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S10. Admixture f3 statistics show that the West Eurasian component originated from a population similar to the early Neolithic farmers
Since we have in Mota an unadmixed African population, we can look for the origin of the West Eurasian backflow by modelling contemporary Ari as a mixture of Mota and possible source populations. We do this by using the admixture f3-statistics (63) in the form f3(X, Mota; AriCultivator), where X is a contemporary Eurasian population from our global panel or a Eurasian ancient genome. For the latter, we used a representative of Mesolithic hunter-gatherers (Loschbour), and one of the Early Neolithic farmers (LBK, also known as Stuttgart) (9); these two genomes were chosen for their high coverage, allowing us to use most of the SNPs available for contemporary populations and Mota. The genomic positions included in the global dataset were called in these two genomes using samtools, calling sites with base quality ≥20 and mapping quality ≥30. Then, the vcf files were converted to plink-format files using vcftools (59), and finally merged with the global dataset (already containing Mota), using PLINK (60). All f3 statistics were computed using the 3PopTest program from the ADMIXTOOLS package (63).
LBK (an early Neolithic farmer) and Sardinians are the two most likely sources (showing the most negative admixture f3 values) for the Eurasian admixture in the Ari. A number of other analyses have shown Sardinians to be the closest contemporary population to early Neolithic farmers that came into Europe from the Near East (9), as contemporary populations from that region have been affected by large-scale populations movements in the last few millennia (65). Thus, the West Eurasian backflow originated from the direct descendants of the same early farmers who brought agriculture into Europe. Given that we have a putative source for the West Eurasian component, we can re-estimate its extent by using LBK as its source in our estimation of the f4 ratio, from which λMota,LBK can be derived without having to worry about West African ancestry in the source (as we had to for the Druze; Fig. S7).
the error associated with the ALDER estimates, the two are in reality not that incompatible as they are less than 3 standard errors (SE) apart: the upper boundary based on the ancient genome is 2.81 SE different to the ALDER estimate if we use a generation time of 29 years, and 2.41 SE if we use 25 years. Furthermore, the magnitude of the admixture proportion in Yoruba is rather low, a level at which we expect ALDER estimates to be less accurate. Indeed, we see that the proportion inferred by ALDER (2.7%) is much lower than the direct estimate based on the f4 ratio using Mota as a reference (6%).
We next tested whether the West Eurasian component found in Yoruba, which had been previously suggested to be older than Mota [dated to 9.6k±1.8k yrs ago using ALDER (16)], comes from the same source found for the Ari. We use the D statistics (66, 67) in the form D(Yoruba, Mota; X, Han), where X is a contemporary Eurasian population from our global panel or a Eurasian ancient genome. Sardinians and LBK were again found to be the most likely source of the West Eurasian component (giving the strongest positive values that indicate excess affinity between X and Yoruba compared to Mota, Table S6). This result suggests that there was a single source for the West Eurasian component found throughout Africa. So, how can the date estimated by ALDER (9,618±1,825 assuming a generation time of 29 years, and 8,300±1,575 with 25 years) be reconciled with the timing directly inferred by the age of our ancient genome (4.5 k yrs)? Given the error associated with the ALDER estimates, the two are in reality not that incompatible as they are less than 3 standard errors (SE) apart: the upper boundary based on the ancient genome is 2.81 SE different to the ALDER estimate if we use a generation time of 29 years, and 2.41 SE if we use 25 years. Furthermore, the magnitude of the admixture proportion in Yoruba is rather low, a level at which we expect ALDER estimates to be less accurate. Indeed, we see that the proportion inferred by ALDER (2.7%) is much lower than the direct estimate based on the f4 ratio using Mota as a reference (6%).
Finally, we repeated the analysis detailed above using Mbuti as our target (Table S7). The signal was slightly weaker in this case, but Sardinians were again highlighted as the most likely source of the West Eurasian component in this population (LBK was ranked 6th in this analysis).
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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LOL that link was already posted, you nutjob! That euronut persistence is surely strong in you.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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As I posted elsewhere, look at the g25 results ran on Mota.
Notice that the first set is closest to Mota especially the Hadza but in the second set comprising both Ethio-Semitic and Cushitic speakers the distance is about equivalent between Neolithic Moroccans and Natufians.
-------------------- Mahirap gisingin ang nagtutulog-tulugan. Posts: 26239 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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