technology and drive to include more
preliminary haplogroup identification to classify these Nubians into HV, H, K, U, or R haplogroups (Table 3)
diverse sources of data; Genomes of North African populations are sparse but accumulating quickly (eg.
Hollfelder et al. 2017, Scheunemann & Peltzer et al. 2017)
• Nubians have a dynamic history with their neighbors to the north – trade, conquest, colonialism – all of which Merged reads Merged reads Average coverage of
Ind No. Total Reads
may have contributed to their genetic ancestry. Mitochondrial data provide valuable insight into the ancestry used mapped MtGenome
of Nubian individuals and serve as a primary resource for migration and population history reconstruction; for 202 527704 5296 4247 1.8275
instance, how genetic diversity or continuity from the past has shaped modern inhabitants of the Nile Valley 206 583599 1401 1295 0.1893
• Nubian genetic makeup before Arab expansion is speculative, inferred from marker typing, or based on non- 210 4477904 2784 2321 0.3536
genetic markers, but thought to be closely related to Egyptians (Babiker et al. 2011, Irish 2005) 212 745183 3250 2614 0.2934
216 433395 2166 2056 0.5756
Egypt Ext. Blank 1 225890 40936 1111 0.0044
Ext. Blank 2 265217 50940 1319 0.0195
OBJECTIVES Lower
Nubia Lib. Blank 1 99114 43683 446 Neg.
• Assess mitochondrial (mtDNA) genetic diversity in
Lib. Blank 2 42004 15343 232 Neg.
Medieval Nubian population
Table 2. Processed reads statistics of Individuals where it was possible to determine preliminary Haplogroups. At this time, those not included
did not have sufficient coverage of the Hypervariable Region I; may require more enrichment steps.
• Reconstruct population dynamics and ancestry;
Upper
understand the mobility and interactions of this Nubia

group across Upper Nubia; assess continuity in

modern Sudanese
• Establish feasibility of paleogenetic work with
Nubian remains from 4th Cataract region, build
data set that expands in space and time

Figure 1. Map modern North Sudan with ancient sites (marked with red
triangles); 4th cataract region highlighted in orange. Sudan & Nubia 19.

Table 3. Haplogrep output of preliminary haplogroup assignments for 5/20 individuals. Range is in bp of the Hypervariable Region I. Polymorphisms included in determination
M AT E R I A L S are listed in row aligning with SampleID.

• The Nubian site of El-Kurru lies along the Nile River about 140 km upstream of Old Dongola, the capital of the
Medieval Christian kingdom of Makuria DISCUSSION
• International Kurru Archaeological Project excavated fortified Medieval settlement dating to roughly 600- • Haplogroup classifications show ancient Nubians may differ from modern North African individuals; the genetic
1000 CE, cemetery dated to Late Christian 900-1450 CE variation or homogeneity within the ancient populations of the Nile Valley.
• Cemetery contained 11 subadults and 16 adults (1 undetermined) of various ages • Samples from new excavations seem to have better molecular preservation than those from later excavations
• Remains in good to poor preservation, due to taphonomy (ie. wadi, irrigation flooding) or disease (eg. stored in field house for 1 or more years may damage DNA)
• 20 individuals piloted for ancient DNA extraction for NGS and hybridization capture methods • Possible strategy to sample remains same field season or before long-term storage
• Sterile sampling hood in Khartoum
A B Ind No. Year Excavated Sex Estimation Age Estimation • Additional captures required to build full mitochondrial genomes > haplotype profile construction, FST statistics,
005 2014 Unknown Young Adult and population continuity test (as modeled in Brandt et al. 2013)
104 2015 Male Young Adult • Historical sources reference an invading group, the Noba from the S/SW desert, moving against the Kushites.
109 2015 -- Child Extent of their integration is contested: brief encounter, an admixture event, or replacement?
110 2015 Probable Female Older Adult
• Transect approach will answer this question, when including other samples deeper in time
111 2015 Probable Female Adult
113 2015 -- Adolescent
201 2016 Male Middle Adult FUTURE DIRECTIONS
202 2016 -- Child
• Expanding sample cohort: 50 new samples from 4th Cataract region (teeth and petrous samples) – See Fig. 1
203 2016 Male Young Adult
204 2016 Male Older Adult • El-Zuma, El-Detti, Tanqasi – Post-Meritic samples (350-600 CE)
206 2016 Female Young Adult • Berber Meroitic Cemetery (350 BCE-350 CE), Tinga Archaeological
207 2016 Male Older Adult Project, Kewa Archaeological Rescue Project – Meroitic Samples (300 BCE – 300 CE)
209 2016 -- Adolescent
• Create a time-series to characterize genetic variation and trace human migrations in
210 2016 Male Older Adult
real-time to reconstruct past population history
211 2016 -- Child
212 2016 -- Infant • Nuclear genome work with El-Kurru samples, interested in malaria adaptation genes within the Nile Valley ie.
C D G6PD
213 2016 -- Infant
214 2016 -- Child
215 2016 Male Older Adult
216 2016 Male Older Adult SELECT REFERENCES
Table 1. Demography of individuals from 2013-2016 field seasons at El-Kurru. Sex estimated with Skuldbøl T, Uildriks M, Rose K, Philips J, & Breidenstein A. (2016). “The Medieval Fortification, Settlement, and Cemetery” in El-Kurru 2015-16: Preliminary Report. Sudan &
reference to non-metric cranial traits present (Buikstra & Ubelaker 1994), morphology of the pubis Nubia, 20, 40-46.
Figure 2. A) Individual 209, excavated 2016. B) Individual 210, (Phenice 1969), and morphology of greater sciatic notch (Buikstra & Ubelaker, 1994). Age estimated Schuenemann, V. J., Peltzer, A., Welte, B., van Pelt, W. P., Molak, M., Wang, C. C., Furtwaegler, A., Urban, C., Reiter, E., Nieselt, K., Teßmann, B. Francken, M., Harvati, K., Haak,
excavated 2016. C) Temporal bone of Individual 202 before from as many features present, including: degree of epiphyseal fusion (Mackay 1961, Scheuer & Black W., Schiffels, S. & Krause, J. (2017). Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nature communications, 8:
2004), tooth formation (Thoma & Goldman 1960, Smith 1991) and dental eruption sequences (Buikstra 15694.
sample preparation from petrous portion. D) Temporal bone
& Ubelaker 1994), and occlusal wear (Gilmore & Grote, 2012). Sub-adults were assessed for biological Hollfelder, N., Schlebusch, C. M., Günther, T., Babiker, H., Hassan, H. Y., & Jakobsson, M. (2017). Northeast African genomic variation shaped by the continuity of indigenous
from Individual 210 before sample preparation from petrous
portion. sex, but will so with molecular testing (designated as ‘ - - ‘). groups and Eurasian migrations. PLoS Genetics, 13(8), e1006976.
Irish, D., & Joel, D. (2005). Population continuity vs. discontinuity revisited: Dental affinities among late Paleolithic through Christian-era Nubians. American Journal of Physical
Anthropology, 128(3), 520-535.
METHODS C. Lalueza Fox (1997). mtDNA analysis in ancient Nubians supports the existence of gene flow between sub-Sahara and North Africa in the Nile valley, Annals of Human Biology, 24(3), 217-227.
Krings, M., Bauer, K., Geisert, H., Malek, A. K., Chaix, L., Simon, C., ... & Pääbo, S. (1999). mtDNA analysis of Nile River Valley populations: a genetic corridor or a barrier to migration?. The American
Journal of Human Genetics, 64(4), 1166-1176.
Buzon, M. R. (2008). A bioarchaeological perspective on Egyptian colonialism in Nubia during the New Kingdom. The Journal of Egyptian Archaeology, 94(1),
Extraction Library Prep & 165-182.
Sample
Amplification mtDNA Capture
Prep

ACKNOWLEDGEMENTS
We would like to thank funding sources for excavation and lab work: the University of Michigan Rackham
Meyer & Kircher 2010,
Pinhasi et al. 2015
MPI Leipzig, adapted K . Bos Meyer et al. 2012
Maricic et al. 2010 International Research Fund, the African Studies Center, and Rackham Graduate Research Funds.
(2012), Dabney et al. 2013
Additional thanks to the National Corporation for the Antiquities and Museums in Khartoum, including Dr.
FGCZ MiSeq Bioinformatics Pipeline Abdelrahman Ali and the International Kurru Archaeological Project team.
1. Raw data demultiplexed using deML (Renaud et al. 2015)
2. Adaptors trimmed via Trimmomatic (Bolger et al. 2014) A special thank you to those who helped gather data in
3. Fragment size and damage profiles generated via MapDamage (Ginolhac 2011) el-Kurru and at the IEM: namely, Annina Kruettli, Enrique
4. Aligned with human mitochondrial genome using Geneius 2.5 (Kearse et al. 2012) Rayo and members of the IKAP team and especially
5. Mt profiles evaluated with HaploGrep 2.0 (Weissensteiner et al. 2016)
the villagers of el-Kurru.