Henn Revisited – “Back Migration” – really?!
Jan 17, 2014 21:45:34 GMT -5
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Post by djoser-xyyman on Jan 17, 2014 21:45:34 GMT -5
As I said many times, it is a very good idea to re-read research papers at least or twice a year. I hope my points are made clearer this time around.
From - Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Abstract
We present dense, genomewide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa;
Prior genetic studies, largely from uniparentally inherited markers, have not resolved the location origin of North African populations or the timing of human dispersal(s) into North Africa. Analyses based on the frequencies of a small number of autosomal genetic polymorphisms and uniparental markers have shown that the genetic landscape follow an east-west pattern with little to no difference between Berber- and Arab-speaking populations [6,7].
, all North African populations except for Tunisians have sub-Saharan ancestry, present in most individuals, though this ancestry varies between 1%–55%. Interestingly, eastern populations (i.e. Libya and Egypt) share ancestry assigned to both the Bantu-speaking Luhya and the Nilotic-speaking Maasai, whereas western populations share ancestry mainly with the Luhya.
According to our ADMIXTURE results, two distinct sub-Saharan ancestries are present in Egyptian individuals at k =6:10; these two ancestry components are highest in the Kenyan Luhya and Maasai populations. However, the ‘‘Luhya’’ ancestry is present at very low proportions, below 10% at k= 6 and below 5% at k= 8 and there is also ‘‘Luhya’’ ancestry detectable in Maasai populations. Thus, we chose the Maasai as the best ancestral sub-Saharan population for extant Egyptians.
We can REJECT a simple model of long-term continuous gene flow between the Near East(QATAR/ARABIA) and North Africa, as evidenced by clear geographic structure and non-zero Fst estimates. Fst estimates between the inferred Maghrebi cluster and sub-Saharan Africans are two to three-times greater than Fst between the Maghrebi and Europeans/Near Easterners ancestral clusters (Table S3).
we first showed that all North African populations are estimated to have diverged from OOA groups more than 12,000 ya (Figure 3). After accounting for putative recent admixture (Figure 1), the indigenous Maghrebi component (k-based) is estimated to have diverged from Near Eastern/Europeans between **18–38 Kya **(Figure 3), under a range of Ne and k values. We hence suggest that the ancestral Maghrebi population separated from Near Eastern/Europeans prior to the Holocene, and that the MAGHREBI POPULATIONS DO **NOT** REPRESENT A LARGE-SCALE DEMIC DIFFUSION OF AGROPASTORALISTS FROM THE NEAR EAST/ARABIA. With model parameters for divergence approximately estimated, we then ask whether North African ancestral populations were part of the initial OOA exit and then returned to Africa [8], or if an in situ model of population persistence for the past 50 Kya is more likely (with variable episodes of migration from the Near East)? We can address this question ONLY indirectly with contemporary samples; however, several auxiliary observations point toward the former hypothesis.
***
Substantially elevated linkage disequilibrium in all of these North African population samples, compared to sub-Saharan populations [32], is consistent with a population bottleneck. Hellenthal et al. [30] also observed that the reduction in the number of haplotype founders required to reconstruct the Mozabite population, as compared to other African populations, could be explained by a population bottleneck. If North African ancestral populations persisted in situ, then we need to invoke two population bottlenecks, one in the ancestors of North Africans (including the Berbers) and one for OOA groups. Alternatively, the ‘‘OOA’’ bottleneck would need to occur in North Africa, rather than when groups moved out of the continent [33]. The second possibility appears at odds with MOST PUBLISHED models of the movement of modern humans outside of Africa.
***
XYYMAN-COMMENT. This her justification for her premise on the backmigration theory. She observed bottleneck in North Africans compared to SSA. Now since SOME OOA models from other researchers do show bottleneck she concluded that North Africans migrated from Qater about 38,000ya. Ie the bottleneck came from the ancestors in QATAR. Now really??!!!, this is bordering on ludicrous and comical. She is proposing the ridiculous idea that the bottleneck is very unlikely to have occurred in two different population!. She did not perform the simple logical analysis of comparing Qatari and North African sequences to resolve the issue. Instead she relied on what is written in the literature/journals. Are they/she for real? She then the politically correct thing by CYA, in the next paragraph. “I may be wrong so to be sure perform genomic sequence data testing “.. Why didn’t she do it to be sure? She didn’t.
(Continuing….)
These models should be further tested with genomic sequence data, which have better power to detect magnitude and timing of bottlenecks, and to estimate the true joint allele frequency spectrum. More recently, the substantial, east-to-west decline of Near Eastern ancestry (Figure 1A) could represent a defined migration associated with Arab conquest 1,400 ya or merely gene flow occurring gradually among neighboring populations along a North African | Arabian Peninsula transect. Although [/b]we observe a declining amount of Maghrebi ancestry from northwest-to northeast,[/b] it is possible that other geographically North African samples (e.g. Egyptians further south than the sampled Siwa Oasis) do not conform to this geographic cline. Finally, we also observe European ancestry that is not clearly accounted for by the inclusion of a Near Eastern sample. Additional migration coming from Europe might be plausible, though the origin and the period where it took place cannot be determined with the present data. The less than 25% European ancestry in populations like Algerians and northern Moroccans could trace back to maritime migrations throughout the Mediterranean [34]. Alternatively, the Qatari could represent a poor proxy for an Arabic source population, causing additional diversity to be assigned European (e.g. European ancestry tracts were not reliably assigned as European with PCADMIX).
From - Genomic Ancestry of North Africans Supports Back-to-Africa Migrations
Abstract
We present dense, genomewide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa;
Prior genetic studies, largely from uniparentally inherited markers, have not resolved the location origin of North African populations or the timing of human dispersal(s) into North Africa. Analyses based on the frequencies of a small number of autosomal genetic polymorphisms and uniparental markers have shown that the genetic landscape follow an east-west pattern with little to no difference between Berber- and Arab-speaking populations [6,7].
, all North African populations except for Tunisians have sub-Saharan ancestry, present in most individuals, though this ancestry varies between 1%–55%. Interestingly, eastern populations (i.e. Libya and Egypt) share ancestry assigned to both the Bantu-speaking Luhya and the Nilotic-speaking Maasai, whereas western populations share ancestry mainly with the Luhya.
According to our ADMIXTURE results, two distinct sub-Saharan ancestries are present in Egyptian individuals at k =6:10; these two ancestry components are highest in the Kenyan Luhya and Maasai populations. However, the ‘‘Luhya’’ ancestry is present at very low proportions, below 10% at k= 6 and below 5% at k= 8 and there is also ‘‘Luhya’’ ancestry detectable in Maasai populations. Thus, we chose the Maasai as the best ancestral sub-Saharan population for extant Egyptians.
We can REJECT a simple model of long-term continuous gene flow between the Near East(QATAR/ARABIA) and North Africa, as evidenced by clear geographic structure and non-zero Fst estimates. Fst estimates between the inferred Maghrebi cluster and sub-Saharan Africans are two to three-times greater than Fst between the Maghrebi and Europeans/Near Easterners ancestral clusters (Table S3).
we first showed that all North African populations are estimated to have diverged from OOA groups more than 12,000 ya (Figure 3). After accounting for putative recent admixture (Figure 1), the indigenous Maghrebi component (k-based) is estimated to have diverged from Near Eastern/Europeans between **18–38 Kya **(Figure 3), under a range of Ne and k values. We hence suggest that the ancestral Maghrebi population separated from Near Eastern/Europeans prior to the Holocene, and that the MAGHREBI POPULATIONS DO **NOT** REPRESENT A LARGE-SCALE DEMIC DIFFUSION OF AGROPASTORALISTS FROM THE NEAR EAST/ARABIA. With model parameters for divergence approximately estimated, we then ask whether North African ancestral populations were part of the initial OOA exit and then returned to Africa [8], or if an in situ model of population persistence for the past 50 Kya is more likely (with variable episodes of migration from the Near East)? We can address this question ONLY indirectly with contemporary samples; however, several auxiliary observations point toward the former hypothesis.
***
Substantially elevated linkage disequilibrium in all of these North African population samples, compared to sub-Saharan populations [32], is consistent with a population bottleneck. Hellenthal et al. [30] also observed that the reduction in the number of haplotype founders required to reconstruct the Mozabite population, as compared to other African populations, could be explained by a population bottleneck. If North African ancestral populations persisted in situ, then we need to invoke two population bottlenecks, one in the ancestors of North Africans (including the Berbers) and one for OOA groups. Alternatively, the ‘‘OOA’’ bottleneck would need to occur in North Africa, rather than when groups moved out of the continent [33]. The second possibility appears at odds with MOST PUBLISHED models of the movement of modern humans outside of Africa.
***
XYYMAN-COMMENT. This her justification for her premise on the backmigration theory. She observed bottleneck in North Africans compared to SSA. Now since SOME OOA models from other researchers do show bottleneck she concluded that North Africans migrated from Qater about 38,000ya. Ie the bottleneck came from the ancestors in QATAR. Now really??!!!, this is bordering on ludicrous and comical. She is proposing the ridiculous idea that the bottleneck is very unlikely to have occurred in two different population!. She did not perform the simple logical analysis of comparing Qatari and North African sequences to resolve the issue. Instead she relied on what is written in the literature/journals. Are they/she for real? She then the politically correct thing by CYA, in the next paragraph. “I may be wrong so to be sure perform genomic sequence data testing “.. Why didn’t she do it to be sure? She didn’t.
(Continuing….)
These models should be further tested with genomic sequence data, which have better power to detect magnitude and timing of bottlenecks, and to estimate the true joint allele frequency spectrum. More recently, the substantial, east-to-west decline of Near Eastern ancestry (Figure 1A) could represent a defined migration associated with Arab conquest 1,400 ya or merely gene flow occurring gradually among neighboring populations along a North African | Arabian Peninsula transect. Although [/b]we observe a declining amount of Maghrebi ancestry from northwest-to northeast,[/b] it is possible that other geographically North African samples (e.g. Egyptians further south than the sampled Siwa Oasis) do not conform to this geographic cline. Finally, we also observe European ancestry that is not clearly accounted for by the inclusion of a Near Eastern sample. Additional migration coming from Europe might be plausible, though the origin and the period where it took place cannot be determined with the present data. The less than 25% European ancestry in populations like Algerians and northern Moroccans could trace back to maritime migrations throughout the Mediterranean [34]. Alternatively, the Qatari could represent a poor proxy for an Arabic source population, causing additional diversity to be assigned European (e.g. European ancestry tracts were not reliably assigned as European with PCADMIX).
