Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
Open accessAbstract
Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.
AI snapshot
Written from the paper’s full text.
TL;DR
Ancient DNA from Egyptian mummies at Abusir el-Meleq shows genetic continuity across the Pre-Ptolemaic, Ptolemaic, and Roman periods, with ancient Egyptians sharing more ancestry with Near Easterners than present-day Egyptians. Modern Egyptians have additional sub-Saharan African ancestry that the authors estimate entered predominantly within the last 2,000 years.
Key findings
- The study obtained 90 complete mitochondrial genomes and genome-wide SNP data from three male individuals from 151 mummified remains; the 90 mtDNA samples grouped as Pre-Ptolemaic (n=44), Ptolemaic (n=27), and Roman (n=19), spanning cal. 1388 BCE–426 CE.
- The three ancient Egyptian groups clustered together genetically, with low FST values (<0.05) and continuity-test P values >0.1, supporting genetic continuity across the ~1,300-year transect.
- Modern Egyptians showed a marked increase in African mtDNA lineages L0–L4 up to 20%; qpAdm and f4-ratio estimated modern Egyptians inherit 8% more African ancestry than the three ancient Egyptians, with ancient African ancestry estimates of 6–15% and modern estimates of 14–21%.
- ALDER estimated a pulse-like admixture event 24 generations ago (~700 years ago), and BEAST estimated an average effective population size of 112,082 individuals (95% HPD 47,839–309,705) for the sampled ancient period.
Methods
- DNA was extracted from 151 mummified human remains from Abusir el-Meleq in Middle Egypt; samples were radiocarbon dated to the late New Kingdom through the Roman Period.
- Double-stranded Illumina libraries were prepared and enriched for human mitochondrial DNA and ~1.24 million nuclear SNPs; 90 mtDNA genomes passed criteria (>10-fold coverage and <3% contamination), and three male individuals passed nuclear quality-control criteria.
- Analyses included mitochondrial haplogroup comparison, FST, population-continuity tests, PCA, MDS, BEAST, ADMIXTURE, outgroup f3-statistics, qpAdm, f4-ratio, ALDER, Y-chromosome haplogroup assignment, and phenotype-associated SNP inspection.
Limitations
- The paper states that all genetic data came from a single site in Middle Egypt and may not represent all of ancient Egypt; southern Egyptian populations may have had a higher sub-Saharan genetic component, so the post-Roman influx argument may need nuance.
- The paper states that archaeological context was greatly diminished because Rubensohn’s records were incomplete and many excavation diaries/notes were destroyed in World War II; collection bias likely favored intact adult skulls, with subadults underrepresented.
- Evident from the text: the nuclear genome-wide analysis rests on only three male individuals, and two had nuclear contamination estimates over 5%, although the authors replicated key results using only the least contaminated sample.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
17 of 37 cited sources checked · 14 supported · 0 flagged · accuracy not yet measured
- Findingown data
qpAdm and the f4-ratio test reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do.
“Both qpAdm35 and the f4-ratio test39 reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results discussed above.”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [35] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015). source
- cites [39] Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Interpretationown data
The data indicate close admixture and affinity at a much earlier date than the ~750 years ago midpoint estimated by Pagani and colleagues.
“Our data seem to indicate close admixture and affinity at a much earlier date, which is unsurprising given the long and complex connections between Egypt and the Middle East.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [17] 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). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Findingcitation
Comparative data from a contemporary population under Roman rule in Asia Minor did not reveal a closer relationship to the ancient Egyptians from the Roman period.
“However, comparative data from a contemporary population under Roman rule in Asia Minor, from the Roman city Ağlasun today in Turkey31, did not reveal a closer relationship to the ancient Egyptians from the Roman period (Fig. 3b,c).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [31] Ottoni, C. et al. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey. R. Soc. Open Sci. 3, 150250 (2016). source
- Study design and conductown data
The study provides the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing authenticity via nucleotide misincorporation patterns and statistical contamination tests.
“Here, we provide the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing the authenticity of the retrieved ancient DNA via characteristic nucleotide misincorporation patterns1314 and statistical contamination tests15 to ensure the ancient origin of our obtained data.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [1314]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [15] 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). source
- Findingown data
ADMIXTURE reveals that the three ancient Egyptians differ from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals.
“Model-based clustering using ADMIXTURE37 (Fig. 4b, Supplementary Fig. 4) further supports these results and reveals that the three ancient Egyptians differ from modern Egyptians by a relatively larger Near Eastern genetic component, in particular a component found in Neolithic Levantine ancient individuals36 (Fig. 4b).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [37] Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009). source
- cites [36] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Study design and conductown data
All samples showed nucleotide misincorporation patterns characteristic of ancient DNA.
“MapDamage 2.0 (ref. 60) has been used to evaluate fragment lengths and nucleotide misincorporation patterns of the provided samples, all of which showed levels that are characteristic for ancient DNA13.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [13] Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007). source
- Findingown data
Ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians do.
“Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times.”
- Also stated in: § Analysis of mitochondrial genomes · plain
“Both analyses reveal higher affinities with modern populations from the Near East and the Levant compared to modern Egyptians (Fig. 3b,c).”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Also stated in: § Analysis of mitochondrial genomes · plain
- Findingown data
f3-statistics point towards sub-Saharan African populations as the missing component when modelling modern Egyptians as a mixture of ancient Egyptian and other populations.
“Our results point towards sub-Saharan African populations as the missing component (Fig. 5c), confirming the results of the ADMIXTURE analysis.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Findingown data
The observed DNA damage patterns differed for source materials, with on average 19% damage in soft tissues and around 10% damage in bone tissue and teeth.
“The observed DNA damage patterns differed for the source materials with on average 19% damage in soft tissues and around 10% damage in bone tissue and teeth (Fig. 2b,c, Supplementary Table 1).”
Quote in the paperNot a substantial claim - Findingown data
Both PCA and Multidimensional Scaling reveal higher affinities of ancient Egyptians with modern populations from the Near East and the Levant compared to modern Egyptians.
“Both analyses reveal higher affinities with modern populations from the Near East and the Levant compared to modern Egyptians (Fig. 3b,c).”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Findingnone given
The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period.
“The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period.”
Quote in the paperSubstantial claim - Findingown data
The genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq.
“Our genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq, indicating that foreign rule impacted the town's population only to a very limited degree at the genetic level.”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Findingreasoning
Ancient Egyptians are more closely related to all modern and ancient European populations tested than modern Egyptians are.
“When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested (Fig. 5b), likely due to the additional African component in the modern population observed above.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Findingown data
mtDNA haplotypes were identical for all samples from the same individuals.
“Importantly, mtDNA haplotypes were identical for all samples from the same individuals.”
Quote in the paperSubstantial claim - Findingown data
The ancient DNA data revealed a high level of affinity between the ancient inhabitants of Abusir el-Meleq and modern populations from the Near East and the Levant.
“The ancient DNA data revealed a high level of affinity between the ancient inhabitants of Abusir el-Meleq and modern populations from the Near East and the Levant.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Findingown data
Modern Egyptians are shifted towards sub-Saharan African populations.
“In contrast, modern Egyptians are shifted towards sub-Saharan African populations.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Findingown data
Effective population size estimates from radiocarbon-dated mitochondrial genomes show similar values in the different ancient time periods, with an average 95% CI between ca. 48,000 and 310,000 inhabitants in the region and period under investigation.
“Our results show similar values of effective population size in the different ancient time periods with an average value of between ca. 48,000 and 310,000 (average 95% CI) inhabitants in the region and period under investigation (Fig. 3d, Supplementary Fig. 2, Supplementary Table 4).”
Quote in the paperNot a substantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Findingown data
Absolute estimates of African ancestry in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21%, depending on method and reference populations.
“Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations (see Supplementary Note 1, Supplementary Fig. 6, Supplementary Tables 5–8).”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Findingown data
In many samples, nuclear DNA damage was relatively low, indicating modern contamination.
“In many samples, nuclear DNA damage was relatively low, indicating modern contamination.”
Quote in the paperSubstantial claim - Findingown data
A substantially larger sub-Saharan African component, found primarily in West-African Yoruba, is seen in modern Egyptians compared to the ancient samples.
“In contrast, a substantially larger sub-Saharan African component, found primarily in West-African Yoruba, is seen in modern Egyptians compared to the ancient samples.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Findingown data
The closest populations on the MDS to the ancient Egyptian meta population (AEGY) are modern populations from Saudi-Arabia, Kuwait, the United Arab Emirates, Yemen and other Near-East populations.
“The closest populations on the MDS with respect to our ancient meta population (AEGY) are modern populations from Saudi-Arabia, Kuwait, the United Arab Emirates, Yemen and other Near-East populations”
Quote in the paperNot a substantial claim - Findingown data
The ancient population from Turkey (TRO) shows more relatedness to modern North-African and Levantine populations than to the ancient Egyptian meta population.
“whereas the individuals from another ancient population from Turkey (TRO) show more relatedness to modern North-African and populations from the Levantine.”
Quote in the paperNot a substantial claim - Interpretationown data
The study demonstrates that the challenges of ancient DNA work on Egyptian mummies can be overcome with enrichment strategies followed by high-throughput DNA sequencing.
“This study demonstrates that the challenges of ancient DNA work on Egyptian mummies can be overcome with enrichment strategies followed by high-throughput DNA sequencing.”
Quote in the paperSubstantial claim - Interpretationown data
DNA damage in Egyptian mummies correlates with tissue type.
“Our results thus suggest that DNA damage in Egyptian mummies correlates with tissue type.”
Quote in the paperNot a substantial claim - Interpretationown data
Present-day Egyptians received additional sub-Saharan admixture in more recent times.
“Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Premisecitation
The first high-throughput sequences obtained from ancient Egyptian mummies were not supported by rigorous authenticity and contamination tests.
“However, the first high-throughput sequences obtained from ancient Egyptian mummies12 were not supported by rigorous authenticity and contamination tests.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [12] Khairat, R. et al. First insights into the metagenome of Egyptian mummies using next-generation sequencing. J. Appl. Genet. 54, 309–325 (2013). source
- Interpretationown data
The substantially lower African component in the ~2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred predominantly within the last 2,000 years.
“While this result by itself does not exclude the possibility of much older and continuous gene flow from African sources, the substantially lower African component in our ∼2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred indeed predominantly within the last 2,000 years.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Interpretationreasoning
The sample's demographic profile is more likely due to collection bias, with collectors favouring intact adult skulls, than to different burial treatments for adults and subadults.
“It is possible that the sample's demographic profile is the result of different burial treatments for adults and subadults, but it seems more likely that it is due to collection bias, with collectors favouring intact adult skulls.”
Quote in the paperNot a substantial claim - Interpretationown data
Foreign rule impacted the town's population only to a very limited degree at the genetic level.
“Our genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq, indicating that foreign rule impacted the town's population only to a very limited degree at the genetic level.”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Interpretationown data
The results revise previous scepticism towards DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures.
“However, our results revise previous scepticism towards the DNA preservation in ancient Egyptian mummies due to climate conditions or mummification procedures8.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [8] Gilbert, M. T. et al. Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003). Am. J. Phys. Anthropol. 128, 110–114 discussion 115–118 (2005). source
- Interpretationown data
The greater closeness of ancient Egyptians to European populations is likely due to the additional African component in the modern population.
“When comparing this pattern with modern Egyptians, we find that the ancient Egyptians are more closely related to all modern and ancient European populations that we tested (Fig. 5b), likely due to the additional African component in the modern population observed above.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Interpretationown data
The analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history.
“This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level.”
Quote in the paperSubstantial claim - Study design and conductown data
The intra-group distances of the three ancient populations (Pre-Ptolemaic, Ptolemaic, Roman Period) were not significantly different from each other.
“However, as the intra-group distances of our three ancient populations were not significantly different from each other, we merged all three ancient populations in a single set”
Quote in the paperSubstantial claim - Interpretationcitation
It is arguable that the complete spectrum of society is represented at Abusir el-Meleq, ranging from Late Period priests' burials to simple inhumations.
“Rather it seems arguable that the complete spectrum of society is represented, ranging from Late Period priests' burials that stand out by virtue of their size and contents to simple inhumations that are buried with little to no grave goods2.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [2] Riggs, C. The Beautiful Burial in Roman Egypt: Art, Identity, and Funerary Religion Oxford University Press (2005). source
- Study design and conductown data
Negative controls processed in parallel with samples showed no substantial mapping rates, suggesting that DNA introduced during laboratory work could be kept at a minimal level.
“Negative controls were processed in parallel with samples. The former show no substantial mapping rates and suggest that the amount of DNA introduced during laboratory work could be kept on a minimal level.”
Quote in the paperSubstantial claim
- May combine two claims. 37
- Classified as probably not a substantial claim. 39
May combine two claims.
Findingown dataModern Egyptians share the ancient haplogroup profile but show a marked increase of African mtDNA lineages L0-L4 up to 20%.
“Modern Egyptians share this profile but in addition show a marked increase of African mtDNA lineages L0–L4 up to 20% (consistent with nuclear estimates of 80% non-African ancestry reported in Pagani et al.17).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Pagani et al. [17] 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). source
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
May combine two claims.
FindingcitationSample JK2911 had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia, consistent with the ancestral affinity shown above.
“This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [41] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
May combine two claims.
Findingown dataBy comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, the study found an influx of sub-Saharan African ancestry after the Roman Period, corroborating Henn and colleagues.
“By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, we found an influx of sub-Saharan African ancestry after the Roman Period, which corroborates the findings by Henn and colleagues16.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [16] Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, e1002397 (2012). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
May combine two claims.
Findingown dataALDER estimated a putative pulse-like admixture event at 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues.
“We then used ALDER40 to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues16.”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [40] Loh, P. R. et al. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233–1254 (2013). source
- cites [16] Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, e1002397 (2012). source
- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
May combine two claims.
Findingown dataGenetic continuity between ancient and modern Egyptians cannot be ruled out by the formal test despite the sub-Saharan African influx, while continuity with modern Ethiopians is not supported.
“Genetic continuity between ancient and modern Egyptians cannot be ruled out by our formal test despite this sub-Saharan African influx, while continuity with modern Ethiopians17, who carry >60% African L lineages, is not supported (Supplementary Data 5).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [17] 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). source
- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
Classified as probably not a substantial claim.
FindingcitationAccording to radiocarbon dates, the samples can be grouped into three time periods: Pre-Ptolemaic (New Kingdom, Third Intermediate Period and Late Period), Ptolemaic and Roman Period.
“According to the radiocarbon dates (Supplementary Data 1, see also ref. 18), the samples can be grouped into three time periods: Pre-Ptolemaic (New Kingdom, Third Intermediate Period and Late Period), Ptolemaic and Roman Period.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [18] Lalremruata, A. et al. Molecular identification of falciparum malaria and human tuberculosis co-infections in mummies from the Fayum depression (Lower Egypt). PLoS ONE 8, e60307 (2013). source
Table 1 (Introduction; page unavailable) gives radiocarbon dates for mummies assigned to the Third Intermediate, Late, Ptolemaic and Roman periods. It does not date any of its samples to the New Kingdom or group samples into the three stated categories; the Materials and Methods instead describe this study’s samples as spanning the Third Intermediate to Roman periods. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
InterpretationreasoningTaken together with Greek papyri written at the site, the evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek.
“Taken together with the multitude of Greek papyri that were written at the site, this evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek45.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [45] Broux, Y. & Depauw, M. in Social Informatics (eds Aiello, L. M., McFarland, D.) 304–313 (Springer, 2015). source
The paper’s §2.3 discusses Demotic letters from Elephantine, not Greek papyri from Abusir el-Meleq. Searches for Abusir el-Meleq, Greek papyri written at the site, and Greek literacy or speech found no passage addressing the claim. Page numbers were not available in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationFor the three samples with contamination estimates above 3%, visual inspection of sequence assemblies was done to identify potential contaminating lineages and ensure consistency of the consensus mitochondrial genome.
“except for three samples (JK2879, JK2883, JK2896) where a visual inspection of sequence assemblies was done as described in Posth et al.61 to identify potential contaminating lineages and ensure consistency of the generated consensus mitochondrial genome.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [61] Posth, C. et al. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe. Curr. Biol. 26, 827–833 (2016). source
The Results and Discussion (page not provided) describe an approach that estimates present-day human contamination while reconstructing mitochondrial sequences. Our copy does not describe visual inspection of sequence assemblies, identify three samples above 3% contamination, or say that inspection was used to check the consensus genome. The cited paper therefore supports the general contamination-and-reconstruction context, but not the specific procedure attributed to it. (LLM, conf=0.78)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
Findingown dataThe 90 mitochondrial genomes fulfilling criteria (>10-fold coverage and <3% contamination) were grouped into Pre-Ptolemaic (n=44), Ptolemaic (n=27) and Roman (n=19) temporal categories.
“The 90 mitochondrial genomes fulfilling our criteria (>10-fold coverage and <3% contamination) were grouped into three temporal categories based on their radiocarbon dates (Supplementary Data 1), corresponding to Pre-Ptolemaic Periods (n=44), the Ptolemaic Period (n=27) and the Roman Period (n=19) (Supplementary Data 1).”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
May combine two claims.
Findingown dataAncient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations, by outgroup f3-statistics.
“We find that ancient Egyptians are most closely related to Neolithic and Bronze Age samples in the Levant, as well as to Neolithic Anatolian and European populations (Fig. 5a,b).”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataOther relevant SNPs in sample JK2911 carry the ancestral allele, including HERC2 and LCT, suggesting dark-coloured eyes and lactose intolerance.
“Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance (Supplementary Table 9).”
Quote in the paperNot a substantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
May combine two claims.
Findingown dataYields of preserved DNA were comparable in bone and teeth but up to ten times lower in soft tissues.
“Yields of preserved DNA were comparable in bone and teeth but up to ten times lower in soft tissues (Fig. 2a, Supplementary Table 1).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataIn both PCA and ADMIXTURE analyses, no significant differences were found between the three ancient samples, despite two having nuclear contamination estimates over 5%, indicating no larger impact of modern DNA contamination.
“In both PCA and ADMIXTURE analyses, we did not find significant differences between the three ancient samples, despite two of them having nuclear contamination estimates over 5%, which indicates no larger impact of modern DNA contamination.”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
May combine two claims.
Findingown dataThe study obtained complete human mitochondrial genomes from 90 ancient Egyptian mummy samples and genome-wide SNP data from three male individuals passing quality control.
“we successfully obtained complete human mitochondrial genomes from 90 samples and genome-wide SNP data from three male individuals passing quality control.”
- Also stated in: § Abstract · plain
“Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies.”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
- Also stated in: § Abstract · plain
May combine two claims.
Findingown dataThe ancient Egyptian samples fall distinct from modern Egyptians and closer towards Near Eastern and European samples in PCA.
“We found the ancient Egyptian samples falling distinct from modern Egyptians, and closer towards Near Eastern and European samples (Fig. 4a, Supplementary Fig. 3, Supplementary Table 5).”
Quote in the paperSubstantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
May combine two claims.
Findingown dataNuclear DNA showed poor preservation compared to mtDNA, with a high mitochondrial/nuclear DNA ratio of on average around 18,000.
“Overall, the nuclear DNA showed poor preservation compared to the mtDNA as depicted by a high mitochondrial/nuclear DNA ratio of on average around 18,000.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThree out of 40 samples fulfilling strict criteria had acceptable nuclear contamination rates: two Pre-Ptolemaic samples had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one Ptolemaic sample had 7.3% contamination and yielded 201,967 SNPs.
“Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates: Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAll three ancient Egyptian groups cluster together in PCA and Multidimensional Scaling, supporting genetic continuity across the 1,300-year transect.
“We find that all three ancient Egyptian groups cluster together (Fig. 3b), supporting genetic continuity across our 1,300-year transect.”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
May combine two claims.
Findingown dataThe three ancient groups have highly similar haplogroup profiles, supported by low FST values (<0.05) and P values >0.1 for the continuity test.
“We observe highly similar haplogroup profiles between the three ancient groups (Fig. 3a), supported by low FST values (<0.05) and P values >0.1 for the continuity test.”
Quote in the paperSubstantial claim- Rests on an assumption: The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataMost of the individuals are early and late adults, and subadult individuals are underrepresented.
“It is notable that most of the individuals are early and late adults, and that subadult individuals are underrepresented (Supplementary Data 1).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe Y-chromosome haplogroups of the three genome-wide individuals support affinity to the Middle East: two were assigned to Middle-Eastern haplogroup J, and one to haplogroup E1b1b1 common in North Africa.
“The affinity to the Middle East finds further support by the Y-chromosome haplogroups of the three individuals for which genome-wide data was obtained, two of which could be assigned to the Middle-Eastern haplogroup J, and one to haplogroup E1b1b1 common in North Africa (Supplementary Table 3).”
Quote in the paperNot a substantial claim- Rests on an assumption: The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
Probably not a substantial claim: may not pass S3 (load-bearing).
FindingreasoningAssuming a generation time of 29 years and equal male and female effective population size, the population size estimate rescales to 112,082 individuals (95% HPD 47,839-309,705).
“which assuming generation time of 29 years and equal male and female effective population size rescales to 112,082 (95% HPD 47,839–309,705) individuals”
Quote in the paperNot a substantial claim- The authors state this as an assumption: Generation time of 29 years and equal male and female effective population size.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataFor JK2134, there was no sufficient coverage after quality filtering at all the specific sites, so the analysis revealed no further clues.
“For JK2134, there was no sufficient coverage after quality filtering at all the specific sites, which is why the analysis revealed no further clues.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataMitochondrial genome coverages ranged from 11-fold to 4284-fold, with an average of 408-fold.
“we achieved coverages ranging from 11-fold up to 4284-fold on the mitochondrial genome, with an average of 408-fold.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe Bayesian SkyGrid plot indicates a fairly stable, slightly decreasing effective population size for the studied population over the last 5,000 years.
“The obtained Bayesian SkyGrid plot indicates a fairly stable slightly decreasing effective population size for the studied population over the last 5,000 years (Fig. 3d and Supplementary Fig. 2).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataDerived alleles for the gene SLC24A5 were present in both JK2888 and JK2911.
“Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe average median population size over the sampled ancient period, expressed as female effective population size times generation time, was estimated to 1,625,187 (95% HPD 693,670-4,490,725).
“The average median population size over the sampled ancient period, expressed as female effective population size times generation time, was estimated to 1,625,187 (95% HPD 693,670–4,490,725)”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataNo derived alleles were found for the genes SLC45A2, LCT and EDAR in both JK2888 and JK2911.
“For further genes such as SLC45A2, LCT and EDAR we were unable to find derived alleles for both JK2888 and JK2911.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationBy the third century BCE Abusir el-Meleq was at the centre of a wider region comprising the northern part of the Herakleopolites province and had close ties with the Fayum and the Memphite provinces.
“Written sources indicate that by the third century BCE Abusir el-Meleq was at the centre of a wider region that comprised the northern part of the Herakleopolites province, and had close ties with the Fayum and the Memphite provinces, involving the transport of wheat, cattle-breeding, bee-keeping and quarrying42.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [42] Falivene, M. R. The Herakleopolite Nome: a Catalogue of Toponyms with Introduction and Commentary Scholars Press (1998). source
May combine two claims.
Study design and conductown dataAll genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt.
“However, we note that all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt.”
Quote in the paperSubstantial claimMay combine two claims.
Study design and conductown dataReplication using only the least contaminated sample (<1% contamination) gave very similar f3-statistics results, confirming that moderate modern DNA contamination in two samples did not affect the analyses.
“We replicated the results based on f3-statistics using only the least contaminated sample (with <1% contamination estimate) and find very similar results (Supplementary Fig. 5), confirming that the moderate levels of modern DNA contamination in two of our samples did not affect our analyses.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationAbusir el-Meleq was inhabited from at least 3250BCE until about 700CE and was of great religious significance because of its active cult to Osiris, the god of the dead, which made it an attractive burial site for centuries.
“The archaeological site Abusir el-Meleq was inhabited from at least 3250BCE until about 700CE and was of great religious significance because of its active cult to Osiris, the god of the dead, which made it an attractive burial site for centuries2.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [2] Riggs, C. The Beautiful Burial in Roman Egypt: Art, Identity, and Funerary Religion Oxford University Press (2005). source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataNo inconsistencies were found between mitochondrial and nuclear haplogroup assignments.
“We furthermore determined whether there are inconsistencies between our haplogroup assignments of the mitochondrial and the nuclear capture respectively, but did not find any”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataThe lowest cross-validation error in ADMIXTURE was obtained using K=16.
“The lowest cross-validation error was obtained using K=16 and we show the results of that run in Supplementary Fig. 4.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationUnder Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society.
“Under Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society55.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [55] Vandorpe, K. Idnetity in Roman Egypt, 260–276 (Oxford University Press, 2012). source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataAll samples except three (JK2879, JK2883, JK2896) had contamination estimates less than the defined threshold of 3%.
“For all samples, the observed contamination estimates prove to be less than our defined threshold of 3%, except for three samples (JK2879, JK2883, JK2896)”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThroughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa.
“Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa515253.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [51] Smith, S. T. in Nubia in the New Kingdom: Lived experience, pharaonic control and local traditions (eds Spencer, N., Stevens, A. & Binder M.) 613–628.
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [52] Smith, S. T. Wretched Kush: Ethnic Identities and Boundaries in Egypt’s Nubian Empire Routledge (2003). source
- cites [53] Van Pelt, W. P. Revising Egypto-Nubian relations in New Kingdom Lower Nubia: From Egyptianization to cultural entanglement. Cambridge Archaeol. J. 23, 523–550 (2013). source
Classified as probably not a substantial claim.
Study design and conductnone givenOnly samples with less than 3% estimated contamination based on deamination and degree of mitochondrial contamination were used for further downstream analysis.
“only samples with less than 3% estimated contamination based on deamination and degree of mitochondrial contamination have been used for further downstream analysis.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationIn the Roman Period, many Roman army veterans settled in the Fayum area and intermarried with local populations.
“Later, in the Roman Period, many veterans of the Roman army—who, initially at least, were not Egyptian but people from disparate cultural backgrounds—settled in the Fayum area after the completion of their service, and formed social relations and intermarried with local populations44.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [44] Alston, R. Soldier and Society in Roman Egypt: A Social History New York (1995). source
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
InterpretationreasoningThe lack of context greatly diminishes the possibility of 'thick description' of the analysed individuals, at least in terms of their names, titles and materially expressed identity.
“This lack of context greatly diminishes the possibility of ‘thick description' of the analysed individuals, at least in terms of their names, titles and materially expressed identity.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationEspecially in the Roman Period there may have been significant legal and social incentives to marry within one's ethnic group, as individuals with Roman citizenship had to marry other Roman citizens to pass on their citizenship.
“Especially in the Roman Period there may have been significant legal and social incentives to marry within one's ethnic group, as individuals with Roman citizenship had to marry other Roman citizens to pass on their citizenship.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationConnections between Egypt and the Middle East date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation.
“These connections date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation54.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [54] Mumford, G. D. Egypt and the Levant, The Oxford Handbook of the Archaeology of the Levant: c. 8000-332 BCE Oxford (2014).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataEffective sample size for all parameters exceeded 100.
“Effective sample size for all parameters exceeded 100.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductown dataFiltering with q=20 preserved haplotyping calls; even stricter filtering with q=40 preserved haplotyping calls to be consistent.
“We ultimately chose a value of q=20 for filtering with ‘log2fasta', but even more strict filtering with q=40 preserved our haplotyping calls to be consistent.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationEspecially from the second millennium BCE onwards, there were intense, historically and archaeologically documented contacts, including large-scale immigration of Canaanite populations known as the Hyksos into Lower Egypt.
“Especially from the second millennium BCE onwards, there were intense, historically- and archaeologically documented contacts, including the large-scale immigration of Canaanite populations, known as the Hyksos, into Lower Egypt, whose origins lie in the Middle Bronze Age Levant54.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [54] Mumford, G. D. Egypt and the Levant, The Oxford Handbook of the Archaeology of the Levant: c. 8000-332 BCE Oxford (2014).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationAll of the material was excavated by Rubensohn in the early twentieth century, whose main interest was to obtain literary papyri from cartonnage rather than to excavate human remains.
“All of the material was excavated by Rubensohn in the early twentieth century, whose main interest was to obtain literary papyri from cartonnage rather than to excavate human remains47.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [47] Rubensohn, O. & Knatz, F. Berichte über die Ausgrabungen bei Abusir el Mäläq im Jahre 1903. Leipzig: Z. Ägypt. Sprache Alt. Bd. 41, 1–21 (1904). source
Classified as probably not a substantial claim. May combine two claims.
Study design and conductown dataThree samples selected for downstream analysis (JK2134, JK2888, JK2911) had acceptable contamination estimates, similar in both UDG and non-UDG libraries.
“Three samples were selected for down-stream analysis: JK2134, JK2888 and JK2911. In all three of these samples, contamination estimates were acceptable, and similar in both UDG and non-UDG libraries”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningSeveral details of the context of the individuals analysed in this study were lost over time.
“However, a general issue concerning the site is that several details of the context of the individuals analysed in this study were lost over time.”
Quote in the paperNot a substantial claimMay combine two claims.
Study design and conductown dataRepeating the f3-statistics analysis using only sample JK2911 (highest SNP coverage, contamination below 1%) gave very similar results as using all three samples, indicating no effect of contamination on the results.
“Since two of the three selected samples had contamination rate estimates over 5%, we repeated this analysis using only sample JK2911, which has the highest SNP coverage and a contamination estimate of below 1%. The result is shown in Supplementary Fig. 5, with very similar results as when using all three samples, indicating no effect of contamination on our results.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe Fayum saw substantial population growth during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration.
“Abusir el-Meleq's proximity to, and close ties with, the Fayum are significant in the context of this study as the Fayum in particular saw a substantial growth in its population during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration3343.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [33] Clarysse, W. & Thompson, D. J. Counting the people in Hellenistic Egypt Cambridge University Press (2004).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [43] Rathbone, D. W. Villages, land and population in Graeco-Roman Egypt. Proc. Cambridge Philolog. Soc. 36, 103–142 (1990). source
May combine two claims.
PremisecitationWidespread mummification treatments in the Ptolemaic and Roman Periods led to a decline in standards and costs, and the generally modest appearance of many burials further supports the assessment of a complete social spectrum.
“The widespread mummification treatments in the Ptolemaic and Roman Periods in particular, leading to a decline in standards and costs48 and the generally modest appearance of many burials further supports this assessment.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [48] David, R. in Ancient Egyptian Materials and Technology (eds Nicholson, P. T., Shaw, I.) 372–389 (Cambridge, 2000).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationIn the early Roman Period, Abusir el-Meleq appears to have been the main centre in its own district.
“In the early Roman Period, the site appears to have been the main centre in its own district42.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [42] Falivene, M. R. The Herakleopolite Nome: a Catalogue of Toponyms with Introduction and Commentary Scholars Press (1998). source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataSamples showed damage on both 3′ and 5′ ends of reads in the range of 5% to 49%, with an average of 14%.
“our samples showed damage on both 3′ and 5′ ends of reads in the range of 5% up to 49%, with an average of 14%.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Premisenone givenAbusir el-Meleq is one of the few sites in Egypt for which such a vast number of individuals with such an extensive chronological spread are available for ancient DNA analysis.
“Abusir el-Meleq is arguably one of the few sites in Egypt, for which such a vast number of individuals with such an extensive chronological spread are available for ancient DNA analysis.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMany of Rubensohn's excavation diaries and notes were destroyed during the Second World War.
“Furthermore, many of his excavation diaries and notes were destroyed during the Second World War19.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [19] Welte, B. Zeitzeugen aus dem Wüstensand- die altägyptischen Mumienschädel aus Abusir el-Meleg Dissertation. BioArchaeologica no. 6, Marie-Leidorf Verlag (2016). source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataIn all three selected samples, the non-UDG library showed DNA damage over 8% in the first base pair of reads, within the expected range for ancient DNA of this age.
“Furthermore, in all three samples the non-UDG library showed DNA damage over 8% in the first base pair of reads, which is within the expected range of damage for ancient DNA of this age.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisereasoningRubensohn's archaeological records are highly incomplete and many of the finds made by him were removed undocumented from their contexts.
“As is customary for the time, Rubensohn's archaeological records are highly incomplete and many of the finds made by him were removed undocumented from their contexts.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningSuch policies are likely to have affected the intermarriage of Romans and non-Romans to a degree.
“Such policies are likely to have affected the intermarriage of Romans and non-Romans to a degree55.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [55] Vandorpe, K. Idnetity in Roman Egypt, 260–276 (Oxford University Press, 2012). source
The paper relies on this without support.
The three individuals with genome-wide data are representative of the ancient Egyptian populations from their respective periods.
“Three out of 40 samples fulfilling these criteria had acceptable nuclear contamination rates: Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”
The paper relies on this without support.
The 90 mitochondrial genomes are representative of the Abusir el-Meleq population in each time period.
“The 90 mitochondrial genomes fulfilling our criteria (>10-fold coverage and <3% contamination) were grouped into three temporal categories based on their radiocarbon dates (Supplementary Data 1), corresponding to Pre-Ptolemaic Periods (n=44), the Ptolemaic Period (n=27) and the Roman Period (n=19) (Supplementary Data 1).”
The authors state this as an assumption.
Generation time of 29 years and equal male and female effective population size.
“which assuming generation time of 29 years and equal male and female effective population size rescales to 112,082 (95% HPD 47,839–309,705) individuals”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Haplogroup grouping lists 21 categories rather than 20
MinorThe list names 20 specific haplogroup categories and then adds a category for all remaining haplogroups, making 21 categories in total.
“we divided our haplogroups in the following 20 groups”
“H, HV, I, J, K, L0, L1, L2, L3, L4, M1, N, R, R0, T, T1, T2, U, W, X and all remaining other haplogroups”
Two different maximum mitochondrial coverage values
MinorThe results give a maximum coverage of 4,236-fold, whereas the methods give 4,284-fold for the mitochondrial samples.
“11- to 4,236-fold coverage”
“coverages ranging from 11-fold up to 4284-fold on the mitochondrial genome”
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The genomic history of the Iberian Peninsula over the past 8000 years
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Reconstructing Prehistoric African Population Structure
Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K. A., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.049 · Cited by 410 · see citing works
“The Early Iron Age in eastern and southern Africa: a critical re-appraisal.”
InfluentialSelf-citationThe Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes
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Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations
van de Loosdrecht, M. S., Bouzouggar, A., Humphrey, L., Posth, C., Barton, N., Aximu‐Petri, A., Nickel, B., Nagel, S., Talbi, E. H., Hajraoui, M. A. E., et al. (2018) · Science · doi:10.1126/science.aar8380 · Cited by 241 · see citing works
Self-citationAncient Genomics of Modern Humans: The First Decade
Skoglund, P., & Mathieson, I. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021749 · Cited by 246 · see citing works
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Dairying, diseases and the evolution of lactase persistence in Europe
Evershed, R. P., Smith, G. D., Roffet‐Salque, M., Timpson, A., Diekmann, Y., Lyon, M., Cramp, L., Casanova, E., Smyth, J., Whelton, H. L., et al. (2022) · Nature · doi:10.1038/s41586-022-05010-7 · Cited by 229 · see citing works
Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa
Prendergast, M. E., Lipson, M., Sawchuk, E., Olalde, Í., Ogola, C. A., Rohland, N., Sirak, K. A., Adamski, N., Bernardos, R. L., Broomandkhoshbacht, N., et al. (2019) · Science · doi:10.1126/science.aaw6275 · Cited by 196 · see citing works
The genetic history of the Southern Arc: A bridge between West Asia and Europe
Lazaridis, I., Alpaslan-Roodenberg, S., Acar, A., Açıkkol, A., Agelarakis, A. P., Aghikyan, L., Akyüz, U., Andreeva, D., Andrijašević, G., Antonović, D., et al. (2022) · Science · doi:10.1126/science.abm4247 · Cited by 194 · see citing works
Harnessing ancient genomes to study the history of human adaptation
Marciniak, S., & Perry, G. H. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.65 · Cited by 182 · see citing works
“Schuenemann et al.(202) 2017 3 1 Genome-wide SNPs Africa 2 1”
A unified genealogy of modern and ancient genomes
Wohns, A. W., Wong, Y., Jeffery, B., Akbari, A., Mallick, S., Pinhasi, R., Patterson, N. J., Reich, D., Kelleher, J., & McVean, G. (2022) · Science · doi:10.1126/science.abi8264 · Cited by 182 · see citing works
The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean
Fernandes, D., Mittnik, A., Olalde, Í., Lazaridis, I., Cheronet, O., Rohland, N., Mallick, S., Bernardos, R. L., Broomandkhoshbacht, N., Carlsson, J., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1102-0 · Cited by 152 · see citing works
Tales of Human Migration, Admixture, and Selection in Africa
Schlebusch, C. M., & Jakobsson, M. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021759 · Cited by 142 · see citing works
“Their presence suggests some level of population continuity across the MSA in North Africa, including the Late Pleistocene populations in the Levant (at Skhul and Qafzeh) and in East Africa (at Aduma) (56, 111).”
BackgroundInfluentialLate Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
Kanzawa‐Kiriyama, H., Jinam, T. A., Kawai, Y., Sato, T. K., Hosomichi, K., Tajima, A., Adachi, N., Matsumura, H., Kryukov, K. A., Saitou, N., et al. (2019) · Anthropological Science · doi:10.1537/ase.190415 · Cited by 126 · see citing works
Arrieta‐Bolaños, E., Hernández-Zaragoza, D. I., & Barquera, R. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.866407 · Cited by 128 · see citing works
“, 2018), the closeness between Egyptian and East African populations (Schuenemann et al., 2017), and the Australian-Papuan-Polynesian allele group signatures prevalent also in other OCE and SEA populations (Friedlaender et al.”
BackgroundThe origin and legacy of the Etruscans through a 2000-year archeogenomic time transect
Posth, C., Zaro, V., Spyrou, M. A., Vai, S., Gnecchi‐Ruscone, G. A., Modi, A., Peltzer, A., Mötsch, A., Nägele, K., Vågene, Å. J., et al. (2021) · Science Advances · doi:10.1126/sciadv.abi7673 · Cited by 127 · see citing works
Self-citationAfrican population history: an ancient DNA perspective
Vicente, M., & Schlebusch, C. M. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.008 · Cited by 109 · see citing works
“Studies on modern-day populations [15,16] and aDNA from Egyptian mummies [13] indicated that gene-flow from the south, across the Sahara into modern-day North Africans, were low and appeared in recent times.”
Loreille, O. M., Ratnayake, S., Bazinet, A. L., Stockwell, T. B., Sommer, D. D., Rohland, N., Mallick, S., Johnson, P. L. F., Skoglund, P., Onorato, A. J., et al. (2018) · Genes · doi:10.3390/genes9030135 · Cited by 104 · see citing works
“SNPs are already being targeted by the ancient DNA community to determine Y haplogroups [74,88,100], assess kinship [89], and test models of human population history and evolution [41,61,62,64–66,100–102].”
BackgroundInfluentialSabin, S. J., Herbig, A., Vågene, Å. J., Ahlström, T., Božović, G., Arcini, C., Kühnert, D., & Bos, K. I. (2020) · Genome biology · doi:10.1186/s13059-020-02112-1 · Cited by 92 · see citing works
The paradox of HBV evolution as revealed from a 16th century mummy
Ross, Z. P., Klunk, J., Fornaciari, G., Giuffra, V., Duchêne, S., Duggan, A. T., Poinar, D., Douglas, M. W., Eden, J., Holmes, E. C., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006750 · Cited by 89 · see citing works
“DNA isolated from ancient bone matrix has also been shown to be better preserved and less damaged than that recovered from corresponding soft tissue from the same remains [58].”
BackgroundVarela, R., Günther, T., Krzewińska, M., Storå, J., Gillingwater, T. H., MacCallum, M., Arsuaga, J. L., Dobney, K. M., Valdiosera, C. E., Jakobsson, M., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.059 · Cited by 95 · see citing works
“This observation is inconsistent with the PCA and the uniparental genetic marker data, indicating that the outgroup f3 statistic may be misleading, possibly due to the complex history of recent sub-Saharan admixture events in North African populations [12, 21] and the sensitivity of the f3 estimator to such patterns.”
Ancient proteins provide evidence of dairy consumption in eastern Africa
Bleasdale, M., Richter, K. K., Janzen, A., Brown, S., Scott, A., Zech, J., Wilkin, S., Wang, K., Schiffels, S., Desideri, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20682-3 · Cited by 85 · see citing works
Self-citationSirak, K. A., Fernandes, D., Lipson, M., Mallick, S., Mah, M., Olalde, Í., Ringbauer, H., Rohland, N., Hadden, C. S., Harney, É., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27356-8 · Cited by 85 · see citing works
Prendergast, M. E., & Sawchuk, E. (2018) · Antiquity · doi:10.15184/aqy.2018.70 · Cited by 81 · see citing works
“…ancient DNA (aDNA) research in Africa has accelerated, from studies of single individuals to analyses of larger groups with wider analytical scope (Morris et al. 2014; Gallego Llorente et al. 2015; Rodríguez-Varela et al. 2017; Schlebusch et al. 2017; Schuenemann et al. 2017; Skoglund et al. 2017).”
BackgroundPlacing Ancient DNA Sequences into Reference Phylogenies
Martiniano, R., Sanctis, B. D., Hallast, P., & Durbin, R. M. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac017 · Cited by 82 · see citing works
“2017 [23] Later Stone Age to Iron Age Kenya and Tanzania 27 Prendergast et al.”
BackgroundMethodThe genomic history of the Middle East
Almarri, M. A., Haber, M., Lootah, R. A., Hallast, P., Turki, S. H. A., Martin, H. C., Xue, Y., & Tyler‐Smith, C. (2021) · Cell · doi:10.1016/j.cell.2021.07.013 · Cited by 72 · see citing works
Stable population structure in Europe since the Iron Age, despite high mobility
Antonio, M. L., Weiß, C. L., Gao, Z., Sawyer, S., Oberreiter, V., Moots, H. M., Spence, J. P., Cheronet, O., Zagorc, B., Praxmarer, E., et al. (2023) · eLife · doi:10.7554/elife.79714 · Cited by 81 · see citing works
Human auditory ossicles as an alternative optimal source of ancient DNAPreprint
Sirak, K. A., Fernandes, D., Cheronet, O., Harney, É., Mah, M., Mallick, S., Rohland, N., Adamski, N., Broomandkhoshbacht, N., Callan, K. A., et al. (2020) · Genome Research · doi:10.1101/gr.260141.119 · Cited by 69 · see citing works
The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context
Aneli, S., Saupe, T., Montinaro, F., Solnik, A., Molinaro, L., Scaggion, C., Carrara, N., Raveane, A., Kivisild, T., Metspalu, M., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac014 · Cited by 66 · see citing works
Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
Furtwängler, A., Reiter, E., Neumann, G. U., Siebke, I., Steuri, N., Hafner, A., Lösch, S., Anthes, N., Schuenemann, V. J., & Krause, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-32083-0 · Cited by 62 · see citing works
Self-citationEthnic Identities in the Land of the Pharaohs
Matić, U. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108885577 · Cited by 65 · see citing works
Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship
Gad, Y. Z., Hassan, N. A.-M., Mousa, D. M., et al. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa223 · Cited by 58 · see citing works
“generation sequencing (NGS) technology (7-9).”
Neukamm, J., Pfrengle, S., Molak, M., Seitz, A., Francken, M., Eppenberger, P., Avanzi, C., Reiter, E., Urban, C., Welte, B., et al. (2020) · BMC Biology · doi:10.1186/s12915-020-00839-8 · Cited by 55 · see citing works
Self-citationMerheb, M. M., Matar, R., Hodeify, R. F., Siddiqui, S. S., Vazhappilly, C. G., Marton, J., Azharuddin, S., & Zouabi, H. A. (2019) · Cells · doi:10.3390/cells8050433 · Cited by 56 · see citing works
“Surprisingly, ancient Egyptians’ mtDNA matches more with ancient Europeans and Anatolians than modern Egyptians [66].”
BackgroundMethodInfluentialOrigin and diffusion of human Y chromosome haplogroup J1-M267
Sahakyan, H., Margaryan, A., Saag, L., Karmin, M., Flores, R., Haber, M., Kushniarevich, A., Khachatryan, Z., Bahmanimehr, A., Parik, J., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-85883-2 · Cited by 44 · see citing works
A genetic history of continuity and mobility in the Iron Age central Mediterranean
Moots, H. M., Antonio, M. L., Sawyer, S., Spence, J. P., Oberreiter, V., Weiß, C. L., Lucci, M., Cherifi, Y. M. S., Pastina, F. L., Genchi, F., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02143-4 · Cited by 43 · see citing works
“Previous research suggests present-day central and western North African populations can be modeled as having four primary ancestry components: a local/autochthonous Maghrebi component derived from paleolithic hunter-gatherer populations in the region (20, 31, 32); a Near Eastern component thought to have been introdu…”
BackgroundHaber, M., Nassar, J., Almarri, M. A., Saupe, T., Saag, L., Griffith, S. J., Doumet‐Serhal, C., Chanteau, J., Saghieh-Beydoun, M., Xue, Y., et al. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.05.008 · Cited by 41 · see citing works
Ancient DNA Studies and African Population History
Vicente, M., & Schlebusch, C. M. (2021) · BRILL eBooks · doi:10.1163/9789004500228_010 · Cited by 42 · see citing works
“In the easternmost part of North Africa, ancient DNA stud - ies of mummies also indicated that gene flow from sub-Saharan was recent and that people in classical Egypt displayed less sub-Saharan admixture compared to present-day Egyptians (Schuenemann et al., 2017).”
InfluentialD’Atanasio, E., Trombetta, B., Bonito, M., Finocchio, A., Vito, G. D., Seghizzi, M., Romano, R., Russo, G., Paganotti, G. M., Watson, E., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1393-5 · Cited by 41 · see citing works
“5 and 2 kya) showing a not negligible ancient sub-Saharan component (~ 6–10 %) [44].”
BackgroundAncient Egyptian Genomes from northern Egypt: Further discussionPreprint
Gourdine, J.-P. F., Keita, S. O. Y., Gourdine, J.-L., et al. (2018) · doi:10.31219/osf.io/ecwf3 · Cited by 42 · see citing works
Zhang, C., Gao, Y., Ning, Z., Lü, Y., Zhang, X., Liu, J., Xie, B., Xue, Z., Wang, X., Yuan, K., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1838-5 · Cited by 41 · see citing works
The Impact of Ancient Genome Studies in Archaeology
Gökçümen, Ö., & Frachetti, M. D. (2020) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-010220-074353 · Cited by 37 · see citing works
Historical RNA expression profiles from the extinct Tasmanian tigerPreprint
Mármol‐Sánchez, E., Fromm, B., Oskolkov, N., Pochon, Z., Kalogeropoulos, P., Eriksson, E., Biryukova, I., Sekar, V., Ersmark, E., Andersson, B., et al. (2023) · Genome Research · doi:10.1101/gr.277663.123 · Cited by 37 · see citing works
“Desiccation, mummification, or both have proven to be a favorable environment for the preservation of oligonucleotides (Hekkala et al. 2011; Schuenemann et al. 2017; Rossi et al. 2021; Pedersen et al. 2022; Richards et al. 2022).”
BackgroundAncient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India
Harney, É., Nayak, A., Patterson, N. J., Joglekar, P. P., Mushrif‐Tripathy, V., Mallick, S., Rohland, N., Sedig, J. W., Adamski, N., Bernardos, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11357-9 · Cited by 32 · see citing works
Leplongeon, A. (2021) · Frontiers in Earth Science · doi:10.3389/feart.2020.607183 · Cited by 34 · see citing works
“…mummies dated to between 3,000 and 1,600 cal BP showed that ancient Egyptians before the major admixture event identified above already had a strong near-eastern component, found in Levantine Neolithic individuals, suggesting an earlier influx of near-eastern ancestry (Schuenemann et al., 2017).”
BackgroundOras, E., Anderson, J., Tõrv, M., Vahur, S., Rammo, R., Remmer, S., Mölder, M., Malve, M., Saag, L., Saage, R., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227446 · Cited by 29 · see citing works
“Due to poor conditions of biomolecule preservation, aDNA analysis of mummified individuals from regions with a hot and humid climate has not been very successful until recently, when a comprehensive study of the mitochondrial DNA (mtDNA) variation of 90 individuals and genome-wide data of three Egyptian mummies from t…”
BackgroundSirak, K. A., & Sedig, J. W. (2019) · World Archaeology · doi:10.1080/00438243.2019.1617190 · Cited by 27 · see citing works
“…and humid regions such as the Near East (e.g., Broushaki et al. 2016; Lazaridis et al. 2016; Feldman et al. 2018; Harney et al. 2018), Africa (e.g., Schuenemann et al. 2017; Skoglund et al. 2017; Elkamel et al. 2018; Fregel et al. 2018; van de Loosdrecht et al. 2018), Southeast Asia (e.g., Lipson…”
BackgroundThe deep population history in Africa
Hollfelder, N., Breton, G., Sjödin, P., & Jakobsson, M. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab005 · Cited by 28 · see citing works
“These individuals from Morocco along with younger samples (7000 and 5000 years old) show decreasing sub-Saharan ancestry over time (36,37), a trend which has also been observed in Egypt (34).”
Cabrera, V. M., Marrero, P., Abu‐Amero, K. K., & Larruga, J. M. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1211-4 · Cited by 27 · see citing works
“Studies of ancient DNA in the area appear to confirm this scenario both in the northwest [92] and the northeast [93].”
BackgroundPopulation history of North Africa based on modern and ancient genomes
Lucas-Sánchez, M., Serradell, J. M., & Comas, D. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa261 · Cited by 26 · see citing works
“Nuclear DNA data from these ancient Egyptians further supports these results and reveals a larger Neolithic Near Eastern component than in modern Egyptians, in agreement with the rest of North Africa ancient samples (34).”
ResultAncestral mitochondrial N lineage from the Neolithic ‘green’ Sahara
Vai, S., Sarno, S., Lari, M., Luiselli, D., Manzi, G., Gallinaro, M., Mataich, S., Hübner, A., Modi, A., Pilli, E., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-39802-1 · Cited by 21 · see citing works
Through 40,000 years of human presence in Southern Europe: the Italian case study
Aneli, S., Caldon, M., Saupe, T., Montinaro, F., & Pagani, L. (2021) · Human Genetics · doi:10.1007/s00439-021-02328-6 · Cited by 20 · see citing works
Keita, S. O. Y. (2023) · American Anthropologist · doi:10.1111/aman.13903 · Cited by 20 · see citing works
Never boring: Non-invasive palaeoproteomics of mummified human skin
Demarchi, B., Boano, R., Ceron, A., Bello, F. D., Favero‐Longo, S. E., Fiddyment, S., Marochetti, E. F., Mangiapane, G., Mattonai, M., Pennacini, C., et al. (2020) · Journal of Archaeological Science · doi:10.1016/j.jas.2020.105145 · Cited by 20 · see citing works
Xu, W., Lin, Y., Zhao, K., Li, H., Tian, Y., Ngatia, J. N., Ma, Y., Sahu, S. K., Guo, H., Guo, X., et al. (2021) · Ecology and Evolution · doi:10.1002/ece3.7056 · Cited by 20 · see citing works
Mbouaka, A. L., Gamble, M., Wurst, C., Jäger, H. Y., Maixner, F., Zink, A., Noedl, H., & Binder, M. (2021) · Archaeological and Anthropological Sciences · doi:10.1007/s12520-021-01350-z · Cited by 19 · see citing works
“However, we can discuss some of the trends which we have observed here in the context of what is known about the community at Sayala and wider Nubia and southern Egypt.”
BackgroundInfluentialGenome-wide association study for systemic lupus erythematosus in an egyptian population
Elghzaly, A. A., Sun, C., Looger, L. L., Hirose, M., Salama, M., Khalil, N. M., Behiry, M. E., Hegazy, M. T., Hussein, M. A., Salem, M. N., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.948505 · Cited by 20 · see citing works
Stable population structure in Europe since the Iron Age, despite high mobilityPreprint
Antonio, M. L., Weiß, C. L., Gao, Z., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.15.491973 · Cited by 19 · see citing works
“…et al., 2017 ; Saag et al., 2019 ; Saag et al., 2017 ; Sánchez-Quinto et al., 2019 ; Schiffels et al., 2016 ; Schroeder et al., 2019 ; Schuenemann et al., 2017 ; Sikora et al., 2017 ; Skoglund et al., 2014 ; Skourtanioti et al., 2020 ; Unterländer et al., 2017 ; Valdiosera et al.,…”
Ruíz, E. (2024) · doi:10.1093/oso/9780197634028.001.0001 · Cited by 18 · see citing works
Mayoral, L., & Olsson, O. (2024) · Journal of Economic Growth · doi:10.1007/s10887-024-09243-1 · Cited by 18 · see citing works
“At times, large contingents of “Asiatics”, i.e., people descending from the Levant or other parts of the Near East, settled within Egypt.”
InfluentialEmery, M. V., Duggan, A. T., Murchie, T. J., Stark, R. J., Klunk, J., Hider, J., Eaton, K., Karpinski, E., Schwarcz, H. P., Poinar, H. N., et al. (2018) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2018.04.036 · Cited by 18 · see citing works
Genomics of rare diseases in the Greater Middle East
Chekroun, I., Shenbagam, S., Almarri, M. A., Mokrab, Y., Uddin, M. J., Alkhnbashi, O. S., Zaki, M. S., Najmabadi, H., Kahrizi, K., Fakhro, K. A., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02075-8 · Cited by 17 · see citing works
“The analysis of modern Egyptians samples alongside ancient, mummified remains has the potential to reveal how modern population structure has formed and uncover genetic variants that may have conferred survival advantages or, conversely, predisposed populations to specific diseases 106 .”
ARIADNA: machine learning method for ancient DNA variant discovery
Kawash, J., Smith, S. D., Karaiskos, S., & Grigoriev, A. (2018) · DNA Research · doi:10.1093/dnares/dsy029 · Cited by 17 · see citing works
Molto, J. E., Loreille, O. M., Mallott, E. K., Malhi, R. S., Fast, S. A., Daniels-Higginbotham, J., Marshall, C. K., & Parr, R. L. (2017) · Genes · doi:10.3390/genes8100262 · Cited by 16 · see citing works
Maixner, F., Mitterer, C., Jäger, H. Y., Sarhan, M. S., Valverde, G., Lücker, S., Piombino‐Mascali, D., Szikossy, I., Molnár, E., Pálfi, G., et al. (2021) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13772 · Cited by 15 · see citing works
Mitochondrial variability in the Mediterranean area: a complex stage for human migrations
Angelis, F. D., Scorrano, G., Martínez‐Labarga, C., Scano, G., Macciardi, F. M., & Rickards, O. (2018) · Annals of Human Biology · doi:10.1080/03014460.2017.1416172 · Cited by 16 · see citing works
“…be the generation of similar ancient DNA data from human groups in Mediterranean Europe (Macciardi et al., 2016; Modi et al., 2016), North Africa (Schueneman et al., 2017) and the Near East to gain a more comprehensive picture of the ancient population history of the most important and crowded…”
BackgroundMethodInfluentialAncient DNA challenges prevailing interpretations of the Pompeii plaster casts
Pilli, E., Vai, S., Moses, V. C., Morelli, S., Lari, M., Modi, A., Diroma, M. A., Amoretti, V., Zuchtriegel, G., Osanna, M., et al. (2024) · Current Biology · doi:10.1016/j.cub.2024.10.007 · Cited by 16 · see citing works
Application of knee MRI in forensic age estimation: A retrospective cohort
Daghighi, M. H., Pourisa, M., Javanpour-Heravi, H., et al. (2020) · Radiography · doi:10.1016/j.radi.2020.06.019 · Cited by 15 · see citing works
Fregel, R., Mendez, F. L., Bokbot, Y., Martín-Socas, D., Camalich-Massieu, M. D., Santana, J., Morales, J., Ávila‐Arcos, M. C., Underhill, P. A., Shapiro, B., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/191569 · Cited by 15 · see citing works
Whole-genome ancestry of an Old Kingdom Egyptian
Morez, A., Irish, J. D., Cooke, A., Anastasiadou, K., Barrington, C., Gilardet, A., Kelly, M., Silva, M. S. D., Speidel, L., Tait, F., et al. (2025) · Nature · doi:10.1038/s41586-025-09195-5 · Cited by 15 · see citing works
“1a) have yielded nuclear DNA, all post-dating the emergence of Dynastic Egypt by thousands of years (from 787 cal. bce to 23 cal. ce) 20 .”
Adachi, N., Kanzawa‐Kiriyama, H., Nara, T., Kakuda, T., Nishida, I., & Shinoda, K. (2021) · Anthropological Science · doi:10.1537/ase.2012132 · Cited by 12 · see citing works
“Three DNA libraries, Higashimyo-1 and -2 and -3, were prepared using 8 μl of DNA extract following Shinoda et al. (2017) and Meyer and Kircher (2010), respectively, for mitochondrial genome analysis (Supplementary Table 1).”
MethodFerreira, J. C., Alshamali, F., Montinaro, F., Cavadas, B., Torroni, A., Pereira, L., Raveane, A., & Fernandes, V. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab194 · Cited by 12 · see citing works
Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data
Lan, T., Lin, Y., Ngatia, J. N., Guo, X., Li, R., Li, H., Sahu, S. K., Xie, W., Yang, X., Guo, H. B., et al. (2019) · Genes · doi:10.3390/genes10070509 · Cited by 13 · see citing works
“The whole-genome sequencing (WGS) data of twelve samples was used in this study, including six woolly mammoths (Mammuthus primigenius), three ancient humans (Homo sapiens) [25,26], one ancient horse [4], one ancient goat [27], and one ancient aurochs [28].”
MethodBioarchaeological evidence of one of the earliest Islamic burials in the Levant
Srigyan, M., Bolívar, H., Ureña, I., Santana, J., Petersen, A. D., Iriarte, E., Kırdök, E., Bergfeldt, N., Mora, A., Jakobsson, M., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03508-4 · Cited by 16 · see citing works
Wilkinson, C. M., Saleem, S. N., Liu, C. Y. J., & Roughley, M. A. (2023) · Journal of Archaeological Science · doi:10.1016/j.jas.2023.105884 · Cited by 14 · see citing works
Williams, M. P., Flegontov, P., Maier, R., & Huber, C. D. (2024) · Genetics · doi:10.1093/genetics/iyae110 · Cited by 11 · see citing works
“4b), we randomly assigned one of the two alleles as homozygous at simulated heterozygous positions mimicking what is commonly performed for low-and medium-coverage aDNA (Schuenemann et al .”
Larmuseau, M., & Ottoni, C. (2018) · Annals of Human Biology · doi:10.1080/03014460.2017.1402956 · Cited by 10 · see citing works
“However recent studies of ancient genomes in Africa, including Egyptian mummies (Llorente et al., 2015; Schlebusch et al., In preparation; Schuenemann et al., 2017; Skoglund et al., 2017), are encouraging for more analyses in climatically less-optimal areas of the Mediterranean in the future.”
BackgroundYang, H., Yu, P., Lu, Y., et al. (2018) · Royal Society Open Science · doi:10.1098/rsos.172140 · Cited by 9 · see citing works
“For instance, the genome of ancient Egyptian mummies was used to research ancient human history and offered the perspective of deciphering Egypt’s past [14].”
BackgroundIshiya, K., Mizuno, F., Wang, L., & Ueda, S. (2019) · Bioinformatics and Biology Insights · doi:10.1177/1177932219873884 · Cited by 9 · see citing works
“12-17 However, the quantity of endogenous DNA in archeological remains is extremely low, which makes it difficult to obtain complete mitochondrial genome sequences.”
BackgroundGenetic Variability of CYP2D6, CYP3A4 and CYP3A5 Among the Egyptian Population
Mutawi, T. M., Zedan, M. M., Yahya, R. S., et al. (2021) · Pharmacogenomics · doi:10.2217/pgs-2020-0140 · Cited by 9 · see citing works
Africa, the Cradle of Human Diversity
Fortes‐Lima, C., Mtetwa, E., & Schlebusch, C. M. (2021) · BRILL eBooks · doi:10.1163/9789004500228 · Cited by 9 · see citing works
Adulis and the transshipment of baboons during classical antiquity
Grathwol, F., Roos, C., Zinner, D. P., Hume, B. C. C., Porcier, S. M., Berthet, D., Cuisin, J., Merker, S., Ottoni, C., Neer, W. V., et al. (2023) · eLife · doi:10.7554/elife.87513 · Cited by 7 · see citing works
Where Asia meets Europe – recent insights from ancient human genomics
Feldman, M., Gnecchi‐Ruscone, G. A., Lamnidis, T. C., & Posth, C. (2021) · Annals of Human Biology · doi:10.1080/03014460.2021.1949039 · Cited by 8 · see citing works
“The Steppe is usually subdivided into three main macro-regions, i.e. the Eastern Steppe (mostly covering Mongolia), the Central or Kazakh Steppe (mostly covering today’s Kazakhstan) and the Pontic-Caspian Steppe (from north of the Caucasus and to Eastern Europe).”
BackgroundInfluentialThe first reported case of the rare mitochondrial haplotype H4a1 in ancient Egypt
Drosou, K., Collin, T. C., Freeman, P., Loynes, R. D., & Freemont, A. J. (2020) · Scientific Reports · doi:10.1038/s41598-020-74114-9 · Cited by 7 · see citing works
Beneker, O., Molinaro, L., Guellil, M., Sasso, S., Kabral, H., Bonucci, B., Gaens, N., D’Atanasio, E., Mezzavilla, M., Delbrassine, H., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03580-z · Cited by 7 · see citing works
Warinner, C. (2022) · Journal of Anthropological Research · doi:10.1086/721976 · Cited by 7 · see citing works
“…evidence of past infections (Maixner et al. 2016), but molecular degradation and postmortemmicrobial colonization is generally high in mummified soft tissue remains (Maixner et al. 2016; Neukamm et al. 2020; Schuenemann et al. 2017), making them challenging subjects for ancient microbial studies.”
BackgroundHernigou, P., Hosny, G. A., & Scarlat, M. M. (2023) · International Orthopaedics · doi:10.1007/s00264-023-06012-4 · Cited by 7 · see citing works
“However, a recent study [53] has examined genome-wide datasets from Egyptian mummies.”
Yousfi, F.-Z. E., Haroun, A. E., Nebhani, C., Belayachi, J., Askander, O., Fahime, E. E., Fares, H., Ennibi, K., Abouqal, R., Razıne, R., et al. (2024) · Archives of Virology · doi:10.1007/s00705-024-06038-y · Cited by 7 · see citing works
Genetic Polymorphism of Head and Neck Cancers in African Populations: A Systematic Review
Okoturo, E., Osasuyi, A., & Opaleye, T. (2020) · OTO Open · doi:10.1177/2473974x20942202 · Cited by 7 · see citing works
“In conclusion, studies on HNSCC candidate genes needs to be undertaken in Africa, with more of these studies in sub-Saharan Africa.”
BackgroundInfluentialMethodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines
Андреева, Т. В., Malyarchuk, A. B., Дмитриевна, С. А., Dudko, N. A., Plotnikova, M. Y., & Rogaev, E. I. (2022) · Russian Journal of Genetics · doi:10.1134/s1022795422090034 · Cited by 8 · see citing works
Rapid identification of medicinal leech by species-specific polymerase chain reaction technology
Shen, Y., Yang, H., Zheng, Y., et al. (2019) · Pharmacognosy Magazine · doi:10.4103/pm.pm_596_18 · Cited by 7 · see citing works
Sweatman, M. B. (2024) · Time and Mind · doi:10.1080/1751696x.2024.2373876 · Cited by 6 · see citing works
The Two Brothers: an enlightening study of ancient Egyptian teeth
Forshaw, R. (2019) · BDJ · doi:10.1038/s41415-019-0149-2 · Cited by 6 · see citing works
Mummy DNA unravels ancient Egyptians’ ancestry
Watson, T. (2017) · Nature · doi:10.1038/546017a · Cited by 6 · see citing works
Iadarola, B., Lavezzari, D., Modi, A., Esposti, C. D., Beltrami, C., Rossato, M., Zaro, V., Napione, E., Latella, L., Lari, M., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-00559-1 · Cited by 5 · see citing works
“Next-generation sequencing for the study of ancient samples has mainly targeted small regions, such as the mitochondrial DNA (mtDNA), the Y-chromosome DNA (Y-DNA)[33] or specific SNPs of interest[34][35].”
BackgroundA new analysis interpreting Nilotic relationships and peopling of the Nile Valley
Godde, K. (2018) · HOMO · doi:10.1016/j.jchb.2018.07.002 · Cited by 5 · see citing works
Exhibiting Ancient Africa at the Museum of Fine Arts, Boston: “Ancient Nubia Now” and Its Audiences
Emberling, G. (2020) · American Journal of Archaeology · doi:10.3764/aja.124.3.0511 · Cited by 5 · see citing works
REGIONAL DIFFERENCES IN INTELLIGENCE IN EGYPT: A COUNTRY WHERE UPPER IS LOWER
Dutton, E., Bakhiet, S. F. A., Ziada, K. E., et al. (2018) · Journal of Biosocial Science · doi:10.1017/s0021932018000135 · Cited by 4 · see citing works
“Similarly, there is sub-Saharan admixture in the modern day Egyptian population (Schuenemann et al., 2017) and its extent increases the further south one goes (Kings et al., 1992).”
BackgroundMatić, U. (2021) · Archaeological Dialogues · doi:10.1017/s1380203821000076 · Cited by 4 · see citing works
Sirak, K. A., van Rensburg, J. J., Brielle, E. S., Chen, B., Lazaridis, I., Ringbauer, H., Mah, M., Mallick, S., Micco, A., Rohland, N., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02322-x · Cited by 4 · see citing works
“We ran three replicates of ADMIXTURE with random seeds with K = 3 to K = 12 ancestral reference populations and present K = 10 based on low cross-validation errors with the goal of not overfitting .”
- Authors
- Schuenemann, V. J., Peltzer, A., Welte, B., van Pelt, W. P., Molak, M., Wang, C.-C., Furtwängler, A., Urban, C., Reiter, E., Nieselt, K., Teßmann, B., Francken, M., Harvati, K., Haak, W., Schiffels, S., & Krause, J.
- Affiliations
- Senckenberg Centre for Human Evolution and Palaeoenvironment (DE)
- Max Planck Institute of Geoanthropology (DE)
- University of Tübingen (DE)
- Museum and Institute of Zoology (PL)
- Corresponding author
- Haak, Wolfgang
- Schiffels, Stephan
- Krause, Johannes
- ORCID
- Venue
- Nature Communications
- Published
- 2017-05-30
- Volume
- 8
- Issue
- 1
- Pages
- 15694-15694
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5459999
- OpenAlex
- W2616275082
- Semantic Scholar
- 3e7f48869eafe2763e934722fd88f440db3bd6d4
- Cited by
- 201
- References
- 67
- Citations by year
- 2026: 12 · 2025: 13 · 2024: 24 · 2023: 15 · 2022: 16 · 2021: 30 · 2020: 42 · 2019: 17 · 2018: 25 · 2017: 6
- FWCI
- 14.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- Europe PMC (PubMed Central) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Max Planck Digital Library (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Deutsche Forschungsgemeinschaft (DFG‐FOR 2237, FOR2237)
- Fundacja na rzecz Nauki Polskiej
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Arts and Humanities › Archeology › Paleopathology and ancient diseases
- Social Sciences › Arts and Humanities › Archeology › Ancient Egypt and Archaeology
- Keywords
- mitochondrial genome, New Kingdom Egypt, Roman Egypt, genetic admixture, ancient human migration
- MeSH terms
- Anthropology, Asia, Cell Nucleus, DNA, Mitochondrial, Egypt, Europe, Genotype, Geography, Haplotypes, Humans, Mummies, Phenotype, Population Dynamics, Gene Library, Genome, Human, Africa South of the Sahara, Principal Component Analysis, History, Ancient
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