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East Africans may have up to a quarter of Asian and European DNA, says report
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[QUOTE]Originally posted by Ish Gebor: [QB] [QUOTE] Southwest Arabia During the Holocene: Recent Archaeological Developments. Abstract Recent fieldwork has considerably increased our knowledge of early Holocene settlement in Southwest Arabia. Neolithic settlement occurred within an environmental context of increased monsoonal moisture that continued during the mid-Holocene. A now well-attested Bronze Age exemplified by village- and town-scale settlements occupied by sedentary farmers developed toward the end of the mid-Holocene moist interval. The high plateau of Yemen was an early focus for the development of Bronze Age complex society, the economy of which relied upon terraced rain-fed and runoff agriculture.[b] On the fringes of the Arabian desert, the precursors of the Sabaean literate civilization have been traced back to between 3600 and 2800 B.P., and even earlier, so that a virtually continuous archaeological record can now be described for parts of Yemen.[/b] In contrast to the highlands these societies relied upon food production from large-scale irrigation systems dependent upon capricious wadi floods. [b]Bronze Age settlement, while showing some links with the southern Levant, now shows equal or stronger linkages with the Horn of Africa across the Red Sea.[/b] Although some regions of Yemen show breaks in occupation, others show continuity into the Sabaean period when a series of major towns grew up in response to the incense trade with the north. It is now clear that these civilizations grew up on the foundations of earlier Bronze Age complex societies. [/QUOTE]--Christopher Edens , T. J. Wilkinson Southwest Arabia During the Holocene: Recent Archaeological Developments Journal of World Prehistory March 1998, Volume 12, Issue 1, pp 55-119 http://www.springerlink.com/content/qt65313874654632/ Where is Dana Marniche when you need her? [/QB][/QUOTE] [QUOTE] [b]S9. f4 ratio analysis shows that Mota has no component of West Eurasian admixture[/b] We used f4 ratio analysis (63) to formally assess the extent of back-migration to Africa by West Eurasians, using the same logic as adopted by Pickrell et al (58) . We quantified the West Eurasian component in Africa, using Yoruba as our non-admixed African reference, with the ratio f4(Han, Orcadian; X, Druze) / f4 (Han, Orcadian; Yoruba, Druze), where X is a contemporary African population or Mota. However, since Druze has a small level of West African ancestry, this f4 ratio is biased and does not show the desired fraction of West Eurasian component. To correct for this, we define λYoruba,Druze as the fraction of Druze-like (i.e. West Eurasian) ancestry population X, and F as the fraction of Yoruba-like (i.e. West African) ancestry in Druze (estimated in other studies to be F=0.05) (64). We can then write the following equation: f4 (Han, Orcadian; X, Druze) / f4 (Han, Orcadian; Yoruba ,Druze) = (1 - λYoruba,Druze – F) / (1 – F) (2) and solve for λYoruba,Druze for each population X. All statistics were computed with the F4Ratio program from the ADMIXTOOLS package. We first checked that subsetting to the SNPs available for Mota did not affect estimates for contemporary African populations (Table S5), which are in line with those estimated by Pickrell et al (58) using all available positions (Pearson Correlation r=0.9998). Mota does not show any evidence of a West Eurasian component, with a λYoruba,Druze value that is negative (-8.7%, ± 2.2%). This contrasts in particular with the Ari, their closest contemporary relatives, which show large West Eurasian components (17.8%±1.0% and 14.9%±1.2% for Ari Cultivator and Ari Blacksmith, respectively). We confirmed that such a difference is not due to a comparison of a single individual to population estimates by recomputing the f4 ratio for each individual belonging to an Ethiopian population in our dataset (Fig. S6). The absence of a West Eurasian component in Mota supports the dating of the backflow into Africa, which, at ~3.5kya, is younger than our ancient genome (dated to 4.5 kya). Given that Mota predates the backflow, it potentially provides a better unadmixed African reference than contemporary Yoruba. Thus, we recomputed the extent of the West Eurasian component in contemporary African populations using Mota, λMota,Druze, instead of Yoruba in our f4 ratio. By using this better reference, we estimated West Eurasian admixture to be significantly larger than previously estimated, with an additional 6-9% of the genome of contemporary African populations being of Eurasian origin (Fig. S6, and Table S5). Importantly, this analysis shows that the West Eurasian component can be found also in West Africa (Fig. S6), albeit at lower levels than in Eastern Africa. Importantly, a sizeable West Eurasian component is also found in the Yoruba and Mbuti, which are often used a representative of an unadmixed African population. [/QUOTE] [QUOTE] [b]S10. Admixture f3 statistics show that the West Eurasian component originated from a population similar to the early Neolithic farmers[/b] 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). [/QUOTE]--R. Pinhasi et al. Supplementary Materials for Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent https://www.sciencemag.org/content/suppl/2015/10/07/science.aad2879.DC1/Gallego-Llorente.SM.pdf [/QB][/QUOTE]
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