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Nature | www.nature.com | 1

Article

Whole-genome ancestry of an Old Kingdom

Egyptian

Adeline Morez Jacobs

1,2,12

✉

, Joel D. Irish

, Ashley Cooke

, Kyriaki Anastasiadou

Christopher Barrington

, Alexandre Gilardet

2,5

, Monica Kelly

, Marina Silva

, Leo Speidel

2,6,13

Frankie Tait

2,14

, Mia Williams

, Nicolas Brucato

, Francois-Xavier Ricaut

, Caroline Wilkinson

Richard Madgwick

, Emily Holt

, Alexandra J. Nederbragt

, Edward Inglis

, Mateja Hajdinjak

Pontus Skoglund

2,15

✉

& Linus Girdland-Flink

1,11,15

✉

Ancient Egyptian society ourished for millennia, reaching its peak during the Dynastic

Period (approximately 3150–30). However, owing to poor DNA preservation,

questions about regional interconnectivity over time have not been addressed because

whole-genome sequencing has not yet been possible. Here we sequenced a 2× coverage

whole genome from an adult male Egyptian excavated at Nuwayrat (Nuerat, تاريون).

Radiocarbon dated to 2855–2570cal. , he lived a few centuries after Egyptian

unication, bridging the Early Dynastic and Old Kingdom periods. The body was

interred in a ceramic pot within a rock-cut tomb

, potentially contributing to the DNA

preservation. Most of his genome is best represented by North African Neolithic

ancestry, among available sources at present. Yet approximately 20% of his genetic

ancestry can be traced to genomes representing the eastern Fertile Crescent, including

Mesopotamia and surrounding regions. This genetic anity is similar to the ancestry

appearing in Anatolia and the Levant during the Neolithic and Bronze Age

2–5

. Although

more genomes are needed to fully understand the genomic diversity of early Egyptians,

our results indicate that contacts between Egypt and the eastern Fertile Crescent were

not limited to objects and imagery (such as domesticated animals and plants, as well as

writing systems)

6–9

but also encompassed human migration.

For thousands of years, the Egyptian Dynastic civilization (approxi-

mately 3150–30) developed monumental architecture, sophisti-

cated technology and relatively stable belief systems, becoming the

longest-lasting civilization known. Following the political unification of

the northern and southern regions of Egypt (Lower and Upper Egypt) at

the end of the fourth millennium , the Old Kingdom (2686–2125)

witnessed considerable advances, including the construction of the

first step pyramid complex of King Djoser and the ‘Great Pyramid of

Giza’ built by King Khufu. The population has been considered to be

of local origin, with limited input from neighbouring regions

8,10

. Yet,

more recent archaeological evidence shows that trade connections

existed across the Fertile Crescent since at least the sixth millennium



, if not earlier, with the advent of the Neolithic package (such as

domesticated animals and plants)

6,7

. Cultural exchange continued

to develop through the late fourth millennium  with the growing

Sumerian civilization of Mesopotamia

7–9

. This period overlaps with

the appearance of additional innovations in Egypt (such as the pottery

wheel)

and the earliest evidence of hieroglyphic writing in the form

of ivory tags in Tomb U-j at Abydos, dated 3320–3150 

Our knowledge of ancient Egyptians has increased through decades

of bioarchaeological analyses

12–15

, including dental morphological

studies on their relatedness to other populations in North Africa and

West Asia

16–18

. However, the lack of ancient genomes, particularly for

the early periods of Egyptian Dynastic history, remains a barrier to our

understanding of population continuity and gene flow in the region.

Although individuals from ancient Egypt were subjected to the first

effort to isolate ancient DNA

, direct genome sequencing has remained

elusive because of the challenging regional DNA preservation condi-

tions. So far, only three individuals from Abusir el-Meleq (Fig.1a) have

yielded nuclear DNA, all post-dating the emergence of Dynastic Egypt

by thousands of years (from 787cal.  to 23cal. )

. Moreover, these

are not complete genome sequences but are limited to approximately

90,000–400,000 target-enriched genotypes. Over the millennia span-

ning the Dynastic Period, Egypt witnessed several wide-ranging wars,

occupation by foreign rulers and dramatic episodes of internal politi-

cal collapse (First, Second and Third Intermediate periods)

. Together,

these processes may have substantially altered or reshaped the overall

genetic structure and ancestry of the Egyptian population. Here we

https://doi.org/10.1038/s41586-025-09195-5

Received: 21 June 2024

Accepted: 23 May 2025

Published online: xx xx xxxx

Open access

Check for updates

School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.

Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.

World Museum,

National Museums Liverpool, Liverpool, UK.

Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK.

Centre for Palaeogenetics, Stockholm, Sweden.

Genetics Institute,

University College London, London, UK.

Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse III–Paul

Sabatier (UT3), Toulouse, France.

Face Lab, Liverpool John Moores University, Liverpool, UK.

School of History, Archaeology and Religion, Cardiff University, Cardiff, UK.

School of Earth and

Environmental Sciences, Cardiff University, Cardiff, UK.

Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.

Present address: Department of Biology,

University of Padova, Padova, Italy.

Present address: iTHEMS, RIKEN, Wako, Japan.

Present address: Department of Archaeology, University of Reading, Reading, UK.

These authors jointly

supervised this work: Pontus Skoglund, Linus Girdland-Flink.

✉

e-mail: adelinemorez@gmail.com; pontus.skoglund@crick.ac.uk; linus.girdlandlink@abdn.ac.uk

2 | Nature | www.nature.com

Article

present a whole-genome sequence of an ancient Egyptian individual

(2.02× coverage; Supplementary Table1), recovered from a necropolis

at Nuwayrat (تاريون, Nuerat; Fig.1a).

The Nuwayrat individual

Nuwayrat is located near the village of Beni Hasan, 265km south of

Cairo (Fig.1a). Radiocarbon dating of the skeletal remains showed that

the Nuwayrat individual died between 2855 and 2570cal.  (95.4%

probability; Supplementary Information section1 and Supplementary

Table2), which overlaps with the Early Dynastic and Old Kingdom peri-

ods (Fig.1e). This result supports the initial archaeological assessments

that material culture and funerary practices at the site were consistent

with those of the Third and Fourth Dynasties of the Old Kingdom

1,22

The body was placed in a large pottery vessel inside a rock-cut tomb

(Fig.1b and Extended Data Fig.1). This treatment would have ordinarily

been reserved for individuals of a higher social class relative to others

at the site

, as observed elsewhere during the Early Dynastic Period

and at the Old Kingdom royal cemeteries near the city of Memphis

(Supplementary Information section1).

Although acknowledging known limitations in predicting pheno-

typic traits in understudied populations

, the Nuwayrat individual is

predicted to have had brown eyes, brown hair and skin pigmentation

ranging from dark to black skin, with a lower probability of interme-

diate skin colour (Methods and Supplementary Table10). The indi-

vidual was genetically male (XY sex chromosomes; Supplementary

Table1), consistent with the expression of standard skeletal features

(Methods). Our further osteological examination revealed that he

would have stood 157.4–160.5cm tall

. He lived to an advanced age

for the time (approximately 44–64years; the upper end of this range

is the most probable

25,27

), as evidenced by his heavily worn teeth and

age-related osteoarthritis in most joints and vertebrae, in some cases

severe (Fig.1c). This and various activity-induced musculoskeletal

indicators of stress revealed that he experienced an extended period

of physical labour, seemingly in contrast to his high-status tomb burial.

The patterns of osteoarthritis and stress indicators further imply the

form of physical activity that he routinely engaged in, which some

researchers maintain can provide clues concerning occupation

28,29

In this case, although circumstantial, they are not inconsistent with

those of a potter, as depicted in ancient Egyptian imagery. Estimates of

biological affinity based on dental morphological features and cranial

measurements parallel the genomic results (below). More detailed

information about the Nuwayrat individual is presented in Supplemen-

tary Information section2, with a facial depiction in Supplementary

Information section3 (Extended Data Fig.2).

Multi-isotope analysis (δ

C, δ

N, δ

O and

Sr/

Sr) was con-

ducted on dental enamel and dental collagen from the lower-left

second molar to determine his childhood diet and geographic origin

(Supplementary Information section5). All results are consistent with

having grown up in the hot, dry climate of the Nile Valley (δ

carb VSMOW

=

23.6‰, whereVSMOWindicatesVienna Standard Mean Ocean Water;

Sr/

Sr=0.707888)

30–32

and consuming an omnivorous diet based

on terrestrial animal protein and plants, such as wheat and barley

(δ

VPDB

=−19.6‰, whereVPDBindicatesVienna Pee Dee Belemnite;

AIR

=12.3‰)

, typical for Egyptians until the Coptic period

An elevated δ

N value, frequently observed in isotope studies of

Nuwayrat

Cairo

Red Sea

Western desert

Eastern

desert

Mediterranean Sea

NUE001

Abusir-el Meleq

Early Dynastic

Period

Old Kingdom

Middle Kingdom

New Kingdom

First Intermediate

Period

Second Intermediate

Period

Third Intermediate

Period

Late period

Graeco-Roman

period

Islamic period

Modern period

2.02× 32.89× 0.02 ± 0.01 0.03 ± 2.52 × 10

–3

NUE001 2855–2570 cal. BCE 47.69%

Radiocarbon date

(95.4% probability)

Genome

coverage

mtDNA

coverage

C>T

(First base 5

′)

Contamination

mtDNA Chromosome X

b c

3150 BCE

Reads

mapped

4.9%

Fig. 1 | Geographic location and date of the Nuwayrat individual in context.

a, Geographic location of the Nuwayrat cemetery (red dot) and the previously

sequenced Third Intermediate Period individuals from Abusir el-Meleq

(purple diamond). b, Pottery vessel in which the Nuwayrat individual was

discovered. c, Cervical vertebrae belonging to the Nuwayrat individual with

evidence of extreme osteoarthritis (arrows). d, Summary of genomic and

radiocarbon data. See the detailed breakdown of the quality indicators and

calibration results for the three replicates and the combined date in

Supplementary Table2. e, Egyptian civilization timeline and radiocarbon

date of the Nuwayrat and Third Intermediate Period individuals. mtDNA,

mitochondrial DNA. Photo in b reproduced courtesy of the Garstang Museum

of Archaeology, University of Liverpool.

Nature | www.nature.com | 3

South_Africa_2200BP

Ethiopia_4500BP

Morocco_Epipalaeolithic

NUE001

Egypt

Third_Intermediate_Period

Levant_Palaeolithic

Anatolia_Palaeolithic

North Africa Levant Zagros Caucasus

Anatolia Mesopotamia

Morocco_EN

Morocco_MN

Egyptian.HO

Levant_Neolithic

Levant_Chalcolithic

Modern genomes:

Caucasus

Anatolia

Levant

Arabian Peninsula

Iran

Northeast Africa

Northwest Africa

Morocco Palaeolithic/West Asia cline

Levant/Iran Palaeolithic cline

Ancient genomes:

NUE001

Caucasus Palaeolithic

Caucasus Neolithic

Caucasus Chalcolithic

Anatolia Palaeolithic

Anatolia Neolithic

Anatolia Chalcolithic

Anatolia Bronze Age

Levant Palaeolithic

Levant Neolithic

Levant Chalcolithic

Levant Bronze Age

Zagros Neolithic

Africa

North Africa

West Asia

Caucasus

Europe

Southeast Asia

South Asia

East Asia

North and Central Asia

America (Native Americans)

PC1 (4.32%)

PC2 (1.76%)

PC1 (0.96%)

PC2 (0.44%)

–0.05

0.10

0.05

–0.05

–0.05 0.05 0.10

–0.10

–0.15

–0.20

–0.02 0

0.02

NUE001

Levant_BA

Zagros_Neolithic

Zagros_Chalcolithic

Caucasus_Neolithic

Caucasus_Chalcolithic

Anatolia_Neolithic

Anatolia_Chalcolithic

Anatolia_BA

Mesopotamia_Neolithic

Zagros Chalcolithic

Zagros Bronze Age

Mesopotamia Neolithic

Egypt Third Intermediate Period

Morocco Epipalaeolithic

Morocco Early Neolithic (ktg)

Morocco Middle Neolithic

Fig. 2 | Genetic ancestry of the Nuwayrat genome. a, PCA of present-day

worldwide populations, with projection of the Old Kingdom Egyptian genome

from Nuwayrat (NUE001). b, PCA of present-day populations from North Africa

and West Asia, with projection of ancient North African and West Asian

genomes. c, ADMIXTURE clustering analysis of the Old Kingdom Egyptian

genome in the context of ancient African, West Asian and present-day

Egyptian genomes at K=14ancestral populations. Only a subset of genomes

corresponding to those used in the qpAdm analysis (Fig.3) are displayed. The

full output of the ADMIXTURE analysis is shown in Extended Data Figs.4 and 5.

4 | Nature | www.nature.com

Article

ancient Egyptians, may have been caused by the arid environment

35–37

eating foods raised on manured fields

and/or inclusion of Nile fish

in the diet

Ancient genome sequencing

Seven cementum-enriched DNA extracts were prepared into single-

stranded DNA sequencing libraries

and screened on an Illumina plat-

form. Five of these libraries showed degradation patterns expected for

ancient DNA with evidence of elevated rates of cytosine-to-thymine

substitutions at the first base of the sequence alignments (more than

30%) and low contamination estimates for both nuclear and mitochon-

drial DNA (0–3%; Fig.1d); the two remaining libraries were discarded

because of elevated contamination estimates (Extended Data Fig.3

and Supplementary Table1 (Y11473 and Y11476)). The two libraries

(Y11475 and Y11477) with the highest proportion of reads mapping

to the reference human genome (6.0% and 3.2% of all sequences)

were further sequenced on Illumina NovaSeq 6000 and NovaSeq

X platforms to generate a total of 8.3billion 2×100 sequence read

pairs.

Pre-Bronze Age ancestry sources (Nuwayrat)

Longitude

Mesopotamia_Neolithic

Zagros_Neolithic

Zagros_Chalcolithic

Caucasus_Neolithic

Levant_BA

Levant_Chalcolithic

Caucasus_Chalcolithic

Anatolia_Chalcolithic

Greece_Neolithic

Anatolia_Neolithic

Levant_Neolithic

Spain_EN

Ethiopia_4500BP.SG

Anatolia_Palaeolithic

Levant_Palaeolithic

Date mean (yr BP)

Latitude

Levant_BA

NUE001

Tel Shadud

Hazor

Ebla

Baq'ah

Ashkelon

Ain'Ghazal

Anatolia_BA

P = 0.13 P = 0.15 P = 0.34 P = 0.07 P = 0.08 P = 0.25 P = 0.52 P = 0.12

(NUE001, Morocco_MN; X, Juǀ’hoan)

–0.001 0.001

2 3 5 1 4 5 6 1

Number of same-rank

models P > 0.05

Zagros_Neolithic

Morocco_MN

Morocco_EN_ktg

Mesopotamia_Neolithic

Levant_Neolithic

Levant_Chalcolithic

Caucasus_Neolithic

Anatolia_Neolithic

Anatolia_Chalcolithic

100

Admixture proportion (%)

Northwest

Africa

Levant

Mesopotamia

Anatolia

Caucasus

Iran

(including Zagros)

Europe

Northeast

Africa

6,000

7,000

8,000

9,000

10,000

11,000

60° E50° E40° E30° E20° E10° E0°10° W

5° N

10° N

15° N

20° N

25° N

30° N

35° N

40° N

45° N

100

Bronze Age

Chalcolithic

Neolithic

Palaeolithic

Morocco_MN

Morocco_EN_ktg

Levant_Chalcolithic

Levant_Neolithic

Mesopotamia_Neolithic

Anatolia_Chalcolithic

Anatolia_Neolithic

Caucasus_Chalcolithic

Caucasus_Neolithic

Zagros_Chalcolithic

Zagros_Neolithic

Greece_Neolithic

Spain_EN

Egypt_Old Kingdom

4,000

5,000

0.0030.0020

Fig. 3 | Ancestry models of the Nuwayrat genome. a, Ancestry proportion of

Nuwayrat and comparative Bronze Age Levantine and Anatolian genomes for

the best-fit full model (qpAdm). Alternative same-rank models passing P>0.05

with a lower P value are shown in Supplementary Table6. Values represent

best-fitting model estimates±1 standard error. This analysis was conducted

over n=537,543 SNPs for NUE001, n=518,994 SNPs for Anatolia_BA, n=554,622

SNPs for Ain’ Ghazal, n=493,274 SNPs for Ashkelon, n=578,969 SNPs for

Baq’ah, n=574,452 SNPs for Ebla, n=552,505 SNPs for Hazor and n=513,561

SNPs for Tel Shaddud. b, Estimation of the best source responsible for

deviation of the Nuwayrat genome from the Middle Neolithic Morocco group

as f

(NUE001, Morocco_MN; Mesopotamia_N, Juǀʼhoan). Symbols represent f

value±1 standard error. *Z score>2; **Z score>3. Theanalysis was conducted

over 280,544 SNPs. c,d, Map (c) and timeline (d) of rotating sources used to

infer the proximal ancestry of the Nuwayrat and Bronze Age Levantine and

Anatolian genomes (shown in a), with the dark-yellow area corresponding

to the Fertile Crescent. The timeline in d is based on Egyptian cultural

transition dates.

Nature | www.nature.com | 5

We merged the Nuwayrat genome (NUE001) with those of 3,233

present-day individuals that were either whole-genome sequenced or

genotyped on the Human Origins Array and 805 ancient individuals with

either whole-genome or 1.2million singlenucleotide polymorphism

(SNP) capture data. We first projected the Nuwayrat genome in a prin-

cipal component analysis (PCA) using a population panel representing

present-day worldwide genetic diversity. The Nuwayrat individual is

genetically most similar to present-day people in North Africa and West

Asia (Fig.2a and Extended Data Fig.4), which is consistent with the

results from ADMIXTURE clustering

(Extended Data Fig.5). The mito-

chondrial DNA (haplogroup I/N1a1b2) and chromosome Y (haplogroup

E1b1b1b2b~) haplogroups of the Nuwayrat individual are most common

in present-day North African and West Asian groups (Supplementary

Table4), consistent with the whole-genome affinities. Furthermore,

the Nuwayrat genome had no extended runs of homozygosity above

4cM, indicating no recent consanguinity in his ancestry

Ancestry of the Nuwayrat genome

We used the qpAdm

framework to model the genetic ancestry

components that best represent the Nuwayrat genome using a fully

rotating model competition approach, in which a set of candidate

populations are iteratively used as sources to construct one-source,

two-source and three-source population ancestry models, whereas

the remaining candidates are set as outgroup (right) populations

43,44

(Supplementary Information section4). We used a set of 13 populations

from Neolithic and Chalcolithic West Asia, North Africa and the North

Mediterranean region that predate the Nuwayrat individual as potential

sources (Fig.3c,d and Methods). No single-source model fitted the data

(maximum P value observed=2.39×10

−6

for a model with Morocco_

MN as a single source). Instead, a single two-source model (P=0.12)

met the significance criteria (P>0.05), which consisted of a mixture

of 77.6±3.8% ancestry represented by genomes from the Middle

P = 0.32

Number of same-rank

models P > 0.05

Admixture proportion (%)

Levant_BA

Morocco_MN

Congo_Kindoki_Protohistoric

Date mean (yr BP)

Latitude

Morocco_MN

Anatolia_BA

Caucasus_BA

Iran_BA

Greece_Minoan

Northwest

Africa

Levant

Mesopotamia

Anatolia

Caucasus

Iran

(including Zagros)

Europe

Northeast

Africa

East Africa

West Africa

100

Ethiopia_4500BP.SG

Levant_BA

Mesopotamia_Neolithic

Egypt_Third Intermediate Period

Egypt_Old Kingdom

Present-day Egypt

6,000

7,000

8,000

9,000

10,000

11,000

5,000

4,000

3,000

2,000

1,000

60° E40° E20° E

Longitude

0°

Potential Old Kingdom Egyptian

ancestry

100

NUE001

Morocco_MN

10° N

20° N

30° N

40° N

0°

Caucasus_BA

Levant_BA

Greece_Minoan

Iran_BA

Congo_Kindoki_Protohistoric

Ethiopia_4500BP.SG

.oeN cihtiloealaP

Chl.

Hist.

Fig. 4 | Ancestry models of later Egyptians. a, Ancestry proportions of the

Third Intermediate Period genomes for the best-fit model (qpAdm). Alternative

two-source and three-source models passing P>0.05 are reported in

Supplementary Table7. This analysis was conducted over 290,262 SNPs.

b, Ancestry proportions of the present-day Egyptian genomes for the best-fit

model (qpAdm). For b, alternative two-source and three-source models passing

P>0.05 are reported in Supplementary Table8. This analysis was conducted over

767,305 SNPs. Values represent best-fitting model estimates±1 standard error

(a,b). c,d, Map (c) and timeline (d) of rotating sources used to infer the ancestry

of the two Third Intermediate Period and/or the present-day Egyptian genomes.

The timeline in d is based on Egyptian cultural transition dates. BA, Bronze Age;

Chl., Chalcolithic; Hist., historical period; IA, Iron Age; Neo., Neolithic.

6 | Nature | www.nature.com

Article

Neolithic Moroccan site of Skhirat-Rouazi dated to 4780–4230

(Morocco_MN), and the remainder most closely related to genomes

from 9000 to 8000 Neolithic Mesopotamia (22.4±3.8%; Fig.3a). In

addition, two three-source models showed similar ancestry proportions

but with a minor contribution of a third ancestry component repre-

sented by genomes from the Neolithic/Chalcolithic Levant (4.7±8.2% at

P=0.11 and 1.1±8.7% at P=0.07, respectively; Supplementary Table6).

All accepted qpAdm models showed the presence of ancestry related

to Middle Neolithic Morocco in the Nuwayrat genome; therefore, our

results could indicate shared ancestry across North Africa during

this period and, consequently, that local Egyptian Neolithic popula-

tions contributed genetically to the Early Dynastic and Old Kingdom

people, as indicated from material culture

7,8,10

and bioarchaeological

analyses

14,15

. However, because the genomes from Middle Neo-

lithic Morocco have previously been modelled to comprise both

Iberomaurusian-like and Levantine Neolithic ancestry components

which we corroborated (Extended Data Fig.6, Supplementary Informa-

tion section4 and Supplementary Table5), the affinity to Levantine

Neolithic groups could reflect several migration events. To explore

these alternative hypotheses in detail, further ancient DNA studies on

pre-Bronze Age genomes from North Africa are required.

The second genetic ancestry component detected in the Nuwayrat

individual is most closely related to Neolithic Mesopotamians, out of

the potential sources included in the model competition (Methods).

To further examine the putative affinity to Neolithic Mesopotamia,

we computed a series of f

statistics testing whether a set of groups

share more derived alleles with Nuwayrat than with Middle Neolithic

Morocco in the form f

(NUE001, Morocco_MN; X, Ju_hoan_North.DG);

here X represents the rotating sources of the qpAdm model with the

addition of Levantine Palaeolithic, Anatolian Palaeolithic and Bronze

Age Levantine genomes. The statistic was maximized and statistically

significant with Neolithic Mesopotamia as X (Z score=3.2; Fig.3b).

The affinity is also seen in the statistic f

(NUE001, Morocco_MN;

Mesopotamia_N, X), which is positive for all tested populations as X,

consistent with an ancestry affinity between the individual from Nuway-

rat and Neolithic Mesopotamia, with Z scores>2 for all, except Zagros

and Caucasus groups and Chalcolithic and Bronze Age Levantine groups

(Supplementary Table9).

Although we caution that these results are based on a single Egyptian

genome, they mirror another study that found evidence of gene flow

from the Mesopotamian and Zagros regions into surrounding areas,

including Anatolia, during the Neolithic

. Together with archaeological

evidence for cultural exchange

6,7

, these findings open the possibility that

wider cultural and demographic expansion originating in the Mesopota-

mian region reached both Egypt and Anatolia during this period. How-

ever, more recent migrations from the eastern Fertile Crescent during the

Chalcolithic and Bronze Age further altered the Anatolian and Levantine

genetic landscapes

3–5

. Related movements may have introduced the

Mesopotamian-like ancestry more recently in Egypt. We tested this by

applying the same full qpAdm model to target groups from the Bronze

Age Anatolia and Levant (genomes from the Bronze Age Levant were

grouped into eight archaeological sites

3–5,46,47

, of which all models for

Megiddo and Yehud were rejected; Supplementary Table6). Although

we replicated previous findings that all Levantine Bronze Age groups

trace 18.7–79.8% of their ancestry to Neolithic or Chalcolithic Levan-

tine groups

3–5,46,47

, we also detected ancestry from Neolithic Mesopota-

mia at three sites (Ebla, Baq’ah and Ashkelon), considering the best-fit

models, in proportions (41.8–54.8%) exceeding those in the Nuwayrat

genome (Fig.3a and Supplementary Table6). However, the initial full

qpAdm model, extended to include the Bronze Age Levant as a potential

source, can effectively be rejected for the Nuwayrat genome (P=0.013;

Supplementary Information section4). Notably, the best model for

the Nuwayrat genome fits worse when these groups are included as

reference groups (P=0.021; Supplementary Information section4).

This means that we cannot exclude the possibility that the Neolithic

Mesopotamian-like ancestry in the Nuwayrat genome could have arrived

by means of more recent unsampled intermediaries in the Levant.

Although the timing of the admixture event cannot be estimated

directly (Supplementary Table11 and Supplementary Note4), this find-

ing provides direct evidence of genetic ancestry related to the eastern

Fertile Crescent in ancient Egypt. Archaeological evidence lends sup-

port to the Early Neolithic shared regional ancestry between Egypt

and West Asia. Given its proximity, Egypt was one of the first external

areas to adopt the Neolithic package that emerged across West Asia

as early as the sixth millennium  or before

6,48,49

, which could have

corresponded with movements of people. This period is concomi-

tant with the observed gene flow from Mesopotamia to Anatolia

which may have expan ded into Egypt as well. In support, a substan-

tial change in odontometric and dental tissue proportions occurred

approximately 6000 in the Nile Valley, with general continuity

thereafter

. Along with marked temporal differences in subsistence

(such as domesticated plants and greater sedentism) and material cul-

ture (such as the introduction of pottery), this is indicative of disconti-

nuity between the Mesolithic (eighth to seventh millennium ) and

Neolithic populations

. Cultural exchange and trade then continued

through the fourth millennium  when Mesopotamian Late Uruk

period features filtered into the Nile Valley during the later Predynastic

Period

7–9,51

. Trade might have been routed through the Mediterranean

and Red Seas rather than the Sinai Desert

7,52

. Such seaborne mobility

could explain a scenario in which the source population did not come

into contact with the Chalcolithic/Bronze Age Levantines. Our results

indicate that this millennia-long process might not have only included

cultural transmission but also migration and subsequent admixture.

Moreover, it is notable that both our qpAdm modelling and ADMIX

TURE clustering excluded any substantial ancestry in the Nuwayrat

genome related to the 4,500-year-old genome from Mota, Ethiopia or

other individuals in central, eastern or southern Africa (Figs.2 and 3

and Extended Data Fig.5)

. Nevertheless, we found that the Nuwayrat

genome fits as an equally good source as Levant Chalcolithic groups

for the West Eurasian-related component of East African pastoralist

genomes, but ancient DNA data are still missing for many putative

source regions (Extended Data Fig.7, Supplementary Information

section4 and Supplementary Table12)

54,55

Ancestry in later Egypt

The Nuwayrat genome extends the genetic record of ancient Egypt

beyond previously published data from the Third Intermediate Period

(787–544; Fig.1e). We modelled these latter individuals

using

qpAdm with putative sources from a set of nine populations from

North Africa (including Nuwayrat), West Asia and Greece, who lived

between the Old Kingdom and the Third Intermediate Period and also

included genomes from the Middle Neolithic Morocco and Neolithic

Mesopotamia (see Supplementary Information section4 for more

models that tested the potential overfitting of these sources). We can

reject all one-source models, including one with 100% continuity from

Nuwayrat to the Third Intermediate Period (P=3.00×10

−7

). Two similar

two-source models fit the data (Fig.4a and Supplementary Table7),

differing only in whether the Nuwayrat or Middle Neolithic Moroccan

individuals are one of the best-fit sources. In both models, the main

source of ancestry is the Bronze Age Levant (for example, 64.5±5.6%

in the model with Middle Neolithic Morocco; P=0.32; Supplementary

Information section4). These results are consistent with the Third

Intermediate Period genomes deriving part of their ancestry from

local groups related to the Nuwayrat individual while evidencing a

significant increase in Levantine ancestry.

Evidence of gene flow from the Levant by the time of the Third Inter-

mediate Period could be linked to the proposed Bronze Age Canaan-

ite expansion, starting at the end of the Middle Kingdom period.

On the basis of archaeological findings, whether this was a gradual

Nature | www.nature.com | 7

assimilation process

or a rapid shift, such as the settlement of Hyksos

rulers

56,57

, is still debated. Overall, this period also overlaps with the

well-characterized Late Bronze Age collapse that witnessed rapid soci-

etal and economic upheaval across the Mediterranean region, leading

to or being caused by widespread population movements

58,59

. However,

the temporal and geographical limitations of the current genomic data

do not allow firm conclusions to be drawn.

We next tested how present-day Egyptian ancestry could be traced

to the Bronze Age populations living in North Africa, including the

Nuwayrat individual, West Asia, Europe and sub-Saharan Africa, using

qpAdm. Despite substantial heterogeneity, most present-day Egyp-

tian genomes can be modelled as deriving their ancestry from five

sources related to (1) Nuwayrat (32.1–74.7%); (2) Middle Neolithic

Morocco (28.9–72.7%); (3) Bronze Age Levant (11.6–57.1%); (4) the

4,500-year-old individual from Ethiopia (‘Mota’) (7.4–56.0%); and

(5) two approximately 230-year-old individuals from Congo (4.8–

52.0%) (Fig.4b and Supplementary Table8). Thus, if tracing the

ancestry of many present-day Egyptians in our study to the Bronze

Age, much of it would be found in groups related to Nuwayrat or alter-

natively to sources best represented by Middle Neolithic Morocco

from which approximately 80% of Nuwayrat’s ancestry derives. The

second most common ancestry component is related to the Bronze

Age Levant, consistent with the ancestry detected in the Third Inter-

mediate Period individuals. Bronze Age Caucasus ancestry is present

in a fraction of the present-day Egyptians but is similar to the Bronze

Age Levant ancestry

. Our models show a more recent arrival of East

and West African ancestries in present-day Egyptians, which has also

been previously suggested

and dated to 27 generations ago using

linkage disequilibrium-based admixture dating

. Moreover, we note

that there is a substantial diversity in ancestry across Egypt; approxi-

mately 20% of the present-day Egyptian genomes included here did

not fit the model described above.

Conclusions

Our results demonstrate the feasibility of ancient genome sequenc-

ing from the earliest stages of the Egyptian Dynastic civilization. One

possible explanation for the successful whole-genome retrieval isthe

pot burial, which may have favoured a degree of DNA preservation not

previously reported in Egypt. This contributes to the road map for

future research to obtain ancient DNA from Egypt

. Although our anal-

yses are limited to a single Egyptian individual who, on the basis of his

relatively high-status burial, may not be representative of the general

population, our results revealed ancestry links to earlier North African

groups and populations of the eastern Fertile Crescent. Analogous

links were indicated in our biological affinity analyses of dental traits

and craniometrics of the Nuwayrat individual, as well as in previous

morphological studies based on full samples. The genetic links with the

eastern Fertile Crescent also mirror previously documented cultural

diffusion (such as domesticated plants and animals, writing systems

and thepottery wheel), opening up the possibility of some settlement

of people in Egypt during one or more of these periods. The Nuwayrat

genome also allowed us to investigate the Bronze Age roots of ancestry

in later Egypt, highlighting the interplay between population move-

ment and continuity in the region. Future whole-genome sequencing of

DNA frommore individuals will allow for a more detailed and nuanced

understanding of ancient Egyptian civilization and its inhabitants.

Online content

Any methods, additional references, Nature Portfolio reporting summa-

ries, source data, extended data, supplementary information, acknowl-

edgements, peer review information; details of author contributions

and competing interests; and statements of data and code availability

are available at https://doi.org/10.1038/s41586-025-09195-5.

1. Garstang, J. in The Burial Customs of Ancient Egypt (ed. Garstang, J.) 26–30 (Archibald

Constable, 1907).

2. Lazaridis, I. etal. Ancient DNA from Mesopotamia suggests distinct pre-pottery and

pottery Neolithic migrations into Anatolia. Science 377, 982–987 (2022).

3. Skourtanioti, E. etal. Genomic history of Neolithic to Bronze Age Anatolia, Northern

Levant, and Southern Caucasus. Cell 181, 1158–1175.e28 (2020).

4. Haber, M. etal. Continuity and admixture in the last ive millennia of Levantine history

from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum.

Genet. 101, 274–282 (2017).

5. Agranat-Tamir, L. etal. The genomic history of the Bronze Age Southern Levant. Cell 181,

1146–1157.e11 (2020).

6. Salvatori, S. & Usai, D. The neolithic and ‘pastoralism’ along the Nile: a dissenting view.

J. World Prehist. 32, 251–285 (2019).

7. Wengrow, D. The Archaeology of Early Egypt: Social Transformations in North-East Africa,

10,000 to 2,650 BC (Cambridge Univ. Press, 2006).

8. Bard, K. A. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 61–88 (Oxford Univ.

Press, 2000).

9. Stevenson, A. in The Sumerian World (ed. Crawford, H.) 620–636 (Routledge, 2013).

10. Malek, J. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 89–117 (Oxford Univ.

Press, 2000).

11. Doherty, S. K. The Origins and Use of the Potter’s Wheel in Ancient Egypt (Archaeopress,

2015).

12. Keita, S. O. Y. Further studies of crania from ancient northern Africa: an analysis of crania

from First Dynasty Egyptian tombs. Am. J. Phys. Anthropol. 87, 245–254 (1992).

13. Prowse, T. L. & Lovell, N. C. Concordance of cranial and dental morphological traits and

evidence for endogamy in ancient Egypt. Am. J. Phys. Anthropol. 101, 237–246 (1996).

14. Irish, J. D. Who were the ancient Egyptians? Dental afinities among Neolithic through

postdynastic peoples. Am. J. Phys. Anthropol. 129, 529–543 (2006).

15. Zakrzewski, S. R. in Egyptian Bioarchaeology: Humans, Animals, and the Environment

(eds Ikram, S. etal.) 157–167 (Sidestone, 2015).

16. Dicke-Toupin, C. R. Population Continuity or Replacement at Ancient Lachish?

(Fairbanks, 2012).

17. Irish, J. D. Diachronic and synchronic dental trait afinities of late and post-Pleistocene

peoples from North Africa. Homo 49, 138–155 (1998).

18. Maaranen, N., Zakrzewski, S. & Schutkowski, H. Who were the Hyksos? Curr. Anthropol.

63, 66–69 (2022).

19. Pääbo, S. Molecular cloning of ancient Egyptian mummy DNA. Nature 314, 644–645

(1985).

20. Schuenemann, V. J. etal. Ancient Egyptian mummy genomes suggest an increase of

sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 15694 (2017).

21. Shaw, I. The Oxford History of Ancient Egypt (Oxford Univ. Press, 2000).

22. De Meyer, M. etal. in Under the Potter’s Tree: Studies on Ancient Egypt Presented to Janine

Bourriau Vol. 204 (eds Aston, D. etal.) 679–702 (Peeters, 2011).

23. Power, R. K. & Tristant, Y. From refuse to rebirth: repositioning the pot burial in the Egyptian

archaeological record. Antiquity 90, 1474–1488 (2016).

24. Lasisi, T. & Shriver, M. D. Focus on African diversity conirms complexity of skin pigmentation

genetics. Genome Biol. 19, 13 (2018).

25. Buikstra, J. E. & Ubelaker, D. U. Standards for Data Collection from Human Skeletal Remains

(Arkansas Archeological Survey, 1994).

26. Raxter, M. H. etal. Stature estimation in ancient Egyptians: a new technique based on

anatomical reconstruction of stature. Am. J. Phys. Anthropol. 136, 147–155 (2008).

27. Ican, M. Y., Loth, S. R. & Wright, R. K. Age estimation from the rib by phase analysis:

white males. J. Forensic Sci. 29, 1094–1104 (1984).

28. Kennedy, K. A. R. in Reconstruction of Life from the Skeleton (eds Kennedy, K. A. R. &

Ican, M. Y.) 129–160 (Alan R. Liss, 1989).

29. Capasso, L., Kenney, K. A. R. & Wilczak, C. A. Atlas of Occupational Markers on Human

Remains (Edigratifal, 1998).

30. Buzon, M. R. & Simonetti, A. Strontium isotope (

Sr/

Sr) variability in the Nile Valley:

identifying residential mobility during ancient Egyptian and Nubian sociopolitical

changes in the New Kingdom and Napatan periods. Am. J. Phys. Anthropol. 151, 1–9

(2013).

31. Stantis, C., Nowell, G. M., Prell, S. & Schutkowski, H. Animal proxies to characterize the

strontium biosphere in the northeastern Nile Delta. Bioarchaeology of the Near East 13,

1–13 (2019).

32. Touzeau, A. etal. Egyptian mummies record increasing aridity in the Nile Valley from

5500 to 1500 yr before present. Earth Planet. Sci. Lett. 375, 92–100 (2013).

33. Richards, M. P. in Archaeological Science: An Introduction (eds Richards, M. P. & Britton, K.)

125–144 (Cambridge Univ. Press, 2019).

34. Touzeau, A. etal. Diet of ancient Egyptians inferred from stable isotope systematics.

J. Archaeol. Sci. 46, 114–124 (2014).

35. Macko, S. A. etal. Documenting the diet in ancient human populations through stable

isotope analysis of hair. Philos. Trans. R. Soc. London, B: Biol. Sci. 354, 65–76 (1999).

36. Thompson, A. H., Richards, M. P., Shortland, A. & Zakrzewski, S. R. Isotopic palaeodiet

studies of ancient Egyptian fauna and humans. J. Archaeol. Sci. 32, 451–463 (2005).

37. Thompson, A. H., Chaix, L. & Richards, M. P. Stable isotopes and diet at ancient Kerma,

Upper Nubia (Sudan). J. Archaeol. Sci. 35, 376–387 (2008).

38. Poulallion, E. etal. High δ

N values in Predynastic Egyptian archeological remains:

a potential indicator for localised soil fertilisation practices in extreme conditions.

Preprint at bioRxiv https://doi.org/10.1101/2024.11.18.624066 (2024).

39. Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing

of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).

40. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in

unrelated individuals. Genome Res. 19, 1655–1664 (2009).

41. Ringbauer, H., Novembre, J. & Steinrücken, M. Parental relatedness through time revealed

by runs of homozygosity in ancient DNA. Nat. Commun. 12, 5425 (2021).

42. Maier, R. etal. On the limits of itting complex models of population history to f-statistics.

eLife 12, e85492 (2023).

8 | Nature | www.nature.com

Article

43. Skoglund, P. etal. Reconstructing prehistoric African population structure. Cell 171,

59–71.e21 (2017).

44. Yüncü, E. etal. False discovery rates of qpAdm-based screens for genetic admixture.

Preprint at bioRxiv https://doi.org/10.1101/2023.04.25.538339 (2023).

45. Simões, L. G. etal. Northwest African Neolithic initiated by migrants from Iberia and

Levant. Nature 618, 550–556 (2023).

46. Lazaridis, I. etal. Genomic insights into the origin of farming in the ancient Near East.

Nature 536, 419–424 (2016).

47. Feldman, M. etal. Ancient DNA sheds light on the genetic origins of early Iron Age

Philistines. Sci. Adv. 5, eaax0061 (2019).

48. Zvelebil, M. & Lillie, M. in Europe’s First Farmers (ed Price, T. D.) 57–92 (Cambridge Univ.

Press, 2000).

49. Pinhasi, R. & Stock, J. T. Human Bioarchaeology of the Transition to Agriculture

(Wiley, 2011).

50. Martin, N. etal. From hunter-gatherers to food producers: new dental insights into the

Nile Valley population history (Late Paleolithic-Neolithic). Am. J. Biol. Anthropol. 184,

e24948 (2024).

51. Stevenson, A. The Egyptian Predynastic and state formation. J. Archaeol. Res. 24,

421–468 (2016).

52. Redford, D. B. Egypt, Canaan, and Israel in Ancient Times(Princeton Univ. Press, 1992).

53. Llorente, M. G. etal. Ancient Ethiopian genome reveals extensive Eurasian admixture in

Eastern Africa. Science 350, 820–822 (2015).

54. Prendergast, M. E. etal. Ancient DNA reveals a multistep spread of the irst herders into

sub-Saharan Africa. Science 365, eaaw6275 (2019).

55. Wang, K. etal. Ancient genomes reveal complex patterns of population movement,

interaction, and replacement in sub-Saharan Africa. Sci. Adv. 6, eaaz0183 (2020).

56. Bourriau, J. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 172–206 (Oxford Univ.

Press, 2000).

57. Ryholt, K. S. B. & Bülow-Jacobsen, A. The Political Situation in Egypt During the Second

Intermediate Period, C. 1800-1550 B.C. (Museum Tusculanum, 1997).

58. Weiss, B. The decline of Late Bronze Age civilization as a possible response to climatic

change. Clim. Change 4, 173–198 (1982).

59. Ward, W. A., Joukowsky, M. S. & Åström, P. The Crisis Years: The 12th Century B.C.:

From Beyond the Danube to the Tigris (Kendall Hunt, 1992).

60. Harney, É. etal. Ancient DNA from Chalcolithic Israel reveals the role of population

mixture in cultural transformation. Nat. Commun. 9, 3336 (2018).

61. Salter-Townshend, M. & Myers, S. Fine-scale inference of ancestry segments without prior

knowledge of admixing groups. Genetics 212, 869–889 (2019).

62. Elmonem, M. A. etal. The Egypt Genome Project. Nat. Genet. 56, 1035–1037 (2024).

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Methods

Provenance and ethics

The human remains were excavated from the Nuwayrat necropolis

near Beni Hasan, Egypt. They were donated between 1902 and 1904

by the Egyptian Antiquities Service to the members of the Beni Hasan

excavation committee and subsequently donated to the Institute of

Archaeology, University of Liverpool and exported under the John

Garstang export permit. The human remains were then donated to

the World Museum (previously the Liverpool City Museum) in 1950.

Sampling permit was granted by the World Museum.

Ancient DNA extraction, library preparation and sequencing

Sampling and DNA extraction of seven permanent teeth belonging

to an individual from Nuwayrat were carried out in dedicated ancient

DNA facilities at Liverpool John Moores University. Library preparation

and sequencing were carried out at The Francis Crick Institute (Sup-

plementary Table1). Before subsampling, the teeth were decontami-

nated by wiping with 1% sodium hypochlorite, followed by wiping with

molecular biology grade water and ethanol. Approximately 44–66mg

of cementum-enriched powder was extracted from each tooth using a

Dremel drill at the lowest possible rotations per minute (5,000rpm).

DNA was extracted using 1ml of extraction buffer consisting of 0.45ml

of 0.5M EDTA (pH8.0) and 10µl of 10mgml

−1

proteinase K per 50mg of

bone powder. The mixture was incubated overnight (approximately 18h)

at 37°C and purified on the High Pure Viral Nucleic Acid Large Volume

Kit (Roche) using a binding buffer described in ref. 63 and QIAGEN buffer

PE. DNA was eluted in approximately 100µl of QIAGEN elution buffer.

Extracts were turned into single-stranded DNA libraries

(with-

out treatment to remove uracils), double-indexed

and then under-

went paired-end sequencing on a HiSeq 4000 to approximately

seven million reads per library for initial screening (Supplementary

Table1). All samples were processed alongside negative lysate and

extraction controls and positive and negative library controls. On the

basis of the assessment of the initial sequencing results, two libraries

were selected for extra rounds of deeper sequencing on the NovaSeq

6000 and NovaSeq X platforms, following the selection of fragments

greater than 35bp using polyacrylamide gel electrophoresis

for the

library built from the NUE001b5e1 extract (Supplementary Table1),

with a resulting total of 8.3 billion 2×100 sequence pairs.

Radiocarbon dating

New radiocarbon dating was generated for the individual that yielded

DNA from Nuwayrat (NUE001) by Beta Analytic using accelerator mass

spectrometry. We directly dated the upper-left third molar (NUE001b3)

and lower-left first premolar (NUE001b5), both of which yielded DNA

that was deep sequenced (Supplementary Table1). The results are

reported in Supplementary Table2. The femur of this individual

was previously radiocarbon dated

66,67

(Supplementary Information

section 1and Supplementary Table2). All dates were calibrated using

OxCal v.4.4.4 (ref.68) with atmospheric data in IntCal20 (ref.69). We

also combined the three independent dates using the R_Combine()

function in OxCal

(Supplementary Table2). We rounded the calibrated

dates outwards to 10years unless error terms were smaller than ±25bp,

in which case we rounded outwards to 5years

Isotope analysis

Dental collagen and enamel were extracted from the lower-left second

molar. Dentine collagen was extracted for carbon (δ

C) and nitro-

gen (δ

N) isotope analysis following a modified Longin method

72,73

Mass spectrometry was performed using a Flash 1112 series elemental

analyser coupled with a Finnigan DELTA V Advantage (Thermo Fisher

Scientific) using established protocols

. Analytical precision (1σ) of

the in-house calibrated standards

were 0.08 and 0.07 for δ

C and

N, respectively.

For enamel, after surface abrasion, a slice (3.6mm wide) was extrac-

ted, and all adhering dentine was removed. Two fragments were pow-

dered, one of which was pre-ultrasonicated. A minimum of 3.0mg was

analysed for the oxygen isotope composition of enamel carbonate

(δ

). Samples were acidified for 5min with more than 100% ortho-

phosphoric acid (density approximately1.9 gcm

–3

) at 70°C and analysed

in duplicate using a MAT 253 dual-inlet mass spectrometer (Thermo

Fisher Scientific) coupled to a Kiel IV carbonate preparation device

using established protocols

. Isotope values are reported as per mille

(

O) normalized to the Vienna Pee Dee Belemnite (VPDB) scale using

an in-house carbonate standard (BCT63) calibrated against NBS19. The

long-term reproducibility for δ

O BCT63 is ±0.04‰ and ±0.03‰ for

C (1σ). The oxygen carbonate values (δ

C VPDB

) were converted to the

ViennaStandard Mean Ocean Water(VSMOW) scale

and phosphate

(δ

P VSMOW

)

The remaining enamel fragment (56.3mg) was cleaned in an ultra-

sonic bath, digested in 8M HNO

and heated overnight at 120°C. Sr-Spec

was used for strontium extraction, following the revised version of Font

etal.

. Once column-loaded in 1ml of 8M HNO

, matrix elements were

eluted in washes of 8M HNO

, and samples were placed on a hotplate

(120°C) overnight, with a repeat pass following. The sample was redis-

solved in 2% HNO

, and the

Sr/

S ratio was measured using a Neoma

multi-collector inductively coupled plasma mass spectrometry with

tandem mass spectrometry (MC-ICP–MS/MS,Thermo Fisher Scien-

tific). Instrumental mass bias was corrected for using the exponential

law and a normalization ratio of 8.375209 for

Sr/

Sr (ref.78). Residual

krypton (Kr) and rubidium (

Rb) interferences were monitored and cor-

rected using

Kr and

Kr (

Kr/

Kr=0.20175 and

Kr/

Kr=0.66474;

without normalization) and

Rb (

Rb/

Rb=2.5926), respectively.

The accuracy of the method was assessed by measuring the EC-5 coral

standard (

Sr/

Sr: 0.709171±0.000016 (2σ; n=14), consistent with

the expected value for seawater). The data were also corrected against

a National Institute of Standards and Technology Standard Reference

Material 987 value of 0.710248 (ref.79). The procedural blank was less

than 75pg of Sr, negligible relative to sample Sr.

Osteological analyses

Following element inventory, our determination of the Nuwayrat indi-

vidual’s sex was based on standard morphological indicators across the

skeleton (protocol in Buikstra and Ubelaker

). Ageing was estimated

from the dentition, cranium and postcrania

25,27,80–84

. For stature, several

approaches were used

85–87

, with the most likely estimate based on direct

stature reconstruction of ancient Egyptians following ref. 26.

Biological affinity was assessed from two long-recognized methods:

dental non-metric traits

and craniometrics (for example, Howells

First, the rASUDAS application was accessed (https://osteomics.com/

rASUDAS2/)

. It used up to 32 crown and root traits for comparison with

data from seven global population samples. Second, the craniometric

approach used the CRANID program CR6bIND, with 29 measurements

for comparison with a database of 74 premodern through recent global

samples, including Late Dynastic Egyptians and ancient West Asians

Our recording and description of skeletal pathology, related

primarily to age-related breakdown, follow accepted methods

25,92,93

This and activity-induced musculoskeletal stress markers (details in

previous studies

28,29,94

) were used to ascertain the level of physical activ-

ity. Although not without criticism

95,96

, they have been used to infer

occupation by identifying common positions and movements in life. For

that purpose, the latter were compared with illustrations of individuals

engaged in a range of common jobs, as depicted on ancient Egyptian

tomb walls and in statuary (Supplementary Information section2).

Facial reconstruction and depiction

Craniofacial analysis and facial reconstruction from skeletal remains

were carried out using three-dimensional laser scan data of the skull

(collected using an Artec Space Spider scanner), Touch X haptic device

Article

and Geomagic Freeform software

. Egyptian male data

were used to

estimate facial tissues at anatomical points across the skull surface.

The muscles of the head and neck were imported from the Face Lab

database and remodelled to fit the skull following anatomical guide-

lines

. Morphometric standards were used

99,100

to estimate facial

feature morphology, such as eye and nasal shape, lip and ear pattern

and structural creases. A final facial depiction was produced using

two-dimensional photo-editing software. It is important not to con-

sider a facial depiction as a portrait or definitive image because it can

only visualize the available information

101

. In this case, although DNA

analysis indicated the most probable population of origin, there was

no evidence in relation to skin colour and hair colour. Therefore, the

facial depiction was produced in black and white without head hair or

facial hair (Supplementary Information section3).

Bioinformatics data processing and authentication

Read alignment was performed following the pipeline in the study

of Swali etal.

102

. Samples were processed through the nf-core/eager

v.2.3.3 pipeline

103

. First, adaptors were removed, paired-end reads

were merged and bases with a quality below 20 were trimmed using

AdapterRemoval v.2.3.1 (ref.104) with –trimns –trimqualities –collapse

–minadapteroverlap 1 and –preserve5p. Merged reads with a minimum

length of 35bp were mapped to the hs37d5 human reference genome

with Burrows-Wheeler Aligner (BWA-0.7.17 aln)

105

using -l 16500 -n

0.01 -o 2 -t 1 (ref.106). Duplicate reads were removed using DeDup

v.0.12.8 (ref.107). Finally, we removed the alignments with mapping

quality below 30 and containing indels.

We used mapDamage v.2 (ref.108) to visualize the substitution distri-

bution along the reads and evidence the presence of deaminated mol-

ecules typical of ancient DNA. Contamination was estimated using three

different data sources: (1) genome-wide present-day contamination

using the conditional substitution rate

109

computed using PMDtools

v.0.60 (ref.110); (2) present-day mitochondrial DNA-based contami-

nation using schmutzi (commit be61017)

111

; and (3) chromosome X

contamination on libraries assigned as male using ANGSD v.0.933

(ref.112), restricted to the non-recombining region of chromosome X.

All the libraries from NUE001 show little to no contamination, except

two libraries with sequencing identification numbers SKO719A1706

and SKO719A1709 (Extended Data Fig.3 and Supplementary Table1).

Molecular sexing

The biological sex of the sequenced individual was determined using

the R

parameter

113

, which is the ratio of the number of alignments to

the Y chromosome (n

) to the total number of alignments to both sex

chromosomes (n

+ n

), R

= n

/(n

+ n

). All libraries are consistent with

NUE001 being karyotypically male, except the results from the library

SKO719A1706 consistent with being female, which is probably a result

of contamination (Supplementary Table1).

SNP calling in the Nuwayrat individual

We merged the sequencing data from five libraries from the Nuway-

rat individual showing an absence of present-day human DNA con-

tamination, yielding a total of 135,606,409 mapped unique reads of

44.63bp on average, resulting in an average genome-wide coverage

of 2.02×. We called pseudo-haploid positions using SAMTools v.1.9

mpileup

114

with options -B -R -Q30 and SequenceTools 1.5 (ref.115)

with options –randomHaploid and –singleStrandMode. This approach

leverages the single-stranded library preparation to computationally

remove the effects of cytosine-deamination-derived sequence errors.

Specifically, at C/T SNPs, it removes all bases that are aligned onto

the forward strand; at G/A SNPs, it removes all bases on that aligned

to the reverse strand. This allows for a confident pseudo-haploid

genotyping even also at CpG context transitions, which are mostly

not repaired by the uracil-DNA glycosylase (UDG) treatment owing

to methylation

116

Uniparental marker determination

We obtained the mitochondrial DNA consensus of the Nuwayrat individ-

ual from endogenous reads, removing the bases with quality below 20

(-q 20) using schmutzi

111

. The mitochondrial haplogroup was assigned

using Haplogrep 3 (ref.117).

The chromosome Y haplogroup was obtained using pathPhynder

118

with the parameter -m ‘no-filter’, on the basis of approximately 120,000

SNPs extracted from worldwide present-day and ancient male chromo-

some Y variation and the International Society of Genetic Genealogy

v.15.73 (http://www.isogg.org).

Comparison dataset

We merged the genome of the Nuwayrat individual with a comparison

dataset of 977 ancient individuals

2–5,20,43,45–47,53–55,60,119–160

and 4,040 mod-

ern individuals

43,46,122,141,158,161–169

genotyped on either the Human Origins

array

169

(‘Human Origins’ dataset) or the 1.2million SNP array (‘1240k’

dataset)

139

(Supplementary Table3). Most genotypes were directly

accessed from the Allen Ancient DNA Resource v.54.1 (ref.170). We

added nine ancient genomes from Morocco

and 13 ancient genomes

from Mesopotamia

120

from raw mapped Binary AlignmentMap(BAM)

files processed following the above-mentioned bioinformatic pipe-

line, with two modifications: (1) for the double-stranded UDG-treated

genomes from ref. 45, we trimmed the first and last three bases of the

reads and then called pseudo-haploid genotypes at both transition

and transversion sites; and (2) for the non-UDG-treated genomes from

ref. 120, we called pseudo-haploid genotypes at transversion sites only.

We included 100 present-day Egyptian genomes from ref. 164 in both

datasets. Individuals related up to the second degree, as detected in

previous studies, were excluded.

Principal component analysis

We computed two PCA on present-day individuals from the ‘Human Ori-

gins’ dataset using 593,124 substitutions through SMARTPCA (eigensoft

v.6.1.4)

169

. For the first analysis, we kept 3,233 individuals from across

the world and projected NUE001 on the resulting components. For the

second PCA, we kept 722 present-day individuals from North Africa,

West Asia and the Caucasus and projected NUE001 together with 781

ancient genomes from North Africa, West Asia and the Caucasus. Both

analyses used transversions only (111,208 SNPs).

ADMIXTURE clustering

We used a model-based clustering approach from the program

ADMIXTURE v.1.2 (ref.40) to estimate the ancestry components from

genomes in the ‘Human Origins’ dataset. All genomes were transformed

into pseudo-haploid sequences, and transitions were removed. The

remaining 111,208 positions were subsequently pruned for SNPs in

strong linkage disequilibrium using PLINK v.1.9 (ref.171), with the

parameter –indep-pairwise 200 25 0.4 to yield a final set of 71,202

transversion SNPs. ADMIXTURE was run with cross-validation enabled

using --cv flag for all ancestral population numbers from K=3 to K=20.

Runs of homozygosity

The presence and length of runs of homozygosity greater than 4cM

in the Nuwayrat genome were estimated using hapROH v.0.64 (ref.41)

on the 1.2million SNP set of sites.

qpAdm modelling

For all qpAdm modelling in this study, we estimated the ancestry

proportions as a mixture of a set of left (source) rotating popula

tions differentially related to a set of right (outgroup) populations

using ADMIXTOOLS 2 (ref.42) qpadm_rotating() with the option

maxmiss=0.1, removing genotypes missing in more than 10% of pop-

ulations. We restricted the analysis to genomes with both transitions

and transversions (half/plus UDG-treated libraries or single-stranded

libraries called using SequenceTools

115

--singleStrandMode), removing

CpG sites, to increase the robustness of the models. We considered

only models with three or less sources. We restricted the fixed set

of outgroup to populations distantly related to any left populations

and with genomes greater than or equal to 2×: Ju_hoan_North.DG,

Ethiopia_4500BP.SG, Latvia_HG_UDG, USA_Ancient_Beringian.SG,

Vanuatu_400BP_UDG, Japan_HG_Jomon_UDG and China_NEast Asia_

Coastal_EN_UDG. This analysis was conducted on the 1240k dataset.

These parameters are always true unless otherwise stated.

We ranked the non-rejected models first on the basis of the mini-

mal number of source populations, assuming that a fewer number

of source populations is more parsimonious. Then, if several models

with the same number of sources are not rejected, we considered the

P value, given that the number of SNPs in the rotating models are nearly

equal (10% missingness allowed between populations). Supplementary

Information section4 details all models tested.

Nuwayrat genome ancestry modelling. We first estimated the

Nuwayrat genome (NUE001) and contemporary North African and

West Asian populations (Levant_BA (also for each of the eight archaeo-

logical sites separately), Anatolia_BA and Morocco_MN) ancestry pro-

portions as a combination of distal Neolithic populations from North

Africa and West Asia (Morocco_Epipaleolithic, Anatolia_Neolithic,

Levant_Neolithic, Zagros_Neolithic and Caucasus_Neolithic). This

analysis was carried out on 433,280–558,848 SNPs. Then, we estimated

NUE001, Bronze Age Levant (also for each of the eight archaeologi-

cal sites separately) and Bronze Age Anatolia ancestry components,

adding more proximal Neolithic and Chalcolithic North African and

West Asian populations as potential sources (Morocco_EN_ktg,

Morocco_MN, Anatolia_Neolithic, Anatolia_Chalcolithic, Levant_

Neolithic, Levant_Chalcolithic, Zagros_Neolithic, Zagros_Chalcolithic,

Mesopotamia_Neolithic, Caucasus_Neolithic and Caucasus_Chalco-

lithic) as well as two Neolithic Europeans: Spain_EN and Greece_

Neolithic, referred to as the full qpAdm model. This analysis was con-

ducted over 474,731–578,969 SNPs.

Third Intermediate Period ancestry modelling. We estimated the

ancestry proportions of the two Third Intermediate Period Egyptians

using North African and West Asian populations who lived between

the Old Kingdom and Third Intermediate periods as potential sources

(NUE001, Anatolia_BA, Levant_BA, Iran_BA and Caucasus_BA), as well

as a Bronze Age Greek population (Greece_Minoan). We also added

Morocco_MN and Mesopotamia_N to test whether the Third Intermedi-

ate Period Egyptians share a closer ancestry with NUE001 or a source

more related to one of these two ancestries present in NUE001. This

analysis was conducted on 290,262 SNPs.

Present-day Egyptian genome ancestry modelling. We directly

estimated the proportion of NUE001 ancestry in present-day Egyp-

tians

164

as a whole or each individual separately, as well as ancestries

from North African (Morocco_MN), West Asian (Caucasus_BA, Iran_BA

and Levant_BA) and European (Greece_Minoan) populations, as well

as East and West Africa (Ethiopia_4500BP.SG and Congo_Kindoki_

Protohistoric). For each region, we selected the representatives clos-

est to NUE001’s lifetime. Anatolia_BA was removed from the list of

West Asian groups because its inclusion led to a substantial drop-off

of genomes having at least one model passing P=0.05. This analysis

was conducted on 767,305 SNPs.

Ancient East African ancestry modelling. We estimated the

ancestry proportion in ancient East African

43,54,55,144

using both

NUE001 and Levantine Chalcolithic genomes as competing sources

for the Eurasian-like component. We used as potential left sources

NUE001, Levant_Chalcolithic, Ethiopia_4500BP.SG, Dinka.DG, Congo_

Kindoki_Protohistoric and South_Africa_2200BP.SG. For this model,

the following fixed right groups were used: Chimp.REF, Latvia_HG_

UDG, USA_Ancient_Beringian.SG, Vanuatu_400BP_UDG, Japan_HG_

Jomon_UDG and China_NEastAsia_Coastal_EN_UDG. This analysis

was conducted on 141,323–350,110 SNPs.

statistics

statistics of the form f

(NUE001, Morocco_MN; X, Ju_hoan_North.

DG) and f

(NUE001, Morocco_MN; Mesopotamia_N, X), X being the

non-North African groups used in the full qpAdm model, Palaeolithic

Levant or Palaeolithic Anatolia, were estimated to confirm the probable

source of admixture in the Nuwayrat genome when compared with the

Middle Neolithic Moroccan group. f

statistics was computed using

ADMIXTOOLS 2 (ref.42) with the option maxmiss=0.1. We restricted

the analysis to genomes with both transitions and transversions (half/

plus UDG-treated libraries or single-stranded libraries called using

SequenceTools

115

--singleStrandMode). This analysis was conducted

on the 1240k dataset on 280,544 SNPs.

Imputation

The genotypes of the Nuwayrat genome were imputed together with

200 ancient genomes from North Africa and West Asia associated with

the Palaeolithic, Neolithic and Bronze Age culture (Supplementary

Table3). We restricted the imputation to whole-genome sequencing

data greater than 0.5× coverage or 1240k SNP capture data greater than

2× coverage, following recommendations from Sousa da Mota etal.

172

First, we called genotypes using bcftools v.1.19 (ref.173) with the

commands bcftools mpileup with parameters -I -E -a ‘FORMAT/DP’

--ignore-RG and bcftools call -Aim -C alleles. We then imputed the miss-

ing genotypes using Glimpse v.1.1.0 (ref.174). First, we used GLIMPSE_

chunk to split chromosomes into chunks of 2Mb and with a 200-kb

buffer region. Second, imputation was performed with GLIMPSE_

phase on the chunks with default parameters --burn 10, --main 10 and

--pbwt-depth 2, with 1000 Genomes

175

as the reference panel. We then

ligated the imputed chunks with GLIMPSE_ligate.

To remove transitions caused by post-mortem damage before

imputation, for the genomes generated with UDG treatment, we

first hard-trimmed the first and last three base pairs of each read and

removed CpG sites, and for the genome generated without UDG treat-

ment, we removed all transition sites after SNP calling.

We finally restricted the imputed genotypes to those with geno-

type probability ≥0.99 and minor allele frequency ≥0.01 using the

command bcftools filter -i ‘MAX(FORMAT/GP)>=0.99 && INFO/

RAF>=0.01&&INFO/RAF<=0.99’ --set-GTs ‘.’.

The imputed dataset was used for phenotype prediction (see below)

and admixture dating using DATES (Supplementary Information

section4 and Supplementary Table11).

Phenotype prediction

The genotypes responsible for skin, hair and eye colour prediction

were investigated using the HIrisPlex-S system

176–178

using the imputed

genotypes.

Reporting summary

Further information on research design is available in theNature Port-

folio Reporting Summary linked to this article.

Data availability

All mapped sequence data generated for this project are available

from the European Nucleotide Archive under the study accession no.

PRJEB88328.

63. Dabney, J. etal. Complete mitochondrial genome sequence of a Middle Pleistocene

cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110,

15758–15763 (2013).

Article

64. Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex

sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

65. Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated

preparation of single-stranded DNA libraries for the sequencing of DNA from ancient

biological remains and other sources of highly degraded DNA. Nat. Protoc. 15,

2279–2300 (2020).

66. Dee, M. C14 data pottery cofin burial excavated by Garstang in Nuwayrat (World

Museum, Liverpool, UK, 2016).

67. Vanthuyne, B. Early Old Kingdom Rock Circle Cemeteries in the 15th and 16th Nomes

of Upper Egypt. A Socio-archaeological Investigation of the Cemeteries in Dayr

al-Barshā, Dayr Abū

Ḥinnis, Benī Ḥasan al-Shurūq and Nuwayrāt. PhD thesis, KU

Leuven (2017).

68. Bronk Ramsey, C. Oxcal v.4.4.4 calibration program (2021); https://c14.arch.ox.ac.uk/

oxcal.html.

69. Reimer, P. J. etal. The IntCal20 Northern Hemisphere radiocarbon age calibration curve

(0–55 cal kBP). Radiocarbon 62, 725–757 (2020).

70. Ramsey, C. B. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

71. Bayliss, A. & Marshall, P. Radiocarbon Dating and Chronological Modelling: Guidelines

and Best Practice (Historical Association, 2022).

72. Brown, T. A., Nelson, D. E., Vogel, J. S. & Southon, J. R. Improved collagen extraction by

modiied Longin method. Radiocarbon 30, 171–177 (1988).

73. Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230,

241–242 (1971).

74. Scorrer, J. etal. Diversity aboard a Tudor warship: investigating the origins of the Mary

Rose crew using multi-isotope analysis. R. Soc. Open Sci. 8, 202106 (2021).

75. Coplen, T. B. Normalization of oxygen and hydrogen isotope data. Chem. Geol. 72,

293–297 (1988).

76. Chenery, C. A., Pashley, V., Lamb, A. L., Sloane, H. J. & Evans, J. A. The oxygen isotope

relationship between the phosphate and structural carbonate fractions of human

bioapatite. Rapid Commun. Mass Spectrom. 26, 309–319 (2012).

77. Font, L., Nowell, G. M., Graham Pearson, D., Ottley, C. J. & Willis, S. G. Sr isotope analysis

of bird feathers by TIMS: a tool to trace bird migration paths and breeding sites.

J. Anal. At. Spectrom. 22, 513 (2007).

78. Nier, A. O. The isotopic constitution of strontium, barium, bismuth, thallium and mercury.

Phys. Rev. 54, 275–278 (1938).

79. Avanzinelli, R., Conticelli, S. & Francalanci, L. High precision Sr, Nd, and Pb isotopic

analyses using the new generation Thermal Ionisation Mass Spectrometer

ThermoFinnigan Triton-Ti®. Periodico di Mineralogia 74, 147–166 (2015).

80. Ican, M. Y., Loth, S. R. & Wright, R. K. Age estimation from the rib by phase analysis: white

females. J. Forensic Sci. 30, 853–863 (1985).

81. Ican, M. Y. & Loth, S. R. Determination of age from the sternal rib in white males: a test of

the phase method. J. Forensic Sci. 31, 122–132 (1986).

82. Meindl, R. S. & Lovejoy, C. O. Ectocranial suture closure: a revised method for the

determination of skeletal age at death based on the lateral-anterior sutures. Am. J. Phys.

Anthropol. 68, 57–66 (1985).

83. Lovejoy, C. O., Meindl, R. S., Pryzbeck, T. R. & Mensforth, R. P. Chronological

metamorphosis of the auricular surface of the ilium: a new method for the determination

of adult skeletal age at death. Am. J. Phys. Anthropol. 68, 15–28 (1985).

84. Brooks, S. & Suchey, J. M. Skeletal age determination based on the os pubis: a

comparison of the Acsádi-Nemeskéri and Suchey-Brooks methods. Hum. Evol. 5, 227–238

(1990).

85. Trotter, M. & Gleser, G. C. Estimation of stature from long bones of American whites and

Negroes. Am. J. Phys. Anthropol. 10, 463–514 (1952).

86. Robins, G. & Shute, C. C. D. Predynastic Egyptian stature and physical proportions.

Hum. Evol. 1, 313–324 (1986).

87. Bass, W. M. Human Osteology: A Laboratory and Field Manual (Missouri Archaeological

Society, 2006).

88. Richard Scott, G. & Irish, J. D. Human Tooth Crown and Root Morphology (Cambridge Univ.

Press, 2017).

89. Howells, W. W. Skull Shapes and the Map: Craniometric Analyses in the Dispersion of

Modern Homo, Vol. 79 (Harvard Univ. Press, 1989) .

90. Scott, G. R. etal. rASUDAS: a new web-based application for estimating ancestry from

tooth morphology. Forensic Anthropol. 1, 18–31 (2018).

91. Wright, R. Guide to Using the CRANID Programs Cr6bInd: For Linear and Nearest

Neighbours Discriminant Analysis (2012); http://www.scribd.com/document/324417767/

CRANID6b-ManuaL-1-pdf

92. Ortner, D. J. & Putschar, W. Identiication of Paleopathological Conditions in Human

Skeletal Remains (Smithsonian Institution, 1985).

93. Aufderheide, A. C. & Rodríguez-Martín, C. The Cambridge Encyclopedia of Human

Paleopathology (Cambridge Univ. Press, 1998).

94. Hawkey, D. E. & Merbs, C. F. Activity‐induced musculoskeletal stress markers (MSM) and

subsistence strategy changes among ancient Hudson Bay Eskimos. Int. J. Osteoarchaeol.

5, 324–338 (1995).

95. Alves-Cardoso, F. & Assis, S. Exploring ‘wear and tear’ of joints and ‘muscle function’

assumptions in skeletons with known occupation at death. Am. J. Phys. Anthropol. 175,

689–700 (2021).

96. Wallace, I. J. etal. Experimental evidence that physical activity inhibits osteoarthritis:

implications for inferring activity patterns from osteoarthritis in archeological human

skeletons. Am. J. Biol. Anthropol. 177, 223–231 (2022).

97. Wilkinson, C. M. & Mahoney, G. in Craniofacial Identiication (eds Wilkinson, C. M.

& Rynn, C.) 222–237 (Cambridge Univ. Press, 2012).

98. El-Mehallawi, I. H. & Soliman, E. M. Ultrasonic assessment of facial soft tissue thicknesses

in adult Egyptians. Forensic Sci. Int. 117, 99–107 (2001).

99. Wilkinson, C. M. Facial reconstruction—anatomical art or artistic anatomy? J. Anat. 216,

235–250 (2010).

100. Rynn, C., Balueva, T. & Veselovskaya, E. in Craniofacial Identiication (eds Wilkinson, C. M. &

Rynn, C.) 193–202 (Cambridge Univ. Press, 2012).

101. Wilkinson, C. M. Cognitive bias and facial depiction from skeletal remains.

Bioarchaeology Int. 4, 1–14 (2021).

102. Swali, P. etal. Yersinia pestis genomes reveal plague in Britain 4000 years ago.

Nat. Commun. 14, 2930 (2023).

103. Fellows Yates, J. A. etal. Reproducible, portable, and eficient ancient genome

reconstruction with nf-core/eager. PeerJ 9, e10947 (2021).

104. Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming,

identiication, and read merging. BMC Res. Notes 9, 88 (2016).

105. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler

transform. Bioinformatics 26, 589–595 (2010).

106. Meyer, M. etal. A high-coverage genome sequence from an archaic Denisovan individual.

Science 338, 222–226 (2012).

107. Peltzer, A. etal. EAGER: eficient ancient genome reconstruction. Genome Biol. 17, 60

(2016).

108. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0:

fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics

29, 1682–1684 (2013).

109. Meyer, M. etal. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos

hominins. Nature 531, 504–507 (2016).

110. Skoglund, P. etal. Separating endogenous ancient DNA from modern day contamination

in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014).

111. Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and

endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224

(2015).

112. Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation

sequencing data. BMC Bioinf. 15, 356 (2014).

113. Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identiication of

ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482

(2013).

114. Li, H. etal. The sequence alignment/map format and SAMtools. Bioinformatics 25,

2078–2079 (2009).

115. Schiffels, S. SequenceTool. https://github.com/stschiff/sequenceTools (2022).

116. Briggs, A. W. etal. Removal of deaminated cytosines and detection of invivo methylation

in ancient DNA. Nucleic Acids Res. 38, e87–e87 (2010).

117. Schönherr, S., Weissensteiner, H., Kronenberg, F. & Forer, L. Haplogrep3—an interactive

haplogroup classiication and analysis platform. Nucleic Acids Res. 51, W263–W268

(2023).

118. Martiniano, R., De Sanctis, B., Hallast, P. & Durbin, R. Placing ancient DNA sequences into

reference phylogenies. Mol. Biol. Evol. 39, msac017 (2022).

119. Allentoft, M. E. etal. Population genomics of Bronze Age Eurasia. Nature 522, 167–172

(2015).

120. Altınıık, N. E. etal. A genomic snapshot of demographic and cultural dynamism in Upper

Mesopotamia during the Neolithic Transition. Sci. Adv. 8, eabo3609 (2022).

121. Antonio, M. L. etal. Ancient Rome: a genetic crossroads of Europe and the Mediterranean.

Science 366, 708–714 (2019).

122. Broushaki, F. etal. Early Neolithic genomes from the eastern Fertile Crescent. Science

353, 499–503 (2016).

123. Clemente, F. etal. The genomic history of the Aegean palatial civilizations. Cell 184,

2565–2586.e21 (2021).

124. de Barros Damgaard, P. etal. The irst horse herders and the impact of early Bronze Age

steppe expansions into Asia. Science 360, eaar7711 (2018).

125. Damgaard, P. etal. 137 ancient human genomes from across the Eurasian steppes. Nature

557, 369–374 (2018).

126. Feldman, M. etal. Late Pleistocene human genome suggests a local origin for the irst

farmers of central Anatolia. Nat. Commun. 10, 1218 (2019).

127. Fregel, R. etal. Ancient genomes from North Africa evidence prehistoric migrations to

the Maghreb from both the Levant and Europe. Proc. Natl Acad. Sci. USA 115, 6774–6779

(2018).

128. Fu, Q. etal. Genome sequence of a 45,000-year-old modern human from western

Siberia. Nature 514, 445–449 (2014).

129. Fu, Q. etal. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

130. Gokhman, D. etal. Differential DNA methylation of vocal and facial anatomy genes in

modern humans. Nat. Commun. 11, 1189 (2020).

131. Haber, M. etal. A transient pulse of genetic admixture from the crusaders in the near east

identiied from ancient genome sequences. Am. J. Hum. Genet. 104, 977–984 (2019).

132. Haber, M. etal. A genetic history of the near east from an aDNA time course sampling

eight points in the past 4,000 years. Am. J. Hum. Genet. 107

, 149–157 (2020).

133. Hajdinjak, M. etal. Initial Upper Palaeolithic humans in Europe had recent Neanderthal

ancestry. Nature 592, 253–257 (2021).

134. Jones, E. R. etal. Upper Palaeolithic genomes reveal deep roots of modern Eurasians.

Nat. Commun. 6, 8912 (2015).

135. Kılınç, G. M. etal. The demographic development of the irst farmers in Anatolia.

Curr. Biol. 26, 2659–2666 (2016).

136. Lazaridis, I. etal. A genetic probe into the ancient and medieval history of Southern

Europe and West Asia. Science 377, 940–951 (2022).

137. Lazaridis, I. etal. The genetic history of the Southern Arc: a bridge between West Asia and

Europe. Science 377, eabm4247 (2022).

138. Lazaridis, I. etal. Genetic origins of the Minoans and Mycenaeans. Nature 548, 214–218

(2017).

139. Mathieson, I. etal. Genome-wide patterns of selection in 230 ancient Eurasians. Nature

528, 499–503 (2015).

140. Narasimhan, V. M. etal. The formation of human populations in South and Central Asia.

Science 365, eaat7487 (2019).

141. Lazaridis, I. etal. Ancient human genomes suggest three ancestral populations for

present-day Europeans. Nature 513, 409–413 (2014).

142. Lipson, M. etal. Parallel palaeogenomic transects reveal complex genetic history of early

European farmers. Nature 551, 368–372 (2017).

143. Lipson, M. etal. Ancient West African foragers in the context of African population history.

Nature 577, 665–670 (2020).

144. Lipson, M. etal. Ancient DNA and deep population structure in sub-Saharan African

foragers. Nature 603, 290–296 (2022).

145. Mathieson, I. etal. The genomic history of southeastern Europe. Nature 555, 197–203 (2018).

146. McColl, H. etal. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018).

147. Omrak, A. etal. Genomic evidence establishes Anatolia as the source of the European

Neolithic gene pool. Curr. Biol. 26, 270–275 (2016).

148. Patterson, N. etal. Large-scale migration into Britain during the Middle to Late Bronze

Age. Nature 601, 588–594 (2022).

149. Raghavan, M. etal. Upper Palaeolithic Siberian genome reveals dual ancestry of native

Americans. Nature 505, 87–91 (2014).

150. Rodríguez-Varela, R. etal. Genomic analyses of pre-European conquest human remains

from the Canary Islands reveal close afinity to modern North Africans. Curr. Biol. 28,

1677–1679 (2018).

151. 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).

152. Seguin-Orlando, A. etal. Genomic structure in Europeans dating back at least 36,200 years.

Science 346, 1113–1118 (2014).

153. Sirak, K. A. etal. Social stratiication without genetic differentiation at the site of

Kulubnarti in Christian Period Nubia. Nat. Commun. 12, 7283 (2021).

154. van de Loosdrecht, M. etal. Pleistocene North African genomes link Near Eastern and

sub-Saharan African human populations. Science 360, 548–552 (2018).

155. Yaka, R. etal. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

Curr. Biol. 31, 2455–2468.e18 (2021).

156. Yang, M. A. etal. 40,000-year-old individual from Asia provides insight into early population

structure in Eurasia. Curr. Biol. 27, 3202–3208.e9 (2017).

157. Wang, C.-C. etal. Ancient human genome-wide data from a 3000-year interval in the

Caucasus corresponds with eco-geographic regions. Nat. Commun. 10, 1–13 (2019).

158. Wang, C.-C. etal. Genomic insights into the formation of human populations in East Asia.

Nature 591, 413–419 (2021).

159. Yang, M. A. etal. Ancient DNA indicates human population shifts and admixture in northern

and southern China. Science 369, 282–288 (2020).

160. Hofmanová, Z. etal. Early farmers from across Europe directly descended from Neolithic

Aegeans.Proc. Natl Acad. Sci. USA 113, 6886–6891 (2016).

161. Flegontov, P. etal. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and

North America. Nature 570, 236–240 (2019).

162. Jeong, C. etal. The genetic history of admixture across inner Eurasia. Nat. Ecol. Evol. 3,

966–976 (2019).

163. Mallick, S. etal. The Simons Genome Diversity Project: 300 genomes from 142 diverse

populations. Nature 538, 201–206 (2016).

164. Pagani, L. etal. Tracing the route of modern humans out of Africa by using 225 human

genome sequences from Ethiopians and Egyptians. Am. J. Hum. Genet. 96, 986–991 (2015).

165. Pickrell, J. K. etal. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).

166. Skoglund, P. etal. Genomic insights into the peopling of the Southwest Paciic. Nature

538, 510–513 (2016).

167. Vyas, D. N., Al-Meeri, A. & Mulligan, C. J. Testing support for the northern and southern

dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations.

Am. J. Phys. Anthropol. 164, 736–749 (2017).

168. Biagini, S. A. etal. People from Ibiza: an unexpected isolate in the Western Mediterranean.

Eur. J. Hum. Genet. 27, 941–951 (2019).

169. Patterson, N., Moorjani, P., Luo, Y., Mallick, S. & Rohland, N. Ancient admixture in human

history. Genetics 192, 1065–1093 (2012).

170. Mallick, S. etal. The Allen Ancient DNA Resource (AADR) a curated compendium of

ancient human genomes. Sci. Data 11, 1–10 (2024).

171. Purcell, S. etal. PLINK: a tool set for whole-genome association and population-based

linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

172. Sousa da Mota, B. etal. Imputation of ancient human genomes. Nat. Commun. 14, 3660

(2023).

173. Danecek, P. etal. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008

(2021).

174. Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Eficient phasing and

imputation of low-coverage sequencing data using large reference panels. Nat. Genet.

53, 120–126 (2021).

175. The 1000 Genomes Project Consortium. A global reference for human genetic variation.

Nature 526, 68–74 (2015).

176. Chaitanya, L. etal. The HIrisPlex-S system for eye, hair and skin colour prediction from

DNA: introduction and forensic developmental validation. Forensic Sci. Int. Genet. 35,

123–135 (2018).

177. Walsh, S. etal. Developmental validation of the HIrisPlex system: DNA-based eye and

hair colour prediction for forensic and anthropological usage. Forensic Sci. Int. Genet. 9,

150–161 (2014).

178. Walsh, S. etal. Global skin colour prediction from DNA. Hum. Genet. 136, 847–863 (2017).

Acknowledgements A.M.J. was supported by ECR strategic support of early career researchers

in the faculty of science at Liverpool John Moores University, awarded to L.G.-F., andEuropean

Research Council grant no. 852558, awarded to P.S. Open Access funding was provided

by Liverpool John Moores University. This study was supported by the European Research

Council (grant no. 852558 to P.S.). L.S. was supported by a Sir Henry Wellcome Fellowship

(220457/Z/20/Z). P.S. was supported by the European Molecular Biology Organization, the

Vallee Foundation, the Wellcome Trust (217223/Z/19/Z) and The Francis Crick Institute core

funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the

Wellcome Trust. We thanktheGenomics Science Technology Platform at the Francis Crick

Institute for technical assistance.We thank M. Dee (University of Groningen) for providing

advice and support on how to combinethe three radiocarbon dates generated from the

Nuwayrat skeletal remains and M. Stratigos (University of Aberdeen) for useful discussions

about radiocarbon modelling and collagen decay. We are grateful to A. Eladany (University

of Aberdeen) for sharing valuable knowledge on Egyptian archaeology and ethical

recommendations, and B. Vanthuyne (University of Cologne) for sharing literature on the

archaeological site. Liverpool John Moores University colleagues, M. Borrini, C. Eliopoulos,

J. Ohman and A. Wilshaw, provided advice on the osteological proile. We also appreciate the

advice from J. Kabaciński (Polish Academy of Sciences, Poznań Branch).

Author contributions A.M.J., J.D.I., P.S. and L.G.-F. contributed to the conception and design

of the study. A.M.J. and L.G.-F. selected and sampled archaeological material for DNA

extraction. A.M.J., K.A., M.K., F.T., M.W. and M.H. performed DNA laboratory work. A.M.J., C.B.

and A.G. analysed the genetic data. J.D.I. performed osteological analyses. A.C. provided the

archaeological context and interpretation. R.M., E.H., A.J.N. and E.I. performed isotope analysis

and interpretation. C.W. provided facial reconstruction. A.M.J., J.D.I., P.S. and L.G.-F. wrote the

paper with substantial inputs from A.C., K.A., C.B., M.S., L.S., F.T., N.B., F.-X.R., C.W. and M.H.

Competing interests The authors declare no competing interests.

Additional information

Supplementary information The online version contains supplementary material available at

https://doi.org/10.1038/s41586-025-09195-5.

Correspondence and requests for materials should be addressed to Adeline Morez Jacobs,

Pontus Skoglund or Linus Girdland-Flink.

Peer review information Nature thanks Daniel Antoine, Elisabetta Boaretto and the other,

anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer

reports are available.

Reprints and permissions information is available at http://www.nature.com/reprints.

Article

Extended Data Fig. 1 | Archaeological context at the Nuwayrat site.

a, Rock-cut tombs at Nuwayrat enclosing the pottery vessel containing the

pottery coffin burial. b, An impression of the rock-cut tomb based on the

archaeologist John Garstang’s description, with the pottery coffin burial in the

south burial chamber. c, Pottery coffin and archaeological remains of the

Nuwayrat individual, as discovered in 1902. Photos in a and c reproduced

courtesy of the Garstang Museum of Archaeology, University of Liverpool.

Extended Data Fig. 2 | Facial reconstruction and depiction created from the Nuwayrat individual skull. a, Final facial depiction of the Nuwayrat individual.

b, Virtual fit of the skull and facial reconstruction. c, The Nuwayrat individual’s partially complete skeleton.

Article

Extended Data Fig. 3 | Damage patterns at the 5′ end of the reads in each

sequencing run from the Nuwayrat individual. All sequencing runs but one

show a significant increase of C-to-T transitions at the 5 end of DNA fragments,

indicative of authentic ancient DNA.

Extended Data Fig. 4 | ADMIXTURE clustering analysis of the Old Kingdom

Egyptian genome in the context of ancient genomes (K = 3 to 20). ADMIXTURE

was generated on 4,574 present-day and ancient genomes from the ‘HO’ dataset

(Supplementary Data Table3), over 71,202 transversion SNPs. ADMIXTURE

output on the present-day genomes are displayed in Extended Data Fig.5.

Article

Extended Data Fig. 5 | ADMIXTURE clustering analysis of the Old Kingdom

Egyptian genome in the context of present-day genomes (K = 3 to 20).

ADMIXTURE was generated on 4,574 present-day and ancient genomes from

the ‘HO’ dataset (Supplementary Data Table3), over 71,202 transversion SNPs.

ADMIXTURE output on the ancient genomes are displayed in Extended Data

Fig.4.

Extended Data Fig. 6 | Distal ancestries in the Nuwayrat genome and

contemporary groups. The model included Epipaleolithic/Neolithic groups

from North Africa and West Asia as rotating sources in qpAdm (Morocco_

Epipaleolithic, Anatolia_Neolithic, Levant_Neolithic, Zagros_Neolithic,

Caucasus_Neolithic). Details of all models passing p>0.05 are displayed in

Supplementary Data Table5. Values represent best-fitting model estimates ± 1

SE (error bars). This analysis was conducted over n=515,802 SNPs for NUE001,

n=558,549 SNPs for Morocco_MN, n=558,847 SNPs for Levant_BA, and

n=558,848 SNPs for Anatolia_BA.

Article

Extended Data Fig. 7 | Ancestry modelling of ancient East African genomes

with qpAdm. Best-fit models are represented. Details of all models passing

p>0.05 are described in Supplementary Data Table12. N, Neolithic; IA, Iron

Age; EIA, Early iron Age; LIA, Late Iron Age; LSA, Late Stone Age. Values

represent best-fitting model estimates ± 1 SE (error bars). This analysis was

conducted over 141,323-350,110 SNPs (see Supplementary Data Table12).

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Here is a summary article about this individual and story: https://www.nationalgeographic.com/history/article/ancient-egyptian-genome Background on Mesopotamia: https://en.wikipedia.org/wiki/History_of_Mesopotamia > "Although we caution that these results are based on a single Egyptian genome, they mirror another study that found evidence of gene flow from the Mesopotamian and Zagros regions into surrounding areas, including Anatolia, during the Neolithic. Together with archaeological evidence for cultural exchange, these findings open the possibility that wider cultural and demographic expansion originating in the Mesopotamian region reached both Egypt and Anatolia during this period." > "Our results demonstrate the feasibility of ancient genome sequencing from the earliest stages of the Egyptian Dynastic civilization. One possible explanation for the successful whole-genome retrieval is the pot burial, which may have favoured a degree of DNA preservation not previously reported in Egypt. This contributes to the road map for future research to obtain ancient DNA from Egypt. Although our analyses are limited to a single Egyptian individual who, on the basis of his relatively high-status burial, may not be representative of the general population, our results revealed ancestry links to earlier North African groups and populations of the eastern Fertile Crescent. Analogous links were indicated in our biological affinity analyses of dental traits and craniometrics of the Nuwayrat individual, as well as in previous morphological studies based on full samples." > "This genetic affinity is similar to the ancestry appearing in Anatolia and the Levant during the Neolithic and Bronze Age. Although more genomes are needed to fully understand the genomic diversity of early Egyptians, our results indicate that contacts between Egypt and the eastern Fertile Crescent were not limited to objects and imagery (such as domesticated animals and plants, as well as writing systems) but also encompassed human migration."

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