Cited by 201Forensic and Genetic ResearchPaleopathology and ancient diseasesAncient Egypt and Archaeology

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

Open access
Schuenemann, Verena J., Peltzer, Alexander, Welte, Beatrix, van Pelt, W. Paul, Molak, Martyna, Wang, Chuan-Chao, Furtwängler, Anja, Urban, Christian +8 more·2017·Nature Communications

Abstract

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

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

Crossref · 10.1038/ncomms15694

Cites

68 of 68 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

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.
  • May combine two claims. 37
  • Classified as probably not a substantial claim. 39
  • May combine two claims.

    Findingown data

    Modern 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.

    Findingcitation

    Sample 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 data

    By 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 data

    ALDER 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 data

    Genetic 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.

    Findingcitation

    According 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.

    Interpretationreasoning

    Taken 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 conductcitation

    For 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 data

    The 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 data

    Ancient 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 data

    Other 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 data

    Yields 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 claim
  • May combine two claims.

    Findingown data

    In 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 data

    The 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.
  • May combine two claims.

    Findingown data

    The 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 data

    Nuclear 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 claim
  • May combine two claims.

    Findingown data

    Three 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 claim
  • May combine two claims.

    Findingown data

    All 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 data

    The 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 data

    Most 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 claim
  • May combine two claims.

    Findingown data

    The 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).

    Findingreasoning

    Assuming 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 data

    For 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Mitochondrial 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Derived 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    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).

    “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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    No 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    By 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 data

    All 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 claim
  • May combine two claims.

    Study design and conductown data

    Replication 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    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 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 data

    No 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Under 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 data

    All 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    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 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 given

    Only 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    In 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).

    Interpretationreasoning

    The 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    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.

    “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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Connections 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 data

    Effective sample size for all parameters exceeded 100.

    “Effective sample size for all parameters exceeded 100.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Filtering 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Especially 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.

    Premisecitation

    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 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 data

    Three 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Several 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 claim
  • May combine two claims.

    Study design and conductown data

    Repeating 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The 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.

    Premisecitation

    Widespread 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).

    Premisecitation

    In 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 data

    Samples 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 claim
  • Classified as probably not a substantial claim.

    Premisenone given

    Abusir 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Many 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 data

    In 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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisereasoning

    Rubensohn'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 claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Such 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
58 of 58
  • 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”
3 of 3

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

    Minor

    The list names 20 specific haplogroup categories and then adds a category for all remaining haplogroups, making 21 categories in total.

  • Two different maximum mitochondrial coverage values

    Minor

    The results give a maximum coverage of 4,236-fold, whereas the methods give 4,284-fold for the mitochondrial samples.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 5

  1. Dunand, F. & Lichtenberg, R. Mummies and Death in Egypt Cornell University Press (2006).
  2. Clarysse, W. & Thompson, D. J. Counting the people in Hellenistic Egypt Cambridge University Press (2004).
  3. Rubensohn, O. Griechisch-römische Funde in Ägypten. Archäol. Anz. 20, 65–70 (1905).
  4. David, R. in Ancient Egyptian Materials and Technology (eds Nicholson, P. T., Shaw, I.) 372–389 (Cambridge, 2000).
  5. Mumford, G. D. Egypt and the Levant, The Oxford Handbook of the Archaeology of the Levant: c. 8000-332 BCE Oxford (2014).

Cited by

Sorted by citations

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
Venue
Nature Communications
Published
2017-05-30
Volume
8
Issue
1
Pages
15694-15694
ISSN
2041-1723 (ISSN-L)
OpenAlex
W2616275082
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-26.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-26.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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