Genomic insights into the origin of farming in the ancient Near East

The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago largely occurred after the splitting of the Basal Eurasians from other non-Africans.

“The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.”

• cites [11] Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014) sourceSupported

Diverse ancient West Eurasians can be modelled as mixtures of as few as four streams of ancestry related to Western Hunter Gatherers, Eastern Hunter Gatherers, Neolithic Levant/Natufians, and Neolithic Iran.

“This suggests the hypothesis that diverse ancient West Eurasians can be modelled as mixtures of as few as four streams of ancestry related to these populations, which we confirmed using qpWave7 (Supplementary Information, section 7).”

• cites [7] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015) sourcePartly supported

  The paper’s main text (page unavailable in our copy) describes WHG- and EHG-related ancestry and models Yamnaya as a mixture of EHG and a Near Eastern-related population. It does not establish the proposed four streams, identify Neolithic Levant/Natufian and Neolithic Iran as sources, or model diverse ancient West Eurasians in those terms. The citing authors’ statement that they confirmed the hypothesis with qpWave is their own result, not a finding attributed to this source. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

qpAdm estimates of Basal Eurasian ancestry are highest in the earliest populations from Iran (66±13% in the likely Mesolithic sample, 48±6% in Neolithic samples) and the Levant (44±8% in Epipaleolithic Natufians).

“We obtain the highest estimates in the earliest populations from both Iran (66±13% in the likely Mesolithic sample, 48±6% in Neolithic samples), and the Levant (44±8% in Epipaleolithic Natufians) (Fig. 2), showing that Basal Eurasian ancestry was widespread across the ancient Near East.”

• cites [7] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015) sourceCould not verify

  The Abstract discusses Near Eastern-related ancestry in the Yamnaya, and Extended Data Table 1 lists the study's ancient samples. Neither gives qpAdm estimates of Basal Eurasian ancestry for Iran or Natufians. Searches for those populations, the quoted percentages, and “Basal Eurasian” found no passage addressing the claim. (LLM, conf=0.76)

  Experimental — accuracy not yet measured

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

Almost all ancient and present-day West Eurasians have evidence of significant admixture between two or more ancestral populations, as documented by negative f3(Test; Reference1, Reference2) statistics.

“Almost all ancient and present-day West Eurasians have evidence of significant admixture between two or more ancestral populations, as documented by statistics of the form f3(Test; Reference1, Reference2) which if negative, show that a Test population's allele frequencies tend to be intermediate between two Reference populations16 (Extended Data Table 2).”

• cites [16] Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012) sourceSupported

The populations at the four corners of the PCA quadrangle had differentiation of FST=0.08-0.15, comparable to the value of 0.09-0.13 seen between present-day West Eurasians and East Asians (Han).

“We computed squared allele frequency differentiation between all pairs of ancient West Eurasians28 (Methods; Fig. 3; Extended Data Fig. 2b; Extended Data Fig. 4), and found that the populations at the four corners of the quadrangle had differentiation of FST=0.08-0.15, comparable to the value of 0.09-0.13 seen between present-day West Eurasians and East Asians (Han) (Supplementary Data Table 3).”

• cites [28] Fernández, E. et al. Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS Genet. 10, e1004401 (2014) sourceCould not verify

  The Results sections on Genetic distances and Principal Component Analysis report FST comparisons and a PCA of haplogroup frequencies, but do not identify four corners of a PCA quadrangle or report FST=0.08–0.15 for those populations. Searches for the quadrangle and the Han comparison also found no passage giving the claimed 0.09–0.13 benchmark. The cited paper therefore does not verify the numerical comparison in the quoted claim. (LLM, conf=0.76)

  Experimental — accuracy not yet measured

The dataset combines the newly reported ancient individuals with previously published ancient data to form a dataset of 281 ancient individuals.

“We combined our data with previously published ancient data7,8,9,10,8,10-15 to form a dataset of 281 ancient individuals.”

• cites [7] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015) sourcePartly supported

  The Abstract (page not available) says the authors combined their data with previously published ancient samples, supporting that part of the claim. It reports a total of 94 ancient Europeans, not 281 ancient individuals. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [8] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015) sourcePartly supported

  The ‘Genome-wide ancient DNA from West Eurasia’ section says the authors combined 67 previously published samples with newly reported data. But it gives the resulting dataset as 230 ancient individuals, not 281; the cited paper therefore supports the combination but not the claimed total. No page number is available in our copy. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [9] Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015) sourceSupported
• cites [10] Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015) sourceNot checked — no full text of the source
• cites [11] Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014) sourceSupported
• cites [12] Günther, T. et al. Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proc. Nat. Acad Sci. USA (2015) sourceNot checked — no full text of the source
• cites [13] Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014) sourceSupported
• cites [14] Olalde, I. et al. A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures. Mol. Biol. Evol. 32, 3132–3142 (2015) sourceSupported
• cites [15] Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014) sourcePartly supported

  The Methods section ('Genome sequencing and read processing'; page unavailable) says the study processed its ancient genomes alongside previously published ancient datasets. It does not report a combined dataset of 281 ancient individuals, so the cited paper supports the combination but not that total. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

The inner ear region of the petrous bone can yield up to ~100 times more endogenous DNA than other skeletal elements.

“First, we sampled from the inner ear region of the petrous bone3,4 that can yield up to ~100 times more endogenous DNA than other skeletal elements4.”

• cites [3] Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014) sourceSupported
• cites [4] Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10, e0129102 (2015) sourcePartly supported

  The Discussion reports substantially higher endogenous DNA yields from petrous samples than from a metatarsal bone of the same individual, supporting the comparison with another skeletal element. But the reported difference is 267- to 410-fold, not an upper limit of approximately 100-fold; the paper also notes that this comparison rests on a single non-petrous bone. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

PCA on present-day West Eurasian populations replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East.

“PCA on present-day West Eurasian populations (Methods) (Extended Data Fig. 1) on which we projected the ancient individuals (Fig. 1b) replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East (Extended Data Fig. 1)7,8,13.”

• cites [7] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015) sourcePartly supported

  The paper's PCA discussion (page unavailable) says that an analysis including 777 present-day West Eurasians replicates the positioning of present-day Europeans relative to the Near East, supporting the broad geographic contrast. It does not describe that contrast as horizontal PC1 or report parallel PC2 clines in Europe and the Near East. The Online Methods (page unavailable) confirm that ancient samples were projected onto a PCA using present-day West Eurasians. (LLM, conf=0.83)

  Experimental — accuracy not yet measured
• cites [8] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015) sourcePartly supported

  The Methods (‘Population history analysis’; page not provided) confirm that the paper performed PCA on 777 West Eurasian individuals and projected ancient individuals onto it. The passages in our copy do not describe a Europe–Near East contrast on PC1 or parallel European and Near Eastern clines on PC2, so they do not support those specific findings. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [13] Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014) sourcePartly supported

  The PCA results passage (labeled Abstract in our copy; page unavailable) reports a Europe–Near East discontinuity and north–south clines in both regions, supporting the main pattern. It does not specify that the contrast lies on horizontal PC1 or that the clines lie on PC2, so those axis assignments are not verified by our copy. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

West Eurasians harbour significantly less Neanderthal ancestry than East Asians.

“West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22.”

• cites [19] Prufer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014) sourcePartly supported

  In “Denisovan gene flow in mainland Asia” (page unavailable), the paper says populations in Asia and America appear to have more regions of Neandertal origin than populations in Europe. This supports the direction of the comparison, but the passage does not establish statistical significance for Neandertal ancestry or address West Eurasians as a whole. The reported Z-score concerns Denisovan, not Neandertal, ancestry. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [20] Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012) sourcePartly supported

  In “Denisovan and Neandertal gene flow,” the paper estimates 24% less Neandertal ancestry in Europe than in eastern Asia and South America (95% CI 12–36%), supporting a significant difference for the populations studied. Its European samples were French and Sardinian; it does not establish the claim for West Eurasians as a whole. (LLM, conf=0.83)

  Experimental — accuracy not yet measured
• cites [21] Wall, J. D. et al. Higher levels of neanderthal ancestry in East Asians than in Europeans. Genetics 194, 199–209 (2013) sourcePartly supported

  The D-statistics and estimates of f section reports significantly higher frequencies of putative Neanderthal haplotypes in East Asians than in Europeans; the Discussion likewise reports a higher admixture rate in East Asians. The paper establishes this comparison for Europeans, not for West Eurasians as a whole. The proposed dilution explanation is attached to a different citation and is not part of this verdict. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

There is a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals.

“Supporting this theory, we observe a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals19 (Supplementary Information, section 5; Fig. 2).”

• cites [19] Prufer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014) sourcePartly supported

  The paper’s ‘Neandertal gene flow into modern humans’ section reports Neanderthal-derived DNA in people outside Africa, and its Discussion describes allele sharing between Neanderthals and non-African populations (page not supplied). It does not report a correlation with Basal Eurasian ancestry. The citing sentence presents that correlation as the citing authors’ own observation (‘we observe’), rather than a finding of this source. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

The highest estimates of Basal Eurasian ancestry are from the Near East.

“It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East, given the hypothesis that it was there that most admixture between Neanderthals and modern humans occurred19,23.”

• cites [19] Prufer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014) sourceCould not verify

  The 'Neandertal gene flow into modern humans' section estimates Neandertal-derived DNA in people outside Africa, but does not estimate Basal Eurasian ancestry. Searches for Basal Eurasian ancestry and Near Eastern estimates found no passage supporting the claim that the highest estimates are from the Near East. (LLM, conf=0.75)

  Experimental — accuracy not yet measured
• cites [23] Brace, C. L. et al. The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form. Proc. Natl Acad. Sci. USA 103, 242–247 (2006) sourceCould not verify

  The Conclusions discuss craniofacial evidence for Neolithic migration from the Near East, not estimates of Basal Eurasian ancestry. Searches for Basal Eurasian ancestry and Neanderthal admixture found no passage addressing where the highest ancestry estimates occur. The cited paper therefore does not verify this claim in our copy. (LLM, conf=0.76)

  Experimental — accuracy not yet measured

Eastern Eurasians can be modelled as arrayed along a cline with different proportions of ANE ancestry, ranging from ~40% ANE in Native Americans to no less than ~5-10% ANE in diverse East Asian groups including Han Chinese.

“Eastern Eurasians can be modelled as arrayed along a cline with different proportions of ANE ancestry (Supplementary Information, section 11; Extended Data Fig. 8), ranging from ~40% ANE in Native Americans matching previous findings13,15, to no less than ~5-10% ANE in diverse East Asian groups including Han Chinese (Extended Data Fig. 5; Extended Data Fig. 7f).”

• cites [13] Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014) sourcePartly supported

  The Online Methods ('Ancestry estimates from f4-ratios'; page not supplied) describe estimating ANE ancestry in Karitiana, and Extended Data report that Native Americans are closer to ANE than to WHG. Neither passage gives the claimed ~40% estimate. The passages found also do not establish an Eastern Eurasian ANE cline or ~5–10% ANE ancestry in East Asian groups, including Han Chinese. (LLM, conf=0.78)

  Experimental — accuracy not yet measured
• cites [15] Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014) sourceSupported

All the libraries analyzed had rates of C-to-T substitution in the final nucleotide of at least 3%, consistent with genuine ancient DNA.

“We quantified the rate of C-to-T substitution in the final nucleotide of the sequences analyzed, relative to the human reference genome sequence, and found that all the libraries analyzed had rates of at least 3%38, consistent with genuine ancient DNA.”

• cites [38] Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010) sourceSupported

Application of the ghost-population method highlights the impact of Ancient North Eurasian (ANE) ancestry related to the ~22,000 BCE Mal'ta 1 and ~15,000 BCE Afontova Gora 2 on populations living in Europe, the Americas, and Eastern Eurasia.

“Application of this methods highlights the impact of Ancient North Eurasian (ANE) ancestry related to the ~22,000 BCE Mal'ta 1 and ~15,000 BCE Afontova Gora 215 on populations living in Europe, the Americas, and Eastern Eurasia.”

• cites [15] Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014) 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

The Chalcolithic people of western Iran can be modelled as a mixture of the Neolithic people of western Iran, the Levant, and Caucasus Hunter Gatherers (CHG).

“The Chalcolithic people of western Iran can be modelled as a mixture of the Neolithic people of western Iran, the Levant, and Caucasus Hunter Gatherers (CHG), consistent with their position in the PCA (Fig. 1b).”

• cites [7] Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015) sourceCould not verify

  The passages labeled Abstract model Yamnaya and European populations, while Extended Data Table 1 lists the study’s ancient samples; neither addresses Chalcolithic people of western Iran. Searches for western Iran, Chalcolithic ancestry, and the proposed Neolithic Iranian–Levantine–CHG mixture found no passage supporting or contradicting the claim. (LLM, conf=0.76)

  Experimental — accuracy not yet measured

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

It is impossible to model the Ancestral North Indians (ANI) as being derived from any single ancient population in the dataset.

“We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset.”

• cites [34] Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009) sourceCould not verify

  The ‘Relationship of Indians to non-Indians’ section reports that ANI and CEU form a clade, but does not test whether ANI could derive from any single ancient population in a dataset. The Discussion says that the history of ANI before mixture remains a priority for future work. Searches for the claimed single-population modelling result found no passage addressing it. (LLM, conf=0.76)

  Experimental — accuracy not yet measured
• cites [35] Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016) sourceCould not verify

  The Genetic clustering section describes ancient European and Siberian samples, while the Extended Data discuss ancestry estimates and comparisons among those samples (page numbers unavailable). Searches for “Ancestral North Indians,” “ANI,” and single-population ancestry models found no passage addressing whether ANI can be derived from one ancient population. (LLM, conf=0.75)

  Experimental — accuracy not yet measured

The early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians.

“To the west, the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians8.”

• cites [8] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015) sourceSupported

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

The earliest populations of the Near East derived around half of their ancestry from a 'Basal Eurasian' lineage.

“We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other.”

The first farmers of the southern Levant and Zagros Mountains were strongly genetically differentiated.

“The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers.”

The statistic f4(Test, Han; Ust'-Ishim, Chimp) is significantly negative (Z<−3.7) for all ancient Near Easterners as well as Neolithic and later Europeans.

“This statistic is significantly negative (Z<−3.7) for all ancient Near Easterners as well as Neolithic and later Europeans, consistent with their having ancestry from a deeply divergent Eurasian lineage that separated from the ancestors of most Eurasians prior to the separation of Han and Ust’-Ishim.”

The Basal Eurasian lineage had little if any Neanderthal admixture.

“We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other.”

The study reports genome-wide ancient DNA from 44 ancient Near Easterners dating between ~12,000 and 1,400 BCE, spanning Natufian hunter-gatherers to Bronze Age farmers.

“We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers.”

• AssumptionRests on an assumption: The relative homogeneity of present-day West Eurasians reflects extensive migration and admixture that homogenized geographically and genetically disparate sources of ancestry.
• AssumptionRests on an assumption: The spread of the world's first farmers from the Near East was a mechanism for homogenizing West Eurasian ancestry.

The study obtained genome-wide data passing quality control for 45 individuals with a median coverage of 172,819 SNPs.

“We obtained genome-wide data passing quality control for 45 individuals on whom we had a median coverage of 172,819 SNPs.”

The first farmers of the Zagros Mountains descended from local hunter-gatherers.

“The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers.”

The first farmers of the southern Levant descended from local hunter-gatherers.

“The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers.”

A population related to people of the Iran Chalcolithic contributed ~43% of the ancestry of early Bronze Age populations of the steppe.

“To the north, a population related to people of the Iran Chalcolithic contributed ~43% of the ancestry of early Bronze Age populations of the steppe.”

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

Among first farmers, those of the Levant trace ~2/3 of their ancestry to people related to Natufian hunter-gatherers and ~1/3 to people related to Anatolian farmers.

“Among first farmers, those of the Levant trace ~2/3 of their ancestry to people related to Natufian hunter-gatherers and ~1/3 to people related to Anatolian farmers (Supplementary Information, section 7).”

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

Northwest Anatolians-with ancestry from a population related to European hunter-gatherers-are better modelled if this ancestry is taken as more extreme than Bichon.

“Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10).”

In the Human Origins dataset, there is Levantine ancestry in Eastern Africa.

“(a) Levantine ancestry in Eastern Africa in the Human Origins dataset”

The ratio of Neanderthal ancestry in Basal Eurasians relative to non-Basal Eurasians is 9±26% (95% confidence interval −42 to 60%).

“We use a block jackknife47, dropping one of 100 contiguous blocks of the genome at a time, to estimate the value and standard error of this quantity (9±26%). We compute a 95% confidence interval based on the point estimate ±1.96-times the standard error: −42 to 60%.”

• AssumptionThe authors state this as an assumption: Basal Eurasians had no less Neanderthal admixture than Mbuti from sub-Saharan Africa.

There is a cline of ANE ancestry across the east-west extent of Eurasia.

“We also document a cline of ANE ancestry across the east-west extent of Eurasia.”

WHG are a mix of EHG and the Upper Paleolithic Bichon from Switzerland.

“and WHG are a mix of EHG and the Upper Paleolithic Bichon from Switzerland (Supplementary Information, section 7).”

Basal Eurasian ancestry is negatively correlated with Neanderthal ancestry.

“Negative correlation of Basal Eurasian ancestry with Neanderthal ancestry”

The ancient populations of the Chalcolithic Iran, Chalcolithic Armenia, Bronze Age Armenia and Chalcolithic Anatolia were all composed of the same ancestral components, albeit in slightly different proportions.

“Our analysis show that the ancient populations of the Chalcolithic Iran, Chalcolithic Armenia, Bronze Age Armenia and Chalcolithic Anatolia were all composed of the same ancestral components, albeit in slightly different proportions (Fig. 4b; Supplementary Information, section 7).”

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

Genetic differentiation in West Eurasian populations declines over time.

“Genetic structure in ancient West Eurasian populations across time and decline of genetic differentiation over time”

• Also stated in: § Extended Data · plain

  “Reduction of genetic differentiation in West Eurasia over time”

EHG, Mal'ta 1 (MA1) and Afontova Gora 2 (AG2) are positioned near the intersection of clines formed by European hunter-gatherers (WHG, SHG, EHG) and Eastern non-Africans in the space of outgroup f3-statistics of the form f3(Mbuti; Papuan, Test) and f3(Mbuti; Switzerland_HG, Test).

“EHG, and Upper Paleolithic Siberians Mal'ta 1 (MA1) and Afontova Gora 2 (AG2) are positioned near the intersection of clines formed by European hunter-gatherers (WHG, SHG, EHG) and Eastern non-Africans in the space of outgroup f3-statistics of the form f3(Mbuti; Papuan, Test) and f3(Mbuti; Switzerland_HG, Test).”

Eastern Hunter Gatherers (EHG) derive ~3/4 of their ancestry from the ANE.

“Eastern Hunter Gatherers (EHG) derive ~3/4 of their ancestry from the ANE (Supplementary Information, section 11);”

By the Bronze Age, the southern Levant and Zagros farmer populations and Anatolian-related farmers had mixed with each other and with European hunter-gatherers, drastically reducing genetic differentiation.

“By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation.”

The Basal Eurasian lineage separated from other non-African lineages prior to their separation from each other.

“We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other.”

The significantly negative f4(Test, Han; Ust'-Ishim, Chimp) results are consistent with ancient Near Easterners and Neolithic/later Europeans having ancestry from a deeply divergent Eurasian lineage that separated from the ancestors of most Eurasians prior to the separation of Han and Ust'-Ishim.

“This statistic is significantly negative (Z<−3.7) for all ancient Near Easterners as well as Neolithic and later Europeans, consistent with their having ancestry from a deeply divergent Eurasian lineage that separated from the ancestors of most Eurasians prior to the separation of Han and Ust’-Ishim.”

Basal Eurasian ancestry was widespread across the ancient Near East.

“We obtain the highest estimates in the earliest populations from both Iran (66±13% in the likely Mesolithic sample, 48±6% in Neolithic samples), and the Levant (44±8% in Epipaleolithic Natufians) (Fig. 2), showing that Basal Eurasian ancestry was widespread across the ancient Near East.”

• AssumptionRests on an assumption: The qpAdm/f4 reference populations used in the analyses are appropriate proxies for the ancestral populations they represent.

Scandinavian hunter-gatherers (SHG) are a mixture of WHG and a population on the Iran_ChL→Steppe_EMBA cline.

“(b) Scandinavian hunter-gatherers (SHG) are a mixture of WHG and a population on the Iran_ChL→Steppe_EMBA cline.”

Early/Middle Bronze Age steppe populations are a mixture of Iran_ChL and a population on the WHG→SHG cline.

“(a) Early/Middle Bronze Age steppe populations are a mixture of Iran_ChL and a population on the WHG→SHG cline.”

The study rejects the hypothesis that the spread of agriculture in the Near East was achieved by the dispersal of a single farming population displacing the hunter-gatherers they encountered.

“We reject the hypothesis that the spread of agriculture in the Near East was achieved by the dispersal of a single farming population displacing the hunter-gatherers they encountered.”

• AssumptionRests on an assumption: The relative homogeneity of present-day West Eurasians reflects extensive migration and admixture that homogenized geographically and genetically disparate sources of ancestry.
• AssumptionRests on an assumption: The spread of the world's first farmers from the Near East was a mechanism for homogenizing West Eurasian ancestry.

Caucasus hunter-gatherers (CHG) are a mixture of Iran_N and both WHG and EHG.

“(c) Caucasus hunter-gatherers (CHG) are a mixture of Iran_N and both WHG and EHG.”

Somali are a mixture of Mota and a population on the Iran_ChL→Levant_BA cline.

“(e) Somali are a mixture of Mota50 and a population on the Iran_ChL→Levant_BA cline.”

• cites [50]Not matched

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

South Asian populations can be modelled as having West Eurasian-related ancestry similar to that in populations from both the Eurasian steppe and Iran.

“(e) Mixture proportions for South Asian populations showing that they can be modelled as having West Eurasian-related ancestry similar to that in populations from both the Eurasian steppe and Iran.”

Eastern European hunter-gatherers (EHG) are a mixture of WHG and a population on the Onge→Han cline.

“(f) Eastern European hunter-gatherers (EHG) are a mixture of WHG and a population on the Onge→Han cline.”

The study developed a method to infer the existence and genetic affinities of ancient populations from unobserved 'ghost' populations.

“To further assess the robustness of our inferences, we developed a method to infer the existence and genetic affinities of ancient populations from unobserved ‘ghost’ populations (Supplementary Information, section 10; Extended Data Fig. 7).”

There is admixture from a 'ghost' ANE population into both European and Eastern Eurasian ancestry.

“Admixture from a ‘ghost’ ANE population into both European and Eastern Eurasian ancestry”

The interdependence of the ancestry of Europe and the Near East may have been mediated by unsampled geographically intermediate populations that contribute ancestry to both regions.

“This interdependence of the ancestry of Europe and the Near East may have been mediated by unsampled geographically intermediate populations36 that contribute ancestry to both regions.”

• cites [36] Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013) sourceNot checked — no full text of the source

The study tested whether conclusions might be biased by the particular populations sampled by plotting the inferred position of admixed populations in PCA against a weighted combination of their inferred source populations and obtained qualitatively consistent results.

“We tested our conclusions by plotting the inferred position of admixed populations in PCA against a weighted combination of their inferred source populations and obtained qualitatively consistent results (Extended Data Fig. 6).”

Late Neolithic/Bronze Age Europeans are a mixture of the preceding Europe_MNChL population and a population with both EHG and Iran_ChL ancestry.

“(d) Late Neolithic/Bronze Age Europeans are a mixture of the preceding Europe_MNChL population and a population with both EHG and Iran_ChL ancestry.”

All libraries passing quality control and for which sufficient X chromosome data were available had contamination rates of 0-1.5% according to ANGSD X chromosome estimates.

“For the nuclear data from males, we used the ANGSD software44 to estimate a conservative X chromosome estimate of contamination. We determined that all libraries passing our quality control and for which we had sufficient X chromosome data to make an assessment had contamination rates of 0-1.5%.”

• cites [44] Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007) sourceNot checked — no full text of the source