Ancient Egypt, Sudan, North Africa? Will there be any results from these areas?

[Andriy]

I mean in the Near future?

[David Bush]

From Egypt
yes
coming soon

[Philjames]

From Egypt
yes
coming soon

How do you know?

[David Bush]

How do you know?

https://isba9.sciencesconf.org/data/...ISBA9_2022.pdf


The Enigma of Hyksos: An ancient DNA study

Saupe Tina (1, 2), Guellil Meriam (2), Niinemäe Helja (2), Stantis Chris (3),
Scheib Christiana L. (2)
1 - Department of Evolutionary Biology, Institute of Molecular and Cell Biology,
University of Tartu, Tartu, Estonia (Estonia), 2 - Estonian Biocentre, Institute of
Genomics, University of Tartu, Tartu, Estonia (Estonia), 3 - Faculty of Science and
Technology, Department of Archaeology and Anthropology, Bournemouth University,
Dorset, UK (United Kingdom)
The Second Intermediate Period (~1640-1530 BCE) signalised a time of change in
Egyptian history. It was marked by the occupation of Egypt by foreign rulers, known
as the Hyksos, who left their marks on Egyptian culture well beyond the New
Kingdom. While previous studies have pointed to a Western Asian origin for the
Hyksos, potentially in the Levant (Schuenemann et al. 2017), the actual geographical
and genetic origin of the Egyptian conquerors remains unknown. Here, we present
the first full human mitochondrial genomes from the archaeological site of Tell el
Dab'a in the Eastern Nile Delta (Egypt), where the capital of Hyksos once stood, and
whole nuclear and mitochondrial genomes from new sites in the Levant. We
extracted DNA from teeth and petrous bones of 49 individuals in the dedicated
ancient DNA laboratory at the Estonian Biocentre, Institute of Genomics, University of
Tartu, Estonia. After raw data processing, samples (n= 13) with more than 4%
endogenous human content were additionally sequenced to increase coverage, and
samples (n= 16) with a minimum of 0.1% of endogenous human content were
selected for mtDNA target enrichment to generate full mtDNA genomes. We will
analyse our new aDNA data using previously published datasets from the same
geographical region and period to estimate the genetic components and gain new
insights into the Hyksos genetic make-up (Agranat-Tamir et al. 2020; Skourtanioti et
al. 2020).


Insights into ancient Egyptian genomes in the first Millennium BC

Salem Nada (1), Gnecchi Ruscone Guido Alberto (1, 2), Furtwängler Anja (1),
Freund Caecilia (1), Bianco Raffaela (1), Martins Nuno Filipe Gomes (3), Burri
Marta (4), Tiliakou Anthi (1), Spyrou Maria (5), Mötsch Angela (1), Teßmann
Barbara (6), Frenzel Hannah (7), Francken Michael (8), Harvati Katerina (5, 9),
Krause Johannes (1, 2), Stockhammer Philipp W. (1, 10)
1 - Department of Archaeogenetics, Max Planck Institute for the Science of Human
History, Jena (Germany), 2 - Max Planck Institute for Evolutionary Anthropology,
Leipzig, (Germany), 3 - Evolutionary Genomics Section, GLOBE Institute, University
of Copenhagen, Copenhagen (Denmark), 4 - Swiss Ornithological Institute, Sempach,
(Switzerland), 5 - Institute for Archaeological Sciences (INA), University of Tübingen,
Tübingen (Germany), 6 - Berlin society of Anthropology, Ethnology and Prehistory,
Berlin, (Germany), 7 - Institute of Anatomy, Leipzig University, Leipzig (Germany), 8 -
Cultural Heritage Management, Government office of Stuttgart, Baden Württemberg
(Germany), 9 - Senckenberg Centre for Human Evolution and Palaeoenvironment,
University of Tübingen, Tübingen (Germany), 10 - Institute for Pre- and Protohistoric
Archaeology and Archaeology of the Roman Provinces, LMU Munich, Munich
(Germany)
Egypt provides a privileged location to study historical population dynamics as it is at
the crossroads between the ancient civilizations in Africa, Asia, and Europe. In the first
millennium BC, ancient Egypt witnessed foreign domination by the neighboring
populations including Libyans, Nubians, Assyrians, Greeks, Romans, and others,
whose roles vary from trade exchange and interaction to invasion and rule. Despite
being potential to addressing questions on the population's demographic, retrieval of102
ancient DNA from the Egyptian mummies has greatly been challenged by the presence
of contamination. Here we report a preliminary, rigorously tested genome-wide dataset
from mummies using high-throughput DNA sequencing and targeted capture
techniques. The individuals in our study are recovered from Upper and Lower Egypt
sites and spanning around 900 years of ancient Egyptian history, from the Third
Intermediate to the Roman period. Our study aims to characterize the major ancestry
components for ancient Egyptians and to explore the genetic continuation and
admixture through times and regions.

Paleogenomic insights into Nubian ancestry from ancient Middle Nile
populations


Breidenstein Abagail (1), Neukamm Judith (1), Barbieri Chiara (2), Ferrari Giada
(3), Gondek-Wyrozemska Agata T. (4), Abdallah Mohammed Saad (5, 6),
Bushara Murtada (6), Stark Robert J. (7), Ciesielska Joanna (8), Obluski Artur
(8), Star Bastiaan (3), Hassan Hisham Yousef (9), Rühli Frank (1), Schuenemann
Verena (1), Bigham Abigail W. (10)
1 - Institute of Evolutionary Medicine (Switzerland), 2 - Department of Evolutionary
Biology and Environmental Studies (Switzerland), 3 - Centre for Ecological and
Evolutionary Synthesis (Norway), 4 - Norwegian College of Fishery Science
(Norway), 5 - Bolheim Bioarchaeology Laboratory (Sudan), 6 - National Corporation
for Antiquities and Museums (Sudan), 7 - McMaster University, Hamilton, Ontario
(Canada), 8 - Polish Centre of Mediterranean Archaeology (Poland), 9 - Banoon ART
& Cytogenetics Centre, Bahrain Defense Force Hospital (Bahrain), 10 - Department
of Anthropology, UCLA (United States)


The kingdoms of Nubia, located in the Nile River Valley of modern-day northern
Sudan and southern Egypt, served as an important corridor of migration for millennia.
Little is known of the ancient genetic landscape, but this biological perspective can
further our understanding of population movements before this event. Here, we
created a time-transect of genetic diversity in the Middle Nile region, using whole
mitochondrial (MT) genome analysis of ancient DNA samples obtained from several
archaeological sites spanning nearly two thousand years, from the Meroitic period
(ca. 350 BCE) to before the Arab expansion (ca. 1450 CE). We trialed 43 individuals,
extracting DNA using newly developed 8, including petrosal bone extraction, nonheat sample processing, enzymatic pretreatments, and DNA capture techniques,
optimized for samples with very poor DNA preservation. Following strict
contamination and authentication assessments, we retrieved whole mitogenomes for
six individuals: two with African ancestry and four with Eurasian ancestry. The
ancient Nubians showed most genetic affinity with modern East Africans, Middle
Easterners, and Egyptians. These results indicate that Nubians had a strong African
component with evidence of gene flow from Eurasia dating back to at least Meroitic
through Christian times. Although these individuals encompass varying
archaeological contexts and span two millennia, these initial results hint at the
complexity of the region's genetic makeup and begin to reconstruct the impact of
migrations from outside Africa. Lastly, our work represents the first successful
retrieval of full MT sequence data from Middle Nile inhabitants, further demonstrating
the viability of paleogenomic work in Sudan.



Human mitochondrial hapologroups and ancient DNA preservation across
Egyptian history

Urban Christian (1), Neukamm Judith (1), Eppenberger Patrick (1), Brändle
Martin (2), Rühli Frank (1), Schuenemann Verena (1)
1 - Institute of Evolutionary Medicine (University of Zurich Switzerland), 2 - Faculty of
Biology, Philipps-Universität Marburg (Germany)
Egypt represents an ideal location for genetic studies on population migration and
admixture due to its geographic location and rich history. However, there are only a
few reliable genetic studies on ancient Egyptian samples. In a previous study, we
assessed the genetic history of a single site: Abusir el-Meleq from 1388 BCE to 426
CE. We now focus on widening the geographic scope to give a general overview of
the population genetic background, focusing on mitochondrial haplogroups present
among the whole Egyptian Nile River Valley. We collected 81 tooth, hair, bone, and
soft tissue samples from 14 mummies and 17 skeletal remains. The samples span
approximately 4000 years of Egyptian history and originate from six different
excavation sites covering the whole length of the Egyptian Nile River Valley. NGS127
based ancient DNA 8 were applied to reconstruct 18 high-quality mitochondrial
genomes from 10 different individuals. The determined mitochondrial haplogroups
match the results from our Abusir el-Meleq study. Our results indicate very low rates
of modern DNA contamination independent of the tissue type. Although authentic
ancient DNA was recovered from different tissues, a reliable recovery was best
achieved using teeth or petrous bone material. Moreover, the rate for successful
ancient DNA retrieval between Egyptian mummies and skeletal remains did not differ
significantly. Our study provides preliminary insights into population history across
different regions and compares tissue-specific DNA preservation for mummies and
skeletal remains from the Egyptian Nile River Valley

[drobbah]

If all those studies come out in 2023, that would be huge for those of us with ancestry primarily from NE Africa.I am particularly interested in the Sudan paper and the paper that has samples from Upper Egypt

[drobbah]

4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists

Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the site of Kadruka. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kilometres away. Our findings support established models for the southwards dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide the first direct evidence for a genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.

[Qrts]

The Enigma of Hyksos: An ancient DNA study

Saupe Tina (1, 2), Guellil Meriam (2), Niinemäe Helja (2), Stantis Chris (3),
Scheib Christiana L. (2)

There's a newer, more detailed abstract for this study:

https://submissions.e-a-a.org/eaa202...?Abstract=2459
New genomic evidence of a Bronze Age Levantine-Egyptian Nexus

West Asia, especially the Eastern Mediterranean coast (also known as the Levant), has played its role in the migration history of humans as the bridge between Europe, Asia, and Africa. During the Bronze Age (~3500-1150 BCE), groups from the Levant started to move towards Northern Africa and with the beginning of the 2nd Intermediate Period (~1640-1530 BCE), one particular group, known as the Hyksos, ruled the northeastern region of the Nile Delta sharing their cultural artefacts such as ceramics and burial practices with locals in Ancient Egypt and leaving their marks on the Egyptian culture. While previous studies have pointed to a “Levantine” origin of the Hyksos, the actual geographical and genetic origin remains debated.
To investigate the presence of the “Levantine” ancestral component and the connectedness between genetic data and shared burial practices, we extracted DNA of human skeletal elements at the dedicated ancient DNA laboratory at the Institute of Genomics, Tartu (Estonia) of ancient individuals dated to the Late Middle Bronze Age from six archaeological sites geographically located in the Levant ((Pella (Jordan), Jericho (Palestine), Tell Mozan and Umm el-Marra (Syria)) and Egypt (Tell el-Dabca). We generated genome-wide data of 16 ancient individuals from the Levant with an average genomic coverage between 0.004× and 0.048× (more than 6,000 single nucleotide polymorphisms (SNPs)) and were able to obtain partial and fully covered mitogenomes of 25 ancient individuals using mitochondrial DNA target enrichment via hybridisation capture.
We compared the first preliminary genetic results of the newly generated dataset with published available data and found a genetic overlap in the Levant with present-day individuals indicating a stable ancestral composition. We further plan to investigate the genetic impact of the “Levantine” component in the ancient and present-day individuals from Egypt and find a presence of the legacy of the Hyksos.

[Andriy]

https://isba9.sciencesconf.org/data/...ISBA9_2022.pdf


The Enigma of Hyksos: An ancient DNA study

Saupe Tina (1, 2), Guellil Meriam (2), Niinemäe Helja (2), Stantis Chris (3),
Scheib Christiana L. (2)
1 - Department of Evolutionary Biology, Institute of Molecular and Cell Biology,
University of Tartu, Tartu, Estonia (Estonia), 2 - Estonian Biocentre, Institute of
Genomics, University of Tartu, Tartu, Estonia (Estonia), 3 - Faculty of Science and
Technology, Department of Archaeology and Anthropology, Bournemouth University,
Dorset, UK (United Kingdom)
The Second Intermediate Period (~1640-1530 BCE) signalised a time of change in
Egyptian history. It was marked by the occupation of Egypt by foreign rulers, known
as the Hyksos, who left their marks on Egyptian culture well beyond the New
Kingdom. While previous studies have pointed to a Western Asian origin for the
Hyksos, potentially in the Levant (Schuenemann et al. 2017), the actual geographical
and genetic origin of the Egyptian conquerors remains unknown. Here, we present
the first full human mitochondrial genomes from the archaeological site of Tell el
Dab'a in the Eastern Nile Delta (Egypt), where the capital of Hyksos once stood, and
whole nuclear and mitochondrial genomes from new sites in the Levant. We
extracted DNA from teeth and petrous bones of 49 individuals in the dedicated
ancient DNA laboratory at the Estonian Biocentre, Institute of Genomics, University of
Tartu, Estonia. After raw data processing, samples (n= 13) with more than 4%
endogenous human content were additionally sequenced to increase coverage, and
samples (n= 16) with a minimum of 0.1% of endogenous human content were
selected for mtDNA target enrichment to generate full mtDNA genomes. We will
analyse our new aDNA data using previously published datasets from the same
geographical region and period to estimate the genetic components and gain new
insights into the Hyksos genetic make-up (Agranat-Tamir et al. 2020; Skourtanioti et
al. 2020).


Insights into ancient Egyptian genomes in the first Millennium BC

Salem Nada (1), Gnecchi Ruscone Guido Alberto (1, 2), Furtwängler Anja (1),
Freund Caecilia (1), Bianco Raffaela (1), Martins Nuno Filipe Gomes (3), Burri
Marta (4), Tiliakou Anthi (1), Spyrou Maria (5), Mötsch Angela (1), Teßmann
Barbara (6), Frenzel Hannah (7), Francken Michael (8), Harvati Katerina (5, 9),
Krause Johannes (1, 2), Stockhammer Philipp W. (1, 10)
1 - Department of Archaeogenetics, Max Planck Institute for the Science of Human
History, Jena (Germany), 2 - Max Planck Institute for Evolutionary Anthropology,
Leipzig, (Germany), 3 - Evolutionary Genomics Section, GLOBE Institute, University
of Copenhagen, Copenhagen (Denmark), 4 - Swiss Ornithological Institute, Sempach,
(Switzerland), 5 - Institute for Archaeological Sciences (INA), University of Tübingen,
Tübingen (Germany), 6 - Berlin society of Anthropology, Ethnology and Prehistory,
Berlin, (Germany), 7 - Institute of Anatomy, Leipzig University, Leipzig (Germany), 8 -
Cultural Heritage Management, Government office of Stuttgart, Baden Württemberg
(Germany), 9 - Senckenberg Centre for Human Evolution and Palaeoenvironment,
University of Tübingen, Tübingen (Germany), 10 - Institute for Pre- and Protohistoric
Archaeology and Archaeology of the Roman Provinces, LMU Munich, Munich
(Germany)
Egypt provides a privileged location to study historical population dynamics as it is at
the crossroads between the ancient civilizations in Africa, Asia, and Europe. In the first
millennium BC, ancient Egypt witnessed foreign domination by the neighboring
populations including Libyans, Nubians, Assyrians, Greeks, Romans, and others,
whose roles vary from trade exchange and interaction to invasion and rule. Despite
being potential to addressing questions on the population's demographic, retrieval of102
ancient DNA from the Egyptian mummies has greatly been challenged by the presence
of contamination. Here we report a preliminary, rigorously tested genome-wide dataset
from mummies using high-throughput DNA sequencing and targeted capture
techniques. The individuals in our study are recovered from Upper and Lower Egypt
sites and spanning around 900 years of ancient Egyptian history, from the Third
Intermediate to the Roman period. Our study aims to characterize the major ancestry
components for ancient Egyptians and to explore the genetic continuation and
admixture through times and regions.

Paleogenomic insights into Nubian ancestry from ancient Middle Nile
populations


Breidenstein Abagail (1), Neukamm Judith (1), Barbieri Chiara (2), Ferrari Giada
(3), Gondek-Wyrozemska Agata T. (4), Abdallah Mohammed Saad (5, 6),
Bushara Murtada (6), Stark Robert J. (7), Ciesielska Joanna (8), Obluski Artur
(8), Star Bastiaan (3), Hassan Hisham Yousef (9), Rühli Frank (1), Schuenemann
Verena (1), Bigham Abigail W. (10)
1 - Institute of Evolutionary Medicine (Switzerland), 2 - Department of Evolutionary
Biology and Environmental Studies (Switzerland), 3 - Centre for Ecological and
Evolutionary Synthesis (Norway), 4 - Norwegian College of Fishery Science
(Norway), 5 - Bolheim Bioarchaeology Laboratory (Sudan), 6 - National Corporation
for Antiquities and Museums (Sudan), 7 - McMaster University, Hamilton, Ontario
(Canada), 8 - Polish Centre of Mediterranean Archaeology (Poland), 9 - Banoon ART
& Cytogenetics Centre, Bahrain Defense Force Hospital (Bahrain), 10 - Department
of Anthropology, UCLA (United States)


The kingdoms of Nubia, located in the Nile River Valley of modern-day northern
Sudan and southern Egypt, served as an important corridor of migration for millennia.
Little is known of the ancient genetic landscape, but this biological perspective can
further our understanding of population movements before this event. Here, we
created a time-transect of genetic diversity in the Middle Nile region, using whole
mitochondrial (MT) genome analysis of ancient DNA samples obtained from several
archaeological sites spanning nearly two thousand years, from the Meroitic period
(ca. 350 BCE) to before the Arab expansion (ca. 1450 CE). We trialed 43 individuals,
extracting DNA using newly developed 8, including petrosal bone extraction, nonheat sample processing, enzymatic pretreatments, and DNA capture techniques,
optimized for samples with very poor DNA preservation. Following strict
contamination and authentication assessments, we retrieved whole mitogenomes for
six individuals: two with African ancestry and four with Eurasian ancestry. The
ancient Nubians showed most genetic affinity with modern East Africans, Middle
Easterners, and Egyptians. These results indicate that Nubians had a strong African
component with evidence of gene flow from Eurasia dating back to at least Meroitic
through Christian times. Although these individuals encompass varying
archaeological contexts and span two millennia, these initial results hint at the
complexity of the region's genetic makeup and begin to reconstruct the impact of
migrations from outside Africa. Lastly, our work represents the first successful
retrieval of full MT sequence data from Middle Nile inhabitants, further demonstrating
the viability of paleogenomic work in Sudan.



Human mitochondrial hapologroups and ancient DNA preservation across
Egyptian history

Urban Christian (1), Neukamm Judith (1), Eppenberger Patrick (1), Brändle
Martin (2), Rühli Frank (1), Schuenemann Verena (1)
1 - Institute of Evolutionary Medicine (University of Zurich Switzerland), 2 - Faculty of
Biology, Philipps-Universität Marburg (Germany)
Egypt represents an ideal location for genetic studies on population migration and
admixture due to its geographic location and rich history. However, there are only a
few reliable genetic studies on ancient Egyptian samples. In a previous study, we
assessed the genetic history of a single site: Abusir el-Meleq from 1388 BCE to 426
CE. We now focus on widening the geographic scope to give a general overview of
the population genetic background, focusing on mitochondrial haplogroups present
among the whole Egyptian Nile River Valley. We collected 81 tooth, hair, bone, and
soft tissue samples from 14 mummies and 17 skeletal remains. The samples span
approximately 4000 years of Egyptian history and originate from six different
excavation sites covering the whole length of the Egyptian Nile River Valley. NGS127
based ancient DNA 8 were applied to reconstruct 18 high-quality mitochondrial
genomes from 10 different individuals. The determined mitochondrial haplogroups
match the results from our Abusir el-Meleq study. Our results indicate very low rates
of modern DNA contamination independent of the tissue type. Although authentic
ancient DNA was recovered from different tissues, a reliable recovery was best
achieved using teeth or petrous bone material. Moreover, the rate for successful
ancient DNA retrieval between Egyptian mummies and skeletal remains did not differ
significantly. Our study provides preliminary insights into population history across
different regions and compares tissue-specific DNA preservation for mummies and
skeletal remains from the Egyptian Nile River Valley

Will all these papers be published in 2023?

[Andriy]

Please remind me which mitochondrial haplogroups were found in Abusir?

[David Bush]

Please remind me which mitochondrial haplogroups were found in Abusir?

https://www.yfull.com/samples-from-paper/418/