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Cited by 85Forensic and Genetic ResearchGenetic diversity and population structureRace, Genetics, and Society

The Genomic History of the Bronze Age Southern Levant

Open access
Agranat-Tamir, Lily, Waldman, Shamam, Martin, Mario A.S., Gokhman, David, Mishol, Nadav, Eshel, Tzilla, Cheronet, Olivia, Rohland, Nadin +27 more·2020·Cell
DOI 10.1016/j.cell.2020.04.024PMC PMC10212583
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Abstract

Summary We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the “Canaanite” material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations, and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different “Canaanite” groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze Age migrations into the region over the past 3000 years.

AI snapshot

Written from the paper’s full text.

TL;DR

Genome-wide ancient DNA from 73 Bronze and Iron Age individuals in the Southern Levant, combined with published data, shows that most Canaanite-associated groups were genetically similar and can be modeled as mixtures of local Neolithic Levant and Zagros/Caucasus-related ancestry. The non-local component increased over time, and present-day Levantine and Jewish groups are consistent with >50% Middle Eastern-related ancestry plus post-Bronze Age East African and European contributions.

Key findings

  • The study reports 73 new individuals from five sites and assembles a combined dataset of 93 individuals from nine sites. Most Bronze and Iron Age Levant individuals form a tight genetic cluster, except three Megiddo outliers and the previously identified Ashkelon IA1 population; qpWave found all Bronze/Iron Age Levant groups consistent with pairwise clades except the Megiddo outliers, Ashkelon IA1, and Sidon.
  • Most Middle-to-Late Bronze Age groups fit a two-source model with 48–57% Neolithic Levant-related ancestry, except Yehud with a point estimate of 66%; Ashkelon ASH_LBA and ASH_IA2 carried 54%±5% and 42%±5% Neolithic Levant-related ancestry, respectively. Baqah failed this model (P = 0.0003). Zagros-related ancestry increased over time, with a significantly positive slope of β=1.4·10−4±0.4·10−4, amounting to ≈14% per thousand years.
  • Three Megiddo outliers had much higher Caucasus-/Zagros-related ancestry; Neolithic Levant component was ≈22–27% in I2200 and ≈9–26% in I10100. Strontium isotope analysis suggested the outlier siblings were raised locally, implying they were descendants of recent migrants; for two outliers, the only working northeast source was contemporaneous Armenia_MLBA.
  • Present-day Jewish and Levantine Arabic-speaking populations were consistent with >50% Middle Eastern-related ancestry. Post-Bronze Age additions included an East African-related component averaging ~10.6% excluding Ethiopian Jews, who harbor ~80% East African component, and a European-related component averaging ~8.7% excluding Ashkenazi Jews, who harbor ~41% European-related component.

Methods

  • New ancient DNA was extracted mostly from petrous bones of 73 individuals from Tel Megiddo (35), Baq‛ah (21), Yehud (13), Tel Hazor (3), and Tel Abel Beth Maacah (1). DNA was converted to double-indexed half UDG-treated libraries enriched for about 1.2 million SNPs; median autosomal SNP coverage was 288,863 (range 4,883–945,269). Strontium isotopes were measured for 12 individuals, plus 8 without DNA, and AMS radiocarbon dates were generated for 20 individuals.
  • These data were combined with published data for 13 Bronze Age and 7 Iron Age Southern Levant individuals. After removing low-coverage individuals and close relatives, 62 individuals remained for further analysis.
  • Main analyses included PCA, ADMIXTURE, f4-statistics, qpWave, and qpAdm. For present-day populations, the authors developed LINADMIX and pseudo-haplotype ChromoPainter (PHCP), validated with simulations and perturbations.

Limitations

  • Stated: the number of individuals and their time span are insufficient to determine whether the increase in Zagros-related ancestry happened continuously during the Middle and Late Bronze Age or through multiple distinct migration events.
  • Stated: qpAdm could not produce a single working model for the majority of present-day West Eurasian populations because of sub-Saharan African-related admixture; LINADMIX and PHCP have high uncertainty in separating Megiddo_MLBA and Iran_ChL contributions, and other potential ancestry sources remain possible.
  • Stated: the genetic data are compatible with both a Caucasus and a Zagros source for the non-local ancestry, and the Caucasus conclusion may be revised once ancient DNA from the Middle-to-Late Bronze Age Zagros becomes available. Evident: there is no ancient DNA sampling from the northeastern ancient Near East, and Sidon and Baq‛ah show heterogeneity or deviations that may reflect limited sampling and site-specific cosmopolitanism.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2020.04.024

Cites

69 of 69 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

28 of 44 cited sources checked · 13 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    The Bronze Age Sidon group could be modeled as a major (93±2%) ancestral source for present-day groups in the region.

    “The Bronze Age Sidon group could be modeled as a major (93±2%) ancestral source for present-day groups in the region (Haber et al., 2017).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Haber et al., 2017 source

      The Main Text (page unavailable) reports a qpAdm model in which Sidon_BA accounts for 93% ± 1.6% of present-day Lebanese ancestry, consistent with the rounded 93 ± 2% figure. It does not establish that percentage for other present-day groups in the region, so the claim is broader than the reported model. (LLM, conf=0.90)

      Experimental — accuracy not yet measured
  • Premisecitation

    The ancestry of the previously published Bronze Age Southern Levant individuals could be modeled as a mixture of earlier local groups and groups related to the Chalcolithic people of the Zagros Mountains (Iran_ChL).

    “The ancestry of these individuals could be modeled as a mixture of earlier local groups and groups related to the Chalcolithic people of the Zagros Mountains, located in present-day Iran and designated in previous studies as Iran_ChL (Haber et al., 2017; Lazaridis et al., 2016).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Haber et al., 2017 source
    • cites Lazaridis et al., 2016 source
  • Premisecitation

    The ancestry of Chalcolithic individuals from Peqi'in cave included an additional component related to earlier Anatolian farmers, which was excluded as a substantial source for later Bronze Age groups from the Southern Levant, except for coastal groups from Sidon and Ashkelon.

    “A study of Chalcolithic individuals from Peqi’in cave in the Galilee (present-day Israel) showed that the ancestry of this earlier group included an additional component related to earlier Anatolian farmers, which was excluded as a substantial source for later Bronze Age groups from the Southern Levant, with the exception of the coastal groups from Sidon and Ashkelon (Feldman et al., 2019; Harney”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Feldman et al., 2019 source

      Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites Harney et al., 2018 source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
  • Findingcitation

    We identified 17 individuals as being first, second, or third degree relatives of other individuals in the dataset.

    “We used the method described in (Olalde et al., 2019) to identify 17 individuals as being first, second, or third degree relatives of other individuals in the dataset.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Olalde et al., 2019 source

      The paper’s analysis overview says it excluded first-degree relatives from its dataset, showing that Olalde et al. assessed close relationships. The passages found do not describe a method for identifying first-, second-, and third-degree relatives. The 17 individuals are the citing authors’ own result, not a finding attributed to Olalde et al. (LLM, conf=0.73)

      Experimental — accuracy not yet measured
  • Findingcitation

    The genetic distinctiveness of the Sidon individuals is compatible with previous findings that Chalcolithic Levantine individuals from Peqi'in Cave are consistent with contributing some ancestry to the Sidon individuals, but not to the 'Ain Ghazal ones.

    “The genetic distinctiveness of the Sidon individuals is also compatible with previous findings that Chalcolithic Levantine individuals from Peqi’in Cave are consistent with contributing some ancestry to the Sidon individuals, but not to the ‘Ain Ghazal ones (Harney et al.,”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Harney et al., 2018 source
  • Classified as probably not a substantial claim. 20
  • May combine two claims. 33

  • Classified as probably not a substantial claim.

    Premisecitation

    Previous ancient DNA studies published genome-scale data for 13 individuals from four Bronze Age sites in the Southern Levant.

    “Previous ancient DNA studies published genome-scale data for 13 individuals from four Bronze Age sites in the Southern Levant: three individuals from ‘Ain Ghazal in present-day Jordan, dated to ~2300 BCE (Intermediate Bronze Age) (Lazaridis et al., 2016); five from Sidon in present-day Lebanon, dated to ~1750 BCE (Middle Bronze Age) (Haber et al., 2017); two from Tel Shadud in present-day Israel,”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites Lazaridis et al., 2016 source

      The paper’s Abstract (page unavailable) reports genome-wide ancient DNA from the southern Levant, including individuals from ‘Ain Ghazal and individuals from the Bronze Age. But it identifies the ‘Ain Ghazal samples it mentions as Pre-Pottery Neolithic (8,300–6,700 BCE); our copy does not establish three ‘Ain Ghazal individuals dated to ~2300 BCE. The citation is attached to that specific group, not to the other sites in the citing sentence. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites Haber et al., 2017 source
    • cites Feldman et al., 2019 source

  • May combine two claims.

    Findingown data

    All Bronze and Iron Age Levant individuals form a tight cluster, except for three outliers from Megiddo, and previously identified outliers from the Ashkelon population known as IA1.

    “All Bronze and Iron Age Levant individuals (blue and green shapes) form a tight cluster, except for three outliers from Megiddo, and previously identified outliers from the Ashkelon population known as IA1 (Iron Age I; Feldman et al., 2019).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Feldman et al., 2019 source

  • Classified as probably not a substantial claim.

    Premisecitation

    Ashkelon IA1 has previously been reported to harbor European ancestry.

    “Ashkelon IA1 has previously been reported to harbor European ancestry and so our finding that it is genetically differentiated from contemporary groups is unsurprising (Feldman et al., 2019).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Feldman et al., 2019 source

  • Classified as probably not a substantial claim.

    Premisecitation

    Two previous studies modeled Bronze Age individuals from 'Ain Ghazal and Sidon as derived from a mixture of earlier local groups (Levant_N) and groups related to peoples of the Chalcolithic Zagros mountains (Iran_ChL).

    “Two previous studies of Bronze Age individuals from ‘Ain Ghazal and Sidon modeled them as derived from a mixture of earlier local groups (Levant_N) and groups related to peoples of the Chalcolithic Zagros mountains (Iran_ChL) (Haber et al., 2017; Lazaridis et al., 2016).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Haber et al., 2017 source
    • cites Lazaridis et al., 2016 source

      The section ‘How diverse first farmers of the Near East mixed to form the region’s later populations’ (page unavailable) reports that people related to Chalcolithic western Iranians contributed ancestry to Levantine Bronze Age populations; Extended Data also identifies Levant_N as an admixture reference for Levant_BA. But the paper describes its ‘Ain Ghazal samples as Pre-Pottery Neolithic, not Bronze Age, and the passages do not identify Bronze Age individuals from Sidon. The site-specific attribution is therefore unsupported. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingcitation

    The three Megiddo outliers were found in close proximity to each other at Level K-10, which is radiocarbon dated to 1581-1545 BCE (domestic occupation) and 1578-1421 BCE (burials; both ±1σ), while the bone of one of the three (I10100) was directly dated (1688-1535 BCE, ±2σ).

    “The three were found in close proximity to each other at Level K-10, which is radiocarbon dated to 1581–1545 BCE (domestic occupation) and 1578–1421 BCE (burials; both ±1σ) (Martin et al., 2020; Toffolo et al., 2014), while the bone of one of the three (I10100) was directly dated (1688–1535 BCE, ±2σ).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Martin et al., 2020 source
    • cites Toffolo et al., 2014 source

      The Introduction (p. 4) identifies Level K-10 as containing domestic architecture and intramural burials, and Results Table 4 (p. 17) gives a radiocarbon-based range for the transition from K-10 to K-9. Our copy does not establish that the three individuals were found close together, give the claimed occupation and burial ranges, or identify I10100 and its direct bone date. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

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

    Premisecitation

    Earlier genetic analyses modeled the genomes of Middle to Late Bronze Age people of the Southern Levant as having almost equal shares of earlier local populations (Levant_N) and populations related to the Chalcolithic Zagros, suggesting a movement from the northeast into the Southern Levant.

    “Earlier genetic analyses modeled the genomes of Middle to Late Bronze Age people of the Southern Levant as having almost equal shares of earlier local populations (Levant_N) and populations that are related to the Chalcolithic Zagros (Feldman et al., 2019; Haber et al., 2017; Lazaridis et al., 2016), suggesting a movement from the northeast into the Southern Levant.”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites Feldman et al., 2019 source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites Haber et al., 2017 source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites Lazaridis et al., 2016 source

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

    Premisecitation

    Ashkenazi and Moroccan Jews both have a history in Europe.

    “The European-related component is highest in the European control populations (English and Tuscan), as well as in Ashkenazi and Moroccan Jews, both having a history in Europe (Atzmon et al., 2010; Carmi et al., 2014; Schroeter, 2008).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites Atzmon et al., 2010 source

      The Introduction (page unavailable) places Ashkenazi Jews in the Rhine Valley and Eastern Europe. It also says North African Jewish communities admixed with Sephardic Jews who migrated from the Iberian Peninsula, but it does not specifically discuss Moroccan Jews or establish that Moroccan Jews themselves lived in Europe. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites Carmi et al., 2014 source

      The Abstract identifies Ashkenazi Jews as having Central and Eastern European ancestry, and the Results describe a substantial ancestral European contribution to their gene pool. Our copy does not address whether Moroccan Jews have a history in Europe, so it supports only the Ashkenazi part of the claim. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Schroeter, 2008

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationown data

    Our results suggest that both LINADMIX and PHCP are highly informative for individuals with ancestry sources similar to those analyzed here.

    “Thus, although ADMIXTURE, the basis of LINADMIX, is known to have certain pitfalls as a tool for quantifying ancestry proportions (Lawson et al., 2018), in the case of individuals with ancestry sources similar to those we have analyzed here, our results suggest that both LINADMIX and PHCP are highly informative.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Lawson et al., 2018 source

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

    Premisecitation

    Petrous bones are known to yield up to one hundred times more DNA than other skeletal elements.

    “Of the samples that produced working data, all but one came from petrous bones, which are known to yield up to one hundred times more DNA than other skeletal elements (Gamba et al., 2014; Pinhasi et al., 2015, 2019).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Gamba et al., 2014 source

      The Results section (‘The petrous bone and differential DNA yields’) supports substantially higher endogenous DNA yields from petrous bones than from other skeletal elements. It reports up to 183-fold higher yields than other bones, however, rather than the claimed upper figure of 100-fold. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites Pinhasi et al., 2015, 2019

      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

    One of the two Iron Age populations in the Philistine coastal city of Ashkelon (ASH_IA1) showed evidence of mobility of populations related to southern Europe around the Bronze Age to Iron Age transition.

    “For example, one of the two Iron Age populations in the Philistine coastal city of Ashkelon (ASH_IA1) showed evidence of mobility of populations related to southern Europe around the Bronze Age to Iron Age transition (Feldman et al., 2019).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Feldman et al., 2019 source

  • May combine two claims.

    Findingown data

    The sampled individuals from the different sites are usually genetically similar, albeit with subtle but in some cases significant differences, especially in residents of the coastal regions of Sidon and Ashkelon.

    “We show that the sampled individuals from the different sites are usually genetically similar, albeit with subtle but in some cases significant differences, especially in residents of the coastal regions of Sidon and Ashkelon.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    ADMIXTURE results are qualitatively consistent with the PCA, suggesting that all individuals but the outliers from Megiddo and the Ashkelon IA1 population have similar ancestry.

    “The ADMIXTURE results are qualitatively consistent with the PCA, suggesting that all individuals but the outliers from Megiddo and the Ashkelon IA1 population have similar ancestry (Figure 1C).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    The median number of autosomal SNPs covered was 288,863 (range 4,883-945,269).

    “The median number of autosomal SNPs covered was 288,863 (range 4,883–945,269).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    After removing low-coverage individuals and closely related family members, 62 individuals were left for further analysis.

    “After removing low-coverage individuals and closely related family members, 62 individuals were left for further analysis (Table S1).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Three individuals in the Baq'ah are exceptions, suggesting that the difficulty in modelling individuals from this site as a mixture of Neolithic Levant and Chalcolithic Zagros might reflect ancestry heterogeneity.

    “Another exception is three individuals in the Baq’ah (Table S2), which suggests that the difficulty in modelling individuals from this site as a mixture of Neolithic Levant and Chalcolithic Zagros might reflect ancestry heterogeneity (Figure 3).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Two of the three Megiddo outliers are a brother and a sister, leaving in the final dataset two individuals marked as outliers.

    “Two of the three Megiddo outliers are a brother and a sister (Family 4, I2189 and I2200), leaving in the final dataset two individuals marked as outliers.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Sidon individuals are significantly differentiated in qpWave despite roughly clustering with other Southern Levant Bronze Age groups in PCA and ADMIXTURE.

    “The significant differentiation of the Sidon individuals in qpWave—despite the fact that they roughly cluster with the other Southern Levant Bronze Age groups in PCA and ADMIXTURE—is notable especially as we find that they are consistent with forming a clade with the two groups from coastal Ashkelon that do not have European-related admixture (the Bronze Age and later Iron Age groups ASH_LBA and”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Bronze and Iron Age Ashkelon (ASH_LBA and ASH_IA2) carry 54%±5% and 42%±5% Neolithic Levant-related ancestry, respectively.

    “We used qpAdm to estimate that Bronze and Iron Age Ashkelon (ASH_LBA and ASH_IA2) carry 54%±5% and 42%±5% Neolithic Levant-related ancestry, respectively.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Megiddo outliers not only fail to form a clade with the other populations, but also with each other.

    “The Megiddo outliers not only fail to form a clade with the other populations, but also with each other.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    There is evidence of substructure within the Sidon individuals, with some but not all consistent with forming a clade with inland Southern Levant populations.

    “However, we did find evidence of substructure within the Sidon individuals, with some but not all consistent with forming a clade with inland Southern Levant populations, a finding that could reflect substantial cosmopolitan nature of this coastal site (Methods S1C, see Discussion).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Methods S1C

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingown data

    The oldest individuals in our collection, from the Intermediate Bronze Age, already carried significant Zagros-related ancestry, suggesting that gene flow into the region started before ca. 2400 BCE.

    “We observed that the oldest individuals in our collection, from the Intermediate Bronze Age, already carried significant Zagros-related ancestry, suggesting that gene flow into the region started before ca. 2400 BCE.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Neolithic Levant component is ≈22-27% in I2200, and ≈9-26% in I10100.

    “The Neolithic Levant component is ≈22–27% in I2200, and ≈9–26% in I10100.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The addition of Iran_ChL to the set of outgroups does not change this result or cause model failure.

    “The addition of Iran_ChL to the set of outgroups does not change this result or cause model failure.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In sensitive qpAdm modeling, the only working northeast source population for these two individuals is the contemporaneous Armenia_MLBA, while the earlier Iran_ChL and Armenia_EBA do not fit.

    “Direct support for this hypothesis comes from the fact that in sensitive qpAdm modeling (including closely related sets of outgroups), the only working northeast source population for these two individuals is the contemporaneous Armenia_MLBA, while the earlier Iran_ChL and Armenia_EBA do not fit (Table S2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Both methods estimated the ancestry proportion of the distant source population with errors of up to 4% and the proportions of the closely related source populations with errors of up to 10%.

    “Both methods estimated the ancestry proportion of the distant source population with errors of up to 4% and the proportions of the closely related source populations with errors of up to 10%.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The reason these individuals are distinct from the rest is that their Caucasus- or Zagros-related genetic component is much higher, reflecting ongoing gene flow into the region from the northeast.

    “The reason these individuals are distinct from the rest is that their Caucasus- or Zagros-related genetic component is much higher, reflecting ongoing gene flow into the region from the northeast (Table S2, Figure S2B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    The European-related component is highest in the European control populations (English and Tuscan), as well as in Ashkenazi and Moroccan Jews.

    “The European-related component is highest in the European control populations (English and Tuscan), as well as in Ashkenazi and Moroccan Jews, both having a history in Europe (Atzmon et al., 2010; Carmi et al., 2014; Schroeter, 2008).”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Europe_LNBA is a representative of ancient Europeans from the Late Neolithic and Bronze Age.

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

    Findingnone given

    The English and Tuscan populations have a very low Middle Eastern-related component.

    “As expected, the English and Tuscan populations have a very low Middle Eastern-related component.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Eastern African-related component is present in Arabic-speaking groups but is lower in non-Ethiopian Jewish groups.

    “These include an Eastern African-related component that is present in Arabic-speaking groups but is lower in non-Ethiopian Jewish groups, as well as Zagros-related contribution to Levantine populations, which is highest in the northernmost population examined, suggesting a contribution of populations related to the Zagros even after the Bronze and Iron Ages.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Present-day Somalis are an appropriate representative of an Eastern African source for modeling present-day populations.

  • May combine two claims.

    Findingreasoning

    The only inland population that resembles Sidon is Abel Beth Maacah, perhaps because of its geographic proximity.

    “The only inland population that resembles Sidon is Abel Beth Maacah, perhaps because of its geographic proximity (Figure 1A, Figure 2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    An Eastern African-related ancestry entered the region after the Bronze Age, with an approximate south-to-north gradient.

    “We also see an Eastern African-related ancestry entering the region after the Bronze Age, with an approximate south-to-north gradient.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Present-day Somalis are an appropriate representative of an Eastern African source for modeling present-day populations.

  • May combine two claims.

    Findingown data

    Both Arabic-speaking and Jewish populations are compatible with having more than 50% Middle Eastern-related ancestry.

    “We found that both Arabic-speaking and Jewish populations are compatible with having more than 50% Middle Eastern-related ancestry.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Megiddo_MLBA is a representative of the Middle to Late Bronze Age component.
    • The authors state this as an assumption: Iran_ChL is a representative of the Zagros and the Caucasus.

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

    Study design and conductcitation

    We restricted the plot to 68 individuals represented by at least 30,000 autosomal SNPs, a coverage threshold where the ability to infer ancestry was robust to sampling noise.

    “We restricted the plot to 68 individuals represented by at least 30,000 autosomal SNPs (Figure 1B), a coverage threshold where the ability to infer ancestry was robust to sampling noise (Methods S1B).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Methods S1B

      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), S4 (based). May combine two claims.

    Interpretationnone given

    This movement might not have been limited to a short pulse, and instead could have involved multiple waves throughout the Bronze Age.

    “This movement might not have been limited to a short pulse, and instead could have involved multiple waves throughout the Bronze Age.”
    Quote in the paperNot a substantial claim

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

    Interpretationnone given

    The failure of Baqah to fit the model may be a result of ancestry heterogeneity across the Baqah individuals.

    “This may be a result of ancestry heterogeneity across the Baqah individuals (see below).”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    These results do not change qualitatively when using a larger set of outgroup populations.

    “These results do not change qualitatively when we used a larger set of outgroup populations (Table S2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Some level of gene flow into the Levant took place during the later phases of the Bronze Age, and the source of this gene flow was the Caucasus.

    “This shows that some level of gene flow into the Levant took place during the later phases of the Bronze Age, and suggests that the source of this gene flow was the Caucasus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    During the 2nd millennium BCE, Sidon was a major port city connected in trading relations with the eastern Mediterranean basin, which could have led to significant genetic inflow, making its population more heterogeneous than that of inland cities.

    “During the 2nd millennium BCE, Sidon was a major port city, and was connected in trading relations with the eastern Mediterranean basin, which could have led to a significant genetic inflow, making its population more heterogeneous than that of inland cities.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Gene flow into the Levant from people related to those in the Caucasus or Zagros was already occurring by the Intermediate Bronze Age, and it lingered, episodically or continuously, at least in inland sites, during the Middle-to-Late Bronze Age.

    “Taken together, our analyses show that gene flow into the Levant from people related to those in the Caucasus or Zagros was already occurring by the Intermediate Bronze Age, and that it lingered, episodically or continuously, at least in inland sites, during the Middle-to-Late Bronze Age.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The authors verified their conclusions and the robustness of the estimations using a different representative for the Bronze Age Levantine groups as a source and using perturbations to the ADMIXTURE parameters.

    “We further verified these conclusions, as well as the robustness of the estimations, using a different representative for the Bronze Age Levantine groups as a source (Tables S4–S5, Methods S1J), and using perturbations to the ADMIXTURE parameters (Table S4, Methods S1K).”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    The Baq‛ah population might be admixed with more eastern groups, which are not yet genetically sampled.

    “The Baq‛ah is located on the fringe of the Syrian desert, hence this population might be admixed with more eastern groups, which are not yet genetically sampled.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Because there is little archaeological evidence of a direct cultural connection between the Southern Levant and the Zagros region in this period, the Caucasus is a more likely source for this ancestry.

    “As there is little archaeological evidence of a direct cultural connection between the Southern Levant and the Zagros region in this period, the Caucasus is a more likely source for this ancestry.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The patterns of present-day populations reflect demographic processes that occurred after the Bronze Age, and are plausibly related to processes known from the historical literature.

    “Taken together, the patterns of the present-day populations reflect demographic processes that occurred after the Bronze Age, and are plausibly related to processes known from the historical literature (Methods S1I).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    PHCP and LINADMIX agree well with respect to the Somali and Europe_LNBA component, and hence also for the combined contribution of Iran_ChL and Megiddo_MLBA.

    “Comparison of PHCP and LINADMIX shows that they agree well with respect to the Somali and Europe_LNBA component, and hence also for the combined contribution of Iran_ChL and Megiddo_MLBA (Methods S1G, Figure S4).”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    All data generated in this study is available.

    “All data generated in this study is available, see Key Resource Table.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    The authors addressed the problem of estimating ancestry proportions by developing two statistical techniques and testing the robustness of their inference based on a comparison between these methods, simulations and perturbations of the input.

    “We addressed the problem by developing two statistical techniques, and then testing the robustness of our inference based on a comparison between these methods, simulations and perturbations of the input (see STAR Methods, Methods S1F–K).”
    Quote in the paperSubstantial claim

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

    Study design and conductcitation

    The authors used UDG to reduce the rate of cytosine-to-thymine errors typical of ancient DNA.

    “We extracted DNA using a method designed to retain short and highly degraded fragments (Dabney et al., 2013; Korlević et al., 2015; Skoglund et al., 2014), and built the DNA into individual barcoded double-stranded libraries in the presence of the enzyme Uracil–DNA–glycosylase (UDG) to reduce the rate of cytosine-to-thymine errors typical of ancient DNA (Rohland et al., 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Rohland et al., 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

    Replicate measurements of 87Sr/86Sr of the SRM-987 standard over the course of this study yielded 87Sr/86Sr = 0.710273 ± 10 (2σ), n = 29.

    “Replicate measurements of 87Sr/86Sr of SRM-987 standard over the course of this study yielded 87Sr/86Sr = 0.710273 ± 10 (2σ), n = 29.”
    Quote in the paperNot a substantial claim
48 of 48

  • The paper relies on this without support.

    There is no archaeological evidence for cultural spread directly from the Zagros into the Southern Levant during the Bronze Age.

    “Whereas people of the Chalcolithic Zagros are so far the best proxy population for this ancestry component, there is no archaeological evidence for cultural spread directly from the Zagros into the Southern Levant during the Bronze Age.”

  • The paper relies on this without support.

    Almost all present-day Levantine and Mediterranean populations have significant sub-Saharan African-related admixture that the ancient groups did not.

    “qpAdm assumes no admixture between groups related to the outgroups and the source populations, but almost all present-day Levantine and Mediterranean populations have significant sub-Saharan African-related admixture that the ancient groups did not.”

  • The authors state this as an assumption.

    qpAdm assumes no admixture between groups related to the outgroups and the source populations.

    “qpAdm assumes no admixture between groups related to the outgroups and the source populations, but almost all present-day Levantine and Mediterranean populations have significant sub-Saharan African-related admixture that the ancient groups did not.”

  • The authors state this as an assumption.

    Present-day Somalis are an appropriate representative of an Eastern African source for modeling present-day populations.

    “Present-day Somalis as representatives of an Eastern African source (in the absence of genetic data on ancient populations from the region)”

  • The authors state this as an assumption.

    Megiddo_MLBA is a representative of the Middle to Late Bronze Age component.

    “Megiddo_MLBA (the largest group) as a representative of the Middle to Late Bronze Age component”

  • The authors state this as an assumption.

    Iran_ChL is a representative of the Zagros and the Caucasus.

    “Iran_ChL as a representative of the Zagros and the Caucasus”

  • The authors state this as an assumption.

    Europe_LNBA is a representative of ancient Europeans from the Late Neolithic and Bronze Age.

    “Europe_LNBA as a representative of ancient Europeans from the Late Neolithic and Bronze Age”

  • The paper relies on this without support.

    The Armenian sites analyzed are the best representatives to date of the Kura-Araxes and Hurrian cultures.

    “The Armenian sites we analyzed are the best representatives to date of these cultures.”
8 of 8

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • C. elegans has a behavioral repertoire that is modest compared to most animals and that has been extensively documented.

    “C. elegans is among the most thoroughly studied organisms. It has a behavioral repertoire that is modest compared to most animals and that has been extensively documented”

    From Understanding Agent Complexity Through Affordances (2025) · cites this paper as Flavell et al., 2020

    The STAR Methods section describes ancient human remains from archaeological sites in Israel and Jordan, not C. elegans. Searches for C. elegans and its behavioral repertoire found no passage in our copy addressing the claim. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

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.

  • Megiddo sibling's sample ID changes

    Minor

    The sibling pair is identified elsewhere as I2189 and I2200, but the site description names I2189 and I2220.

  • PHCP emission formula reverses the stated probability

    Minor

    The prose assigns probability θ to observing the same allele as the donor. The formula instead assigns 1−θ to observing A when both donor alleles are A, and θ when both are B.

2 of 2

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Authors
Agranat-Tamir, L., Waldman, S., Martin, M. A. S., Gokhman, D., Mishol, N., Eshel, T., Cheronet, O., Rohland, N., Mallick, S., Adamski, N., Lawson, A. M., Mah, M., Michel, M., Oppenheimer, J., Stewardson, K., Candilio, F., Keating, D., Gamarra, B., Tzur, S., Novak, M., Kalisher, R., Bechar, S., Eshed, V., Kennett, D. J., Faerman, M., Yahalom-Mack, N., Monge, J. M., Govrin, Y., Erel, Y., Yakir, B., Pinhasi, R., Carmi, S., Finkelstein, I., Carmel, L., & Reich, D.
Affiliations
  • Hebrew University of Jerusalem (IL)
  • Tel Aviv University (IL)
  • University of Vienna (AT)
  • Broad Institute (US)
  • Howard Hughes Medical Institute (US)
  • University College Dublin (IE)
  • Institute for Anthropological Research (HR)
  • Brown University (US)
  • Israel Antiquities Authority (IL)
  • University of California, Santa Barbara (US)
  • University of Pennsylvania (US)
Corresponding author
  • Novak, Mario
  • Pinhasi, Ron
  • Carmi, Shai
  • Finkelstein, Israel
  • Carmel, Liran
  • Reich, David
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2020-05
Volume
181
Issue
5
Pages
1146-1157.e11
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2020.04.024
PMC
PMC10212583
OpenAlex
W3030827112
Semantic Scholar
ad55344c26677c6ac52239c775d0c11db5f67fea
Cited by
85
References
69
Citations by year
2026: 12 · 2025: 18 · 2024: 13 · 2023: 9 · 2022: 15 · 2021: 16 · 2020: 2
FWCI
5.58
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion)
  • IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
Funders
  • National Science Foundation
  • John Templeton Foundation
  • Israel Science Foundation
  • National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
Keywords
population genomics, ancient DNA, Iron Age
MeSH terms
DNA, Ancient, Archaeology, DNA, Mitochondrial, Ethnicity, Genetics, Population, Haplotypes, Humans, Middle East, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Mediterranean Region, Genomics, History, Ancient, Gene Flow, Human Migration

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 2026-10-10.

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

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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