Ancient DNA sheds light on the genetic origins of early Iron Age Philistines
Open accessAbstract
Bronze and Iron Age genomes suggest a European-related gene flow coincided with the Philistines arrival in ancient Ashkelon.
AI snapshot
Written from the paper’s full text.
TL;DR
Genome-wide ancient DNA from a Bronze-to-Iron Age time series at Ashkelon shows long-term local Levantine ancestry, a transient early Iron Age European-related gene flow, and its disappearance by the later Iron Age. The authors interpret this as genetic evidence coinciding with the Philistine arrival, followed by rapid dilution into the local Levantine gene pool.
Key findings
- Of 108 skeletal elements screened, 10 yielded sufficient human DNA: 3 Late Bronze Age (ASH_LBA), 4 early Iron Age I (ASH_IA1), and 3 later Iron Age II (ASH_IA2) individuals.
- All three Ashkelon populations derived most ancestry from the local Levantine gene pool; ASH_LBA fit a two-way model with ~60% Levant_ChL ancestry (60.0 ± 6.5%) and the rest Iran_ChL.
- ASH_IA1 was distinct in its European-related affinity: ADMIXTURE assigned it an average 14% WHG-related component versus 2–9% in earlier Bronze Age Levantine populations; the best-supported two-way model inferred ~43% ancestry from Greek Bronze Age “Crete_Odigitria_BA” (43.1 ± 19.2%) and the rest from ASH_LBA.
- The European-related signal did not persist in ASH_IA2: WHG-related ancestry was 8% in ASH_IA2 versus 14% in ASH_IA1, and ASH_IA2 fit a two-way Levant_ChL + Iran_ChL model. Modeling ASH_IA2 as a mixture of ASH_IA1 and earlier Bronze Age Levantines/Late Period Egyptian inferred 7–38% contribution from ASH_IA1, but no contribution could not be rejected.
Methods
- Ancient DNA was extracted from 108 Ashkelon skeletal elements; 10 libraries were enriched with a 1.24-million-SNP “1240 k capture” and sequenced. The merged dataset included 638 published ancient genomes and 4,943 present-day individuals from 298 populations, totaling 593,124 SNP sites.
- Population-genetic analyses included PCA, ADMIXTURE (K = 9), f4/f3-statistics, and qpAdm/qpWave modeling, alongside mitochondrial and Y-chromosome haplogroup assignment.
- Authentication and quality control included mitochondrial contamination estimates of 0–9% (two individuals above 5%), nuclear contamination up to 4.3% in males, and relatedness testing showing no first- or second-degree relatives among the 10 individuals.
Limitations
- The paper states that DNA preservation in the southern Levant is low, with only 10 of 108 skeletal elements yielding sufficient human DNA; mean coverage for the reported genomes ranged from 0.08 to 0.7 fold. It also cautions that radiocarbon dates should be treated as rough estimates because marine carbon in the diet could make calibrated dates older than true age.
- The paper states that the spatiotemporal origins of the post-Neolithic gene flow remain broadly defined, that alternative two-way models also fit with smaller P values, and that it cannot distinguish small-scale gene flow from population structure between the Early and Late Bronze Age.
- The paper states that candidate source populations may be missing due to geographical and temporal sampling gaps, that better proxies might be found with future data, and that limited statistical power from insufficient coverage or lack of appropriate contemporaneous proxies affects inference. It also notes limited resolution in the ASH_IA2 model, where no contribution from ASH_IA1 cannot be rejected. Evident from the text: the sample is small (10 individuals across three groups), with low coverage and uneven group sizes.
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Cites
Statistics
Claims the paper makes
0 of 9 cited sources checked · 0 supported · 0 flagged
- Findingown data
A second ancestral component maximized in Iran_N is on average higher in ASH_LBA and earlier Bronze Age Levantines (20 to 30%) than in all earlier Levantines (3 to 8%).
“a second component (shown in green) that is maximized in Iran_N is, on average, higher in ASH_LBA and in each of the earlier Bronze Age Levantines compared to all earlier Levantines (20 to 30% and 3 to 8%, respectively).”
Quote in the paperNot a substantial claim - Findingown data
ASH_LBA is assigned the same major ancestral component as all earlier Levantine populations in ADMIXTURE analysis.
“ASH_LBA is assigned the same major ancestral component as all earlier Levantine populations”
Quote in the paperSubstantial claim - Findingown data
The early Iron Age Ashkelon population (ASH_IA1) had high variation in its genetic affinity to European-derived populations.
“The early Iron Age population was distinct in its high genetic affinity to European-derived populations and in the high variation of that affinity”
- Also stated in: § Genetic discontinuity between the Bronze Age and the early Iron Age people of Ashkelon · plain
“the variance is significantly higher in ASH_IA1 than in either ASH_LBA or ASH_IA2 (P < 2.2 × 10−16 for both by a Fligner-Killeen test)”
Quote in the paperSubstantial claim - Also stated in: § Genetic discontinuity between the Bronze Age and the early Iron Age people of Ashkelon · plain
- Findingown data
Compared to earlier Levantines, Bronze Age individuals including ASH_LBA are shifted along PC2 toward ancient Iranian and Caucasus individuals.
“Compared to earlier Levantines [Levantine early farmers from present-day Jordan and Israel labeled “Levant_N” (12) and Chalcolithic individuals from Peqi’in, Israel labeled “Levant_ChL” (11)], the Bronze Age individuals including ASH_LBA are all shifted along PC2 toward ancient Iranian and Caucasus individuals”
Quote in the paperNot a substantial claim - Findingown data
Only 10 of 108 skeletal elements excavated in Ashkelon yielded sufficient amounts of human DNA.
“We extracted and sequenced DNA from 108 skeletal elements excavated in Ashkelon. In line with the low DNA preservation previously reported for the southern Levant (11–14), only 10 yielded sufficient amounts of human DNA (data file S1).”
Quote in the paperNot a substantial claim
- Findingown data
The early Iron Age Ashkelon population (ASH_IA1) had high genetic affinity to European-derived populations.
“The early Iron Age population was distinct in its high genetic affinity to European-derived populations and in the high variation of that affinity”
- Also stated in: § Genetic discontinuity between the Bronze Age and the early Iron Age people of Ashkelon · plain
“the four ASH_IA1 individuals from the following Iron Age I period are, on average, shifted along PC1 toward the European cline and are more spread out along PC1, overlapping with ASH_LBA on one extreme and with the Greek Late Bronze Age “S_Greece_LBA” (25) on the other”
Quote in the paperSubstantial claim - Also stated in: § Genetic discontinuity between the Bronze Age and the early Iron Age people of Ashkelon · plain
- Findingown data
All three Ashkelon populations derive most of their ancestry from the local Levantine gene pool.
“We find that all three Ashkelon populations derive most of their ancestry from the local Levantine gene pool.”
Quote in the paperSubstantial claim - Findingown data
The excess European affinity of the early Iron Age individuals does not persist in the later Iron Age population.
“we observe that the excess European affinity of the early Iron Age individuals does not persist in the later Iron Age population”
Quote in the paperSubstantial claim - Findingown data
ASH_LBA derives around 60% of its ancestry from Levant_ChL (60.0 ± 6.5%) and the rest from Iran_ChL in a fitting qpAdm two-way admixture model.
“modeling ASH_LBA as a two-way admixture using qpAdm (12, 17) produced a fitting model (χ2P = 0.445), in which ASH_LBA derives around 60% of their ancestry from Levant_ChL (60.0 ± 6.5%; estimate ±1 SE) and the rest from Iran_ChL.”
Quote in the paperNot a substantial claim - Findingown data
Genetic clustering assigns ASH_IA1 an average of 14% contribution from a cluster maximized in Mesolithic European hunter-gatherers (WHG).
“genetic clustering assigns ASH_IA1 with an average of 14% contribution from a cluster maximized in the Mesolithic European hunter-gatherers labeled “WHG””
Quote in the paperSubstantial claim - Findingown data
The variance of the square-rooted f4 statistic is significantly higher in ASH_IA1 than in either ASH_LBA or ASH_IA2 (P < 2.2 × 10−16 for both by Fligner-Killeen test).
“the variance is significantly higher in ASH_IA1 than in either ASH_LBA or ASH_IA2 (P < 2.2 × 10−16 for both by a Fligner-Killeen test)”
Quote in the paperSubstantial claim - Findingown data
ASH_IA2 individuals are intermediate along PC1 between ASH_LBA and earlier Bronze Age Levantines (Jordan_EBA/Lebanon_MBA).
“The ASH_IA2 individuals are intermediate along PC1 between the ASH_LBA ones and the earlier Bronze Age Levantines (Jordan_EBA/Lebanon_MBA) in the west Eurasian PCA”
Quote in the paperSubstantial claim - Findingown data
ASH_LBA shares excess alleles with ancient Iranian/Caucasus-related populations (CHG, Iran_N, Iran_ChL) compared to Neolithic/Chalcolithic Levantines (Levant_N, Levant_ChL).
“estimated excess allele sharing between ASH_LBA and ancient Iranian/Caucasus-related populations (such as CHG, Iran_N, and Iran_ChL) compared to the Neolithic/Chalcolithic Levantines (Levant_N and Levant_ChL)”
Quote in the paperSubstantial claim - Findingown data
The best supported model (χ2P = 0.675) infers ASH_IA1 derives around 43% of ancestry from Greek Bronze Age Crete_Odigitria_BA (43.1 ± 19.2%) and the rest from ASH_LBA.
“The best supported one (χ2P = 0.675) infers that ASH_IA1 derives around 43% of ancestry from the Greek Bronze Age “Crete_Odigitria_BA” (43.1 ± 19.2%) and the rest from the ASH_LBA population.”
Quote in the paperSubstantial claim - Findingown data
Alternative two-way models for ASH_LBA using Anatolia_EBA/Anatolia_BA/Armenia_ChL as the second source also fit, albeit with smaller P values.
“alternative two-way models also fit, albeit with smaller P values. In these models, Anatolia_EBA/Anatolia_BA/Armenia_ChL are used as the second source, replacing Iran_ChL (χ2P = 0.053 to 0.060; table S3).”
Quote in the paperNot a substantial claim - Findingown data
The WHG-maximized component is inferred only in small proportions (2 to 9%) in earlier Bronze Age Levantine populations.
“This component is inferred only in small proportions in earlier Bronze Age Levantine populations (2 to 9%).”
Quote in the paperSubstantial claim - Findingown data
European hunter-gatherer-related ancestry contributes considerably less to ASH_IA2 than to ASH_IA1 (8 and 14%, respectively).
“showing that the European hunter-gatherer–related ancestry contributes considerably less to ASH_IA2 than to ASH_IA1 (8 and 14%, respectively; Fig. 2B).”
Quote in the paperSubstantial claim - Findingown data
ASH_LBA and both earlier Bronze Age Levantine populations (Jordan_EBA and Lebanon_MBA) are symmetrically related to all test populations within the data's resolution (|f4| < 3 SE).
“We find that ASH_LBA and both earlier Bronze Age populations are symmetrically related to all test populations within our data’s resolution (|f4| < 3 SE).”
Quote in the paperSubstantial claim - Findingown data
PC1 coordinates positively correlate with the proportion of WHG ancestry modeled in the Ashkelon individuals.
“We find that the PC1 coordinates positively correlate with the proportion of WHG ancestry modeled in the Ashkelon individuals (fig. S9 and table S6)”
Quote in the paperNot a substantial claim - Findingown data
Despite being chronologically closer to ASH_IA1, ASH_IA2 individuals position closer, on average, to earlier Bronze Age individuals.
“Notably, despite being chronologically closer to ASH_IA1, the ASH_IA2 individuals position closer, on average, to the earlier Bronze Age individuals.”
Quote in the paperSubstantial claim - Findingown data
There is a marginal excess of affinity between ASH_LBA and populations genetically related to ancient Iran and the Caucasus (such as CHG and Steppe_Eneolithic) compared to Jordan_EBA.
“we observe a marginal excess of affinity between ASH_LBA and populations genetically related to ancient Iran and the Caucasus (such as CHG and Steppe_Eneolithic) when compared to Jordan_EBA (fig. S7).”
Quote in the paperNot a substantial claim - Findingown data
In three-way mixture models with candidate populations, Levant_ChL, and Iran_ChL, only models including Sardinian, Crete_Odigitria_BA, or Iberia_BA provided a good fit (χ2P = 0.715, 49.3 ± 8.5%; χ2P = 0.972, 38.0 ± 22.0%; and χ2P = 0.964, 25.8 ± 9.3%, respectively).
“only the models including “Sardinian,” “Crete_Odigitria_BA,” or “Iberia_BA” as the candidate population provided a good fit (χ2P = 0.715, 49.3 ± 8.5%; χ2P = 0.972, 38.0 ± 22.0%; and χ2P = 0.964, 25.8 ± 9.3%, respectively).”
Quote in the paperSubstantial claim - Study design and conductown data
None of the 10 individuals were first- or second-degree related to each other.
“None of the individuals were either first- or second-degree related to each other (fig. S1).”
Quote in the paperNot a substantial claim - Interpretationnone given
Of the available contemporaneous populations, the southern European gene pool is the best proxy for the incoming European-related gene flow into Ashkelon.
“Of the available contemporaneous populations, we model the southern European gene pool as the best proxy for this incoming gene flow.”
Quote in the paperSubstantial claim - Study design and conductown data
For males (n = 4), nuclear contamination was estimated to a maximum of 4.3%.
“For males (n = 4), nuclear contamination was estimated to a maximum of 4.3% (table S2).”
Quote in the paperNot a substantial claim - Interpretationown data
The European-related gene flow had a limited genetic impact on the long-term population structure of the people in Ashkelon.
“suggesting that it had a limited genetic impact on the long-term population structure of the people in Ashkelon”
Quote in the paperSubstantial claim - Interpretationreasoning
A gene flow from a European-related gene pool entered Ashkelon either at the end of the Bronze Age or at the beginning of the Iron Age.
“suggesting that a gene flow from a European-related gene pool entered Ashkelon either at the end of the Bronze Age or at the beginning of the Iron Age”
Quote in the paperSubstantial claim - Study design and conductown data
The study used multiple measures to authenticate the generated ancient DNA data.
“We used multiple measures to authenticate the generated aDNA data.”
Quote in the paperSubstantial claim - Interpretationown data
WHG reasonably tags a European-related ancestral component within the ASH_IA1 individuals.
“suggesting that WHG reasonably tag a European-related ancestral component within the ASH_IA1 individuals.”
Quote in the paperNot a substantial claim - Interpretationown data
Compared to ASH_LBA, ASH_IA1 has additional European-related ancestry.
“only European hunter-gatherers (including WHG) and populations sharing a history of genetic admixture with European hunter-gatherers (e.g., as European Neolithic and post-Neolithic populations) produced significantly positive f4-statistics (Z ≥ 3), suggesting that, compared to ASH_LBA, ASH_IA1 has additional European-related ancestry.”
Quote in the paperSubstantial claim - Study design and conductown data
Within current resolution, it cannot be distinguished whether the marginal ASH_LBA affinity to Iranian/Caucasus-related populations is due to small-scale gene flow between Early and Late Bronze Age or to population structure during this period.
“Within our current resolution, we cannot distinguish whether this affinity is due to a small-scale gene flow from an Iranian/Caucasus-related population entering the Levant between the Early and Late Bronze Age or whether it reflects a certain population structure during this period.”
Quote in the paperNot a substantial claim - Interpretationcitation
The timing of the European-related gene flow is in accord with estimates of the Philistines arrival to the coast of the Levant based on archeological and textual records.
“This timing is in accord with estimates of the Philistines arrival to the coast of the Levant, based on archeological and textual records (2–4).”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [2] A. Yasur-Landau, The Philistines and Aegean Migration at the End of the Late Bronze Age (Cambridge Univ. Press, 2014).
Not checked in the free run.
- cites [3] L. E. Stager, The impact of the Sea Peoples in Canaan (1185–1050 BCE), in The Archaeology of Society in the Holy Land, T. E. Levy, Ed. (Leicester Univ. Press, 1995), pp. 332–348.
Not checked in the free run.
- cites [4] A. E. Killebrew, Biblical peoples and ethnicity, in An Archaeological Study of Canaanites, Egyptians, Philistines, and Early Israel, 1300–1100 BCE. (Society of Biblical Literature, Atlanta, 2005), p. 9.
Not checked in the free run.
- Interpretationreasoning
Mesolithic WHG individuals are unlikely to be a good proxy for the true source of the European-related admixture in the much later early Iron Age.
“However, these Mesolithic individuals are unlikely to be a good proxy for the true source in the much later early Iron Age.”
Quote in the paperSubstantial claim - Interpretationown data
Tested candidate populations from Anatolia, Egypt, and the Levant that did not produce well-fitting models can be excluded as potential sources of the admixture observed in ASH_IA1.
“Nonetheless, the tested candidate populations from Anatolia, Egypt, and the Levant that did not produce well-fitting models can be excluded as potential sources of the admixture observed in ASH_IA1.”
Quote in the paperSubstantial claim - Interpretationreasoning
Transient gene flows such as the one detected here might be overlooked because of a lack of representative samples, potentially leading to erroneous conclusions.
“Transient gene flows, such as the one detected here, might be overlooked because of a lack of representative samples, potentially leading to erroneous conclusions.”
Quote in the paperNot a substantial claim - Interpretationown data
Additional WHG-like ancestry is necessary only to model ASH_IA1 among the three Ashkelon populations.
“Thus, of the three, additional WHG-like ancestry is only necessary to model ASH_IA1.”
Quote in the paperSubstantial claim - Interpretationown data
Within no more than two centuries, the genetic footprint introduced during the early Iron Age is no longer detectable and seems to be diluted by a local Levantine-related gene pool.
“We find that, within no more than two centuries, this genetic footprint introduced during the early Iron Age is no longer detectable and seems to be diluted by a local Levantine-related gene pool.”
Quote in the paperSubstantial claim - Interpretationown data
The replacing population that diluted the European-related component likely stemmed from the Late Bronze Age Levantine gene pool, whether or not from Ashkelon.
“the replacing population is likely to have stemmed from the Late Bronze Age Levantine gene pool, whether or not from Ashkelon.”
Quote in the paperSubstantial claim - Interpretationown data
The apparent symmetry suggests a high degree of genetic continuity throughout at least a millennium between culturally and geographically distinct Bronze Age Levantine groups occupying a region from inland southern Levant to coastal Israel and Lebanon.
“Nonetheless, the apparent symmetry suggests a high degree of genetic continuity throughout at least a millennium between culturally and geographically distinct Bronze Age Levantine groups occupying a region that stretches from the inland southern Levant where present-day Jordan is located and along the coastal regions of present-day Israel and Lebanon.”
Quote in the paperSubstantial claim - Interpretationown data
The genetic distinction of ASH_IA1 is due to a European-related gene flow introduced in Ashkelon during either the end of the Bronze Age or the beginning of the Iron Age.
“Our analysis suggests that this genetic distinction is due to a European-related gene flow introduced in Ashkelon during either the end of the Bronze Age or the beginning of the Iron Age.”
Quote in the paperSubstantial claim - Interpretationown data
The ASH_IA1 individuals were more heterogeneous in their genetic affinities to global populations than both ASH_LBA and ASH_IA2.
“suggesting that the ASH_IA1 individuals were more heterogeneous in their genetic affinities to global populations in respect to both ASH_LBA and ASH_IA2.”
Quote in the paperSubstantial claim - Interpretationown data
The unique cultural features in the early Iron Age are mirrored by the distinct genetic composition detected in ASH_IA1.
“we find that the unique cultural features in the early Iron Age are mirrored by the distinct genetic composition we detect in ASH_IA1.”
Quote in the paperSubstantial claim
- May combine two claims. 16
- Classified as probably not a substantial claim. 16
May combine two claims.
Findingown dataASH_LBA individuals overlap with the cline of present-day Near Easterners and are close to earlier Bronze Age Levantines and Anatolians.
“The ASH_LBA individuals overlap with the cline of present-day Near Easterners and are close to earlier Bronze Age Levantines and Anatolians”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe f4 statistic f4(ASH_IA2, ASH_IA1; test, Mbuti) produced no significantly positive results, and all significantly negative statistics (Z ≤ −3) are with test populations from either Europe or Anatolia.
“This statistic produced no significantly positive results, and all significantly negative statistics (Z ≤ −3) are with test populations from either Europe or Anatolia (fig. S10).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataFor ASH_IA1, the two-way qpAdm model is inadequate (χ2P = 3.80 × 106) and the three-way model with WHG fits (χ2P = 0.765).
“for ASH_IA1, the two-way model is inadequate (χ2P = 3.80 × 106; table S5) and the three-way one fits (χ2P = 0.765).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataASH_LBA and ASH_IA2 fit well with a two-way qpAdm model using Levant_ChL and Iran_ChL (0% WHG contribution), whereas the three-way model infers small nonsignificant WHG proportions (−2.3 ± 2.2% and 2.0 ± 2.2%, respectively).
“ASH_LBA and ASH_IA2 fit well with the two-way model (χ2P = 0.445 and χ2P = 0.313, respectively; table S5), whereas the three-way one infers small nonsignificant proportions (−2.3 ± 2.2 and 2.0 ± 2.2% for ASH_LBA and ASH_IA2, respectively; table S5).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOf 51 tested qpAdm models for ASH_IA1, four are plausible (χ2P > 0.05), all two-way mixtures.
“Of the 51 tested models, we find four plausible ones (χ2P > 0.05), all are two-way mixtures.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe four ASH_IA1 individuals are, on average, shifted along PC1 toward the European cline and are more spread out along PC1, overlapping ASH_LBA on one extreme and Greek Late Bronze Age S_Greece_LBA on the other.
“the four ASH_IA1 individuals from the following Iron Age I period are, on average, shifted along PC1 toward the European cline and are more spread out along PC1, overlapping with ASH_LBA on one extreme and with the Greek Late Bronze Age “S_Greece_LBA” (25) on the other”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataModeling ASH_IA2 as a mixture of ASH_IA1 and earlier Bronze Age Levantines/Late Period Egyptian infers a range of 7 to 38% contribution from ASH_IA1, although no contribution cannot be rejected because of limited resolution.
“By modeling ASH_IA2 as a mixture of ASH_IA1 and earlier Bronze Age Levantines/Late Period Egyptian, we infer a range of 7 to 38% of contribution from ASH_IA1, although no contribution cannot be rejected because of the limited resolution to differentiate between Bronze Age and early Iron Age ancestries in this model (table S8).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataASH_IA1 could also be modeled with modern Sardinian (35.2 ± 17.4%; χ2P = 0.070), Bronze Age Iberia_BA (21.8 ± 21.1%; χ2P = 0.205), or Bronze Age Steppe_MLBA (15.7 ± 9.1%; χ2P = 0.050) as the second source to ASH_LBA.
“ASH_IA1 could also be modeled with either the modern “Sardinian” (35.2 ± 17.4%; χ2P = 0.070), the Bronze Age “Iberia_BA” (21.8 ± 21.1%; χ2P = 0.205), or the Bronze Age “Steppe_MLBA” (15.7 ± 9.1%; χ2P = 0.050) as the second source population to ASH_LBA.”
Quote in the paperNot a substantial claimMay combine two claims.
Study design and conductown dataMitochondrial contamination for all 10 individuals ranged between 0 and 9%, with only two above 5%.
“Mitochondrial contamination for all 10 individuals ranged between 0 and 9%, with only two of them above 5% (table S2).”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataThese data begin to fill a temporal gap in the genetic map of the southern Levant, revealing persistence of the local Levantine gene pool throughout the Bronze Age for over a millennium.
“these data begin to fill a temporal gap in the genetic map of the southern Levant, revealing persistence of the local Levantine gene pool throughout the Bronze Age for over a millennium.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenThe variance for each analyzed group was estimated by a Fligner-Killeen test, which is robust against departures from normality that can be caused by small sample size.
“The variance for each group was estimated by a Fligner-Killeen test, which is robust against departures from normality that can be caused by small sample size.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationNuclear contamination in males was estimated using ANGSD, which compares mismatch rates between polymorphic sites on the X chromosome.
“We next used ANGSD (v0.910) (41), which compares mismatch rates between polymorphic sites on the X chromosome to estimate nuclear contamination in males.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [41] Korneliussen T. S., Albrechtsen A., Nielsen R., ANGSD: Analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014). 25420514 PMC4248462 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenf-statistics were reported only when at least 20,000 SNP positions overlapped between the four tested populations.
“We report the f-statistics in which at least 20,000 SNP positions were overlapping between the four tested populations.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductreasoningTo eliminate genotyping bases with retained damage, the two terminal positions in each read were clipped, and a pseudo-diploid genotype was reconstructed for each individual using pileupCaller.
“To eliminate genotyping bases with retained damage, the two terminal positions in each read were clipped, and subsequently, a pseudo-diploid genotype was reconstructed for each individual using pileupCaller”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationHuman mitochondrial DNA contamination was measured using schmutzi.
“(iii) We measured human mitochondrial DNA contamination using schmutzi (40).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [40] 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). 26458810 PMC4601135 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataThe low significance of the f4-statistics for Bronze Age gene flow might be due to limited statistical power from insufficient coverage or lack of appropriate contemporaneous proxy populations.
“We do not rule out that some gene flow occurred during the Bronze Age as low significance of the f4-statistics might be due to the limited statistical power of our data stemming from either insufficient coverage or a lack of appropriate contemporaneous proxy populations.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAll preamplification procedures were performed in dedicated ancient DNA facilities at MPI-SHH, Jena, Germany.
“All preamplification procedures were performed in the dedicated aDNA facilities of the Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenGenetic sex was inferred for each individual by calculating the ratio of X and Y chromosome coverage normalized by the autosomal average coverage.
“(iv) The genetic sex was inferred for each individual by calculating the ratio of the X and Y chromosome coverage (normalized by the autosomal average coverage).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductown dataADMIXTURE analysis was performed with five replicates for each k using random seeds, and the highest likelihood replicate was chosen.
“We performed five replicates for each k with random seeds and chose the highest likelihood replicate (fig. S3).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [23] Alexander D. H., Novembre J., Lange K., Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655– 1664 (2009). 19648217 PMC2752134 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAutomatically called derived alleles supporting Y-chromosome haplogroup assignment were manually confirmed.
“In addition, the automatically called derived alleles, which support the haplogroup assignment, were manually confirmed.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataFivefold cross-validation errors were calculated for each ADMIXTURE run.
“Fivefold cross-validation (CV) errors were calculated for each run.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductcitationTo reduce potential errors in obtained DNA sequences, DNA damage from cytosine deamination was partially removed using uracil-DNA glycosylase and endonuclease VIII, retaining damage at terminal positions as a measure of aDNA authentication.
“To reduce potential errors in the obtained DNA sequences, we partially removed DNA damage resulting from cytosine deamination using uracil-DNA glycosylase and endonuclease VIII as previously reported (31). In this procedure, the damage is retained in the terminal positions of the DNA fragments and can be leveraged as a measure of aDNA authentication.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [31] Rohland N., Harney E., Mallick S., Nordenfelt S., Reich D., Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2015). 25487342 PMC4275898 source
Not checked in the free run.
Classified as probably not a substantial claim.
Study design and conductown dataBlank extractions and library preparations were included and analyzed for each sample batch to control for potential laboratory contamination.
“(i) To control for potential laboratory contamination, blank extractions and library preparations were included and analyzed for each sample batch (data file S3).”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Study design and conductcitationPairwise allele mismatch rates of all newly reported individuals were calculated to avoid bias from including related individuals in analyzed populations.
“To avoid bias associated with including related individuals into analyzed populations, we calculated the pairwise allele mismatch rates of all newly reported individuals following a method described elsewhere (fig. S1) (42).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [42] Kennett D. J., Plog S., George R. J., Culleton B. J., Watson A. S., Skoglund P., Rohland N., Mallick S., Stewardson K., Kistler L., LeBlanc S. A., Whiteley P. M., Reich D., Perry G. H., Archaeogenomic evidence reveals prehistoric matrilineal dynasty. Nat. Commun. 8, 14115 (2017). 28221340 PMC5321759 source
Not checked in the free run.
Classified as probably not a substantial claim. May combine two claims.
Study design and conductcitationLevels of DNA deamination damage in the mapped reads were estimated using mapDamage (v2.0) and compared to expected values in ancient skeletal element.
“(ii) Levels of DNA deamination damage in the mapped reads were estimated using mapDamage (v2.0) (39) and compared to the expected values in ancient skeletal element.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [39] Jónsson H., Ginolhac A., Schubert M., Johnson P. L. F., Orlando L., mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682– 1684 (2013). 23613487 PMC3694634 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenStrand-ambiguous SNPs were discarded, and quality filters were as those for the HO dataset.
“Strand-ambiguous SNPs were discarded, and quality filters were as those for the HO dataset.”
Quote in the paperNot a substantial claim
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?
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.”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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 measuredPrevious 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,”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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).”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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).”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
Ashkelon IA1 is genetically differentiated from contemporary groups.
“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).”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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).”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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”
From The Genomic History of the Bronze Age Southern Levant (2020) · cites this paper as Feldman et al., 2019
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
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.
Late Bronze Age radiocarbon range disagrees with Table 1
MinorThe text gives 1542 BCE as the recent end of the two dated ASH_LBA individuals' range, but Table 1 dates ASH029 to 1522 BCE.
“two of the individuals were directly carbon-dated to 1746 to 1542 cal BCE”
“| ASH029.A0101 | ASH_LBA | Petrous | 0.14 | 1622–1522 | MBIIC–LBII | 86.6 | 6.9 | F | H66a | |”
Figure 3A names different comparison populations
MinorThe results text says Figure 3A shows a comparison of ASH_IA1 with ASH_LBA, while its caption says the plotted statistic compares ASH_IA1 with ASH_IA2.
“We next formally quantified the genetic differences between ASH_IA1 and the earlier ASH_LBA by calculating f4 (ASH_IA1, ASH_LBA; test, Mbuti) (Fig. 3A).”
“We plot the top and bottom 40 values of f4 (ASH_IA1, ASH_IA2; X, Mbuti) on the map.”
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- Authors
- Feldman, M., Master, D. M., Bianco, R. A., Burri, M., Stockhammer, P. W., Mittnik, A., Aja, A. J., Jeong, C., & Krause, J.
- Affiliations
- Max Planck Institute of Geoanthropology (DE)
- Harvard University (US)
- Seoul National University (KR)
- Corresponding author
- Jeong, Choongwon
- Krause, Johannes
- ORCID
- Venue
- Science Advances
- Published
- 2019-07-05
- Volume
- 5
- Issue
- 7
- Pages
- eaax0061-eaax0061
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC6609216
- OpenAlex
- W2955211334
- Semantic Scholar
- 2848b0288f6bff12a27f35d1c78d61966d056d0e
- Cited by
- 120
- References
- 59
- Citations by year
- 2026: 29 · 2025: 26 · 2024: 8 · 2023: 6 · 2022: 12 · 2021: 14 · 2020: 20 · 2019: 5
- FWCI
- 7.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Science Advances (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- Leon Levy Foundation
- Max Planck Society
- Max Planck−Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Jena, Germany & Cambridge, MA, USA
- 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
- Social Sciences › Arts and Humanities › Archeology › Forensic Anthropology and Bioarchaeology Studies
- Keywords
- Philistines, Ashkelon, Iron Age, Sea Peoples, Bronze Age, population structure, European admixture, migration, ancient DNA, genetic origin, cultural change
- MeSH terms
- DNA, Ancient, Genetics, Population, Humans, White People, History, Ancient, Genome-Wide Association Study, Human Migration
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