Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation

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

Lazaridis et al. showed that the Levant Bronze Age population from the site of 'Ain Ghazal, Jordan (2490-2300 BCE) could be fit statistically as a mixture of around 56% ancestry from a group related to Levantine Pre-Pottery Neolithic agriculturalists and 44% related to populations of the Iranian Chalcolithic.

“Lazaridis et al.24 showed that the Levant Bronze Age population from the site of 'Ain Ghazal, Jordan (2490–2300 BCE) could be fit statistically as a mixture of around 56% ancestry from a group related to Levantine Pre-Pottery Neolithic agriculturalists (represented by ancient DNA from Motza, Israel and 'Ain Ghazal, Jordan; 8300–6700 BCE) and 44% related to populations of the Iranian Chalcolithic (”

• cites Lazaridis et al.24 Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourcePartly supported

  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

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

Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today.

“Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today24,25.”

• cites [24] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourcePartly supported

  The ‘Extreme regional differentiation in the ancient Near East’ section (page not provided) reports that ancient populations at the four corners of its genetic quadrangle had FST values of 0.08–0.15, comparable to 0.09–0.13 between present-day West Eurasians and Han East Asians. But those four corners include the Levant and Iran alongside two European hunter-gatherer groups—not Anatolia. The passage therefore does not establish the stated comparison for populations from all three named regions relative to each other. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [25] Broushaki, F. et al. Early Neolithic genomes from the eastern Fertile Crescent. Science 353, 499–503 (2016). sourcePartly supported

  The supplied Abstract passages say Early Neolithic populations from the Zagros and NW Anatolia descended from distinct ancestral populations and differed conspicuously. They do not establish the claim for Levantine populations or compare the degree of differentiation with that between present-day Europeans and East Asians; searches for those comparisons returned no passage. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

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

Haber et al. suggested that the Canaanite Levant Bronze Age population from the site of Sidon, Lebanon (~1700 BCE) could be modeled as a mixture of the same two groups albeit in different proportions (48% Levant Neolithic-related and 52% Iran Chalcolithic-related).

“Haber et al.26 suggested that the Canaanite Levant Bronze Age population from the site of Sidon, Lebanon (~1700 BCE) could be modeled as a mixture of the same two groups albeit in different proportions (48% Levant Neolithic-related and 52% Iran Chalcolithic-related).”

• cites Haber et al.26 Haber, M. et al. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101, 274-282 (2017). sourceSupported

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

By the Bronze Age, expansion of different Near Eastern agriculturalist populations-Anatolian, Iranian, and Levantine-in all directions and admixture with each other substantially homogenized populations across the region, thereby contributing to the relatively low genetic differentiation that prevails today.

“By the Bronze Age, however, expansion of different Near Eastern agriculturalist populations—Anatolian, Iranian, and Levantine—in all directions and admixture with each other substantially homogenized populations across the region, thereby contributing to the relatively low genetic differentiation that prevails today24.”

• cites [24] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourceSupported

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

The study treated libraries with Uracil-DNA glycosylase (UDG) to reduce characteristic ancient DNA damage at all but the first and last nucleotides.

“We treated the libraries with Uracil–DNA glycosylase (UDG) to reduce characteristic ancient DNA damage at all but the first and last nucleotides29”

• cites [29] Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370, 20130624 (2015). sourcePartly supported

  The Effectiveness of partial uracil-DNA-glycosylase treatment passage says partial UDG removes uracils within ancient DNA molecules while preserving substantial damage at the terminal bases. But it also says terminal-base damage is reduced compared with untreated libraries; the Library construction passage quantifies that reduction at about threefold. Thus the first and last nucleotides are not wholly exceptions to the reduction described in the claim. The indexed copy provides no page number for these passages. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

May combine two claims.

Levant_BA_South and Levant_BA_North are treated as separate populations for analysis, since the symmetry statistic f4(Levant_BA_North, Levant_BA_South; A, Chimp) is significant for a number of test populations A.

“In what follows, we treat Levant_BA_South and Levant_BA_North as separate populations for analysis, since the symmetry statistic f4(Levant_BA_North, Levant_BA_South; A, Chimp) is significant for a number test populations A (|Z| ≥ 3) (Supplementary Data 5), consistent with the different estimated proportions of Levant_N and Iran_ChL ancestry reported in24,26.”

• cites [24] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourcePartly supported

  The section ‘How diverse first farmers of the Near East mixed to form the region's later populations’ estimates that Iran Chalcolithic–related ancestry contributed about 44% to southern Levantine Bronze Age populations. Our copy does not give a corresponding northern estimate or report the stated north–south f4 test. The citing authors present that test and their decision to analyze the populations separately as their own analysis, not as findings of this source. (LLM, conf=0.82)

  Experimental — accuracy not yet measured
• cites [26] Haber, M. et al. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101, 274-282 (2017). sourcePartly supported

  The Main Text (page not provided) estimates Levant_N and Iran_ChL ancestry proportions for Sidon_BA and says Jordan_BA can also be modeled as a mixture of those ancestries. It does not report a north–south comparison of the proportions or the cited f4 symmetry test. The decision to analyze the populations separately and that test are presented as the citing authors’ own analysis, not as findings of this source. (LLM, conf=0.78)

  Experimental — accuracy not yet measured

May combine two claims.

Direct radiocarbon dating suggests that the cave was in use throughout the Late Chalcolithic (4500-3900 BCE), functioning as a central burial location for the region.

“Direct radiocarbon dating suggests that the cave was in use throughout the Late Chalcolithic (4500–3900 BCE), functioning as a central burial location for the region21,23.”

• cites [21] Shalem, D. et al. Peqiʻin: A Late Chalcolithic Burial Site Upper Galilee, Israel (Kinneret Academic College Institute for Galilean Archaeology, 2013).Not matched

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

• cites [23] Segal, D., Carmi, I., Gal, Z., Smithline, H. & Shalem, D. Dating a Chalcolithic burial cave in Peqi’in, upper Galilee, Israel. Radiocarbon 40, 707–712 (1998). sourcePartly supported

  The Discussion says radiocarbon dates confirm cave use over several Chalcolithic centuries and that the cave served as a burial center. It does not establish continuous burial use throughout the specified 4500–3900 BCE span, and its account distinguishes earlier, pre-burial use from the burial phase. Page numbers are unavailable in our copy. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

May combine two claims. The quote only partly states this claim.

The study evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide, requiring X-to-Y-chromosome ratio characteristic of sex, >95% matching to mtDNA consensus, and <2% contamination for males.

“We evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide29, by requiring that the ratio of X-to-Y-chromosome sequences was characteristic of either a male or a female, by requiring >95% matching to the consensus sequence of mitochondrial DNA30, and by requiring (for males) a lack of variation”

• cites [29] Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370, 20130624 (2015). sourceSupported
• cites [30] Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. 110, 2223-2227 (2013). sourcePartly supported

  The citation is attached to the cytosine-to-thymine error criterion. In Results and Discussion (page unavailable), the paper uses end-of-fragment substitutions as evidence of ancient DNA and reports frequencies of 25–30% close to fragment ends. It does not specify a minimum of 3% at the final nucleotide as a library-selection rule. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [32] Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinforma. 15, 356 (2014). sourceCould not verify

  The citation is attached to the minimum 3% terminal cytosine-to-thymine error criterion. The ABBA-BABA section says transitions have high error rates in ancient genomes, but our copy does not give a 3% threshold or describe terminal-base errors as an authenticity test. Searches for those criteria found no supporting passage. (LLM, conf=0.74)

  Experimental — accuracy not yet measured

May combine two claims.

Previously reported median pairwise FST between populations in pre-Neolithic periods is 0.098 (range: 0.023-0.153), in Bronze Age periods 0.015 (range: 0.002-0.045), and in present-day West Eurasian populations 0.011 (range: 0-0.046).

“relative to a previously reported median pairwise FST of 0.098 (range: 0.023–0.153) observed between populations in pre-Neolithic periods, 0.015 (range: 0.002–0.045) in the Bronze Age periods, and 0.011 (range: 0–0.046) in present-day West Eurasian populations24.”

• cites [24] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourcePartly supported

  The section “Extreme regional differentiation in the ancient Near East” reports high FST among early West Eurasian populations and says differentiation had fallen to present-day low levels by the Bronze Age. It also gives 0.046 as the upper bound for present-day West Eurasian pairs. Our copy does not report the three claimed medians or the full ranges for the pre-Neolithic and Bronze Age periods. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

The quote only partly states this claim.

Later Bronze Age individuals all belonged to haplogroup J.

“and later Bronze Age individuals, all of whom belonged to haplogroup J24,26.”

• cites [24] Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419 (2016). sourceCould not verify

  The Abstract says the sample includes Bronze Age individuals, but does not give their haplogroups. The section on Basal Eurasian ancestry identifies haplogroup E in earlier Natufian and Levantine Neolithic populations; searches for Bronze Age haplogroup J and Y-chromosome lineages found no passage establishing that all later Bronze Age individuals belonged to J. (LLM, conf=0.72)

  Experimental — accuracy not yet measured
• cites [26] Haber, M. et al. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101, 274-282 (2017). sourcePartly supported

  The Main Text and Table 1 (page not specified) report that both male Sidon Bronze Age individuals had Y-chromosome haplogroup J. The claim's 'all' is broader than this evidence: three other Sidon individuals were female and had no Y-haplogroup assignment, and the paper does not establish that all later Bronze Age individuals belonged to J. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

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

The allele (G) at rs6903823 has been argued to have been under positive selection by Mathieson et al.

“that has been argued to have been under positive selection by Mathieson et al.31”

• cites [31] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015). sourceCould not verify

  The ‘Twelve signals of selection’ section discusses selection at several named SNPs and loci, but the passages in our copy do not identify rs6903823 or its G allele as a target. Searches for rs6903823 and for ‘rs6903823 G positive selection’ found no passage addressing that specific allele. (LLM, conf=0.72)

  Experimental — accuracy not yet measured

May combine two claims.

The archaeological record is marked by dramatic changes in settlement patterns, large-scale abandonment of sites, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries.

“aspects of the archeological record marked by dramatic changes in settlement patterns43, large-scale abandonment of sites52–55, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries56–59.”

• cites [43] Rowan, Y. M. & Golden, J. The Chalcolithic period of the Southern Levant: a synthetic review. J. World Prehistory 22, 1–92 (2009). sourceNot checked — no full text of the source
• cites [52] Gilead, I. The history of the Chalcolithic settlement in the Nahal Beer Sheva area: the radiocarbon aspect. Bull. Am. Sch. Orient. Res. 296, 1–13 (1994). sourceNot checked — no full text of the source
• cites [53] Bourke, S. et al. The chronology of the Ghassulian Chalcolithic period in the southern Levant: new 14 C determinations from Teleilat Ghassul, Jordan. Radiocarbon 43, 1217–1222 (2001). sourceCould not verify

  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 [54] Bourke, S. J. & Lovell, J. L. Ghassul, chronology and cultural sequencing. Paléorient 30, 179–182 (2004). sourceNot checked — no full text of the source
• cites [55] Gilead, I. in Culture, Chronology and the Chalcolithic: Theory and Transition (eds Lovell, J. L. & Rowan, Y. M.) 12–24 (Oxbow Books, 2011).Not matched

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

• cites [56] van den Brink Edwin, C. in Culture, Chronology and the Chalcolithic: Theory and Transition(eds Lovell, J. L. & Rowan, Y. M.) 61–70 (Oxbow Books, 2011).Not matched

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

• cites [57] Vardi, J. & Gilead, I. Chalcolithic early bronze age I transition in the Southern Levant: the Lithic perspective. Paléorient 39, 111–123 (2013). sourceNot checked — no full text of the source
• cites [58] Milevski, I. The transition from the Chalcolithic to the early bronze age in the Southern Levant in socio-economic context. Paléorient 39, 193–208 (2013). sourceNot checked — no full text of the source
• cites [59] Braun, E. & Roux, V. The late Chalcolithic to early bronze age I transition in the Southern Levant: determining continuity and discontinuity or “Mind the Gap”. Paléorient 29, 15–22 (2013). sourceNot checked — no full text of the source

Classified as probably not a substantial claim. The quote only partly states this claim.

We assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity: mitochondrial genome matching rate, C-to-T substitution rate, and X-chromosome contamination.

“We assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity.”

• cites [30] Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. 110, 2223-2227 (2013). sourcePartly supported

  The Results and Discussion section (“DNA Sequence Authenticity”; page unavailable) uses mitochondrial sequence agreement and C→T substitutions to assess whether DNA in the Tianyuan libraries is ancient and largely from one individual. Our copy does not describe X-chromosome contamination as a third method or say that these three methods were used to assess each library at screening. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [29] Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370, 20130624 (2015). sourcePartly supported

  The Introduction describes C-to-T mismatches and mitochondrial consensus mismatches as evidence of ancient DNA authenticity. The sequencing and analysis section also reports mitochondrial contamination estimates, but our copy does not describe X-chromosome contamination as a screening method. It therefore supports some, but not all, of the three methods attributed to it. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [32] Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinforma. 15, 356 (2014). sourceCould not verify

  The Results and discussion > ABBA-BABA section (page unavailable) describes filtering error-prone transitions when analyzing an ancient Denisovan genome, not screening libraries for authenticity. Searches for mitochondrial matching rates, C-to-T substitution rates, and X-chromosome contamination found no passage describing the three claimed methods. (LLM, conf=0.77)

  Experimental — accuracy not yet measured

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

We excluded two individuals from further analysis because genetic patterns showed they were first-degree relatives of higher coverage samples in the dataset.

“We excluded two individuals from further analysis, as the genetic patterns observed using the method described in Kuhn et al.73. Showed that they were first-degree relatives of higher coverage samples in the dataset.”

• cites [73] Kuhn, J. M. M., Jakobsson, M. & Günther, T. Estimating genetic kin relationships in prehistoric populations. PLoS ONE 13, e0195491 (2018). sourceSupported

Classified as probably not a substantial claim.

We excluded libraries with X-contamination estimates greater than 1.5%.

“we excluded libraries with X-contamination estimates greater than 1.5%32.”

• cites [32] Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinforma. 15, 356 (2014). sourceSupported

May combine two claims.

The dataset is of exceptional quality given the typically poor preservation of DNA in the warm Near East, with a higher proportion of samples yielding appreciable coverage of ancient DNA than has previously been obtained from the region.

“The dataset is of exceptional quality given the typically poor preservation of DNA in the warm Near East, with a higher proportion of samples yielding appreciable coverage of ancient DNA than has previously been obtained from the region, likely reflecting the optimal sampling techniques we used and the favorable preservation conditions at the cave.”

May combine two claims.

The samples from Peqi'in Cave form a tight cluster in PCA, supporting the grouping of these individuals into a single analysis population.

“In a plot of the first and second principal components (Fig. 3a), the samples from Peqi’in Cave form a tight cluster, supporting the grouping of these individuals into a single analysis population”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

The quote only partly states this claim.

Only the model involving Iran_ChL remained plausible after adding Iran_N to the outgroup set.

“Only the model involving Iran_ChL remained plausible.”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

May combine two claims.

The Levant_ChL cluster overlaps in the PCA with a cluster containing Neolithic Levantine samples, although it is slightly shifted upward on the plot toward a cluster corresponding to samples from the Levant Bronze Age.

“The Levant_ChL cluster overlaps in the PCA with a cluster containing Neolithic Levantine samples (Levant_N), although it is slightly shifted upward on the plot toward a cluster corresponding to samples from the Levant Bronze Age, including samples from 'Ain Ghazal, Jordan (Levant_BA_South) and Sidon, Lebanon (Levant_BA_North).”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

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

The quality of ancient DNA obtained from the Peqi'in Cave samples is excellent relative to other sites in the Near East.

“The quality of ancient DNA obtained from the Peqi’in Cave samples is excellent relative to other sites in the Near East.”

May combine two claims.

The Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry.

“while the Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry”

May combine two claims.

The allele (G) at rs6903823 occurs with an estimated frequency of 20% in the Levant_ChL, 17% in the Levant_BA_South, and 15% in the Iran_ChL populations, while it is absent in all other populations.

“occurs with an estimated frequency of 20% in the Levant_ChL, 17% in the Levant_BA_South, and 15% in the Iran_ChL populations, while it is absent in all other populations.”

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

The 22 samples that passed contamination and quality control tests have an average of 0.97× coverage on the 1240 k SNP targets and an average of 358,313 SNPs covered at least once.

“The data from the 22 samples that passed contamination and quality control tests are reported in Supplementary Table 1, with an average of 0.97× coverage on the 1240 k SNP targets, and an average of 358,313 SNPs covered at least once.”

May combine two claims.

Both the increasing genetic diversity over time and the reduced differentiation between populations as measured via FST are consistent with a model in which gene flow reduced differentiation across groups while increasing diversity within groups.

“Both the increasing genetic diversity over time, and the reduced differentiation between populations as measured via FST, are consistent with a model in which gene flow reduced differentiation across groups while increasing diversity within groups.”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

May combine two claims.

A population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.

“These results imply that a population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

May combine two claims.

The Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry.

“This suggests that the Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry.”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

May combine two claims.

The Levant_ChL population is descended from a population related to Levant_N, but also harbors ancestry from non-Levantine populations related to those of Iran or the Caucasus that Levant_N does not share.

“This suggests that the Levant_ChL population is descended from a population related to Levant_N, but also harbors ancestry from non-Levantine populations related to those of Iran or the Caucasus that Levant_N does not share (or at least share to the same extent).”

• AssumptionRests on an assumption: The Peqi’in Cave individuals are representative of the Late Chalcolithic population of the southern Levant.

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

The study attached unique barcodes to libraries to minimize the possibility of contamination.

“We extracted DNA28 and built next-generation sequencing libraries to which we attached unique barcodes to minimize the possibility of contamination.”

• cites [28] Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. 110, 15758-15763 (2013). sourceNot checked — no full text of the source

May combine two claims.

A total of 20 Peqi'in samples appear to be unrelated to each other to the limits of our resolution, and we used these as our analysis set.

“A total of 20 Peqi’in samples appear to be unrelated to each other to the limits of our resolution (that is, genetic analysis suggested that they were not first, second, or third degree relatives of each other), and we used these as our analysis set.”

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

The study restricted to individuals with at least 5000 of the targeted SNPs covered at least once.

“We also restricted to individuals with at least 5000 of the targeted SNPs covered at least once.”

Classified as probably not a substantial claim.

An allele at rs1426654 in the SLC24A5 gene is one of the most important determinants of light pigmentation in West Eurasians.

“an allele at rs1426654 in the SLC24A5 gene which is one of the most important determinants of light pigmentation in West Eurasians41”

• cites [41] Soejima, M. & Koda, Y. Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. Int. J. Leg. Med. 121, 36–39 (2007). sourceNot checked — no full text of the source

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

The Chalcolithic period in the Levant witnessed major cultural transformations in virtually all areas of culture, including craft production, mortuary and ritual practices, settlement patterns, and iconographic and symbolic expression.

“The Chalcolithic period in the Levant witnessed major cultural transformations in virtually all areas of culture, including craft production, mortuary and ritual practices, settlement patterns, and iconographic and symbolic expression43.”

• cites [43] Rowan, Y. M. & Golden, J. The Chalcolithic period of the Southern Levant: a synthetic review. J. World Prehistory 22, 1–92 (2009). sourceNot checked — no full text of the source

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

Y-chromosome haplogroup T is a lineage thought to have diversified in the Near East.

“a lineage thought to have diversified in the Near East46”

• cites [46] Mendez, F. L. et al. Increased resolution of Y-chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa. Hum. Biol. 83, 39–53 (2011). sourceNot checked — no full text of the source

May combine two claims.

The Levant_BA_South population may represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region.

“The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region.”

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

We used qpAdm with additional outgroups and repeated analysis until all but one admixture model was eliminated.

“we repeated qpAdm with each additional outgroup added into the “Right” list until all but one admixture model was eliminated.”

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

We performed ADMIXTURE analysis with 20 replicate analyses for each k between 2 and 14 and retained the highest likelihood replicate.

“For each value of k between 2 and 14, we performed 20 replicate analyses, and we retained the highest likelihood replicate for each k.”

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

We restricted data from sample I1183 to include only sequences with evidence of C-to-T substitution in order to minimize contamination.

“We restricted data from sample I1183 to include only sequences with evidence of C-to-T substitution in order to minimize contamination which was evident in the full data from these samples.”

May combine two claims.

The movements of people within the region of the southern Levant were remarkably dynamic, with some populations, such as the one buried at Peqi'in, being formed in part by exogenous influences.

“We show that the movements of people within the region of the southern Levant were remarkably dynamic, with some populations, such as the one buried at Peqi’in, being formed in part by exogenous influences.”

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

Samples with fewer than 100,000 SNPs have too little data to confidently identify the correct Y-chromosome haplogroup.

“we note that samples with fewer than 100,000 SNPs have too little data to confidently identify the correct haplogroup”