Given that the Mbuti population is known to be relatively isolated from other Pygmy and neighboring non-Pygmy populations, this suggests that central Africa may have been the homeland of a now-extinct archaic form that hybridized with modern humans.
... the results point to relatively recent genetic exchange with an unknown archaic hominin that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene and remained isolated for several hundred thousand years.
. . . .
Interestingly, recent studies attest to the existence of Late Stone Age human remains with archaic features in Nigeria (Iwo Eleru) and the Democratic Republic of Congo (Ishango). The observation that populations from many parts of the world, including Africa, show evidence of introgression of archaic variants suggests that genetic exchange between morphologically divergent forms may be a common feature of human evolution.
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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posted
Here geneticists lacking actual aDNA invent an archaic Homo to crossbreed with AMH Africans based on 3 loci considered recombinational hotspots:
* 13qMB107 in Mbuti, San, Xhosa, SA Bantu * 4qMB179 in Mbuti, Baka, Biaka, Bakola, Luhya, Ngoumba, Yoruba * 18qMB60 in Mbuti, Baka, Biaka, Xhosa, Dinka, Dogon
quote: Michael F. Hammer et al. (2011) Genetic evidence for archaic admixture in Africa
FIG. 4. Frequency of introgressive variants within three sequenced regions in an expanded sample of ≈500 sub-Saharan Africans. The filled bar represents the frequency of a variant marking the divergent haplotype at 4qMB179 (Left), 18qMB60 (Center), and 13qMB179 (Right) in each of 14 population samples. Each horizontal line on the bar charts represents a frequency of 5%.
DISCUSSION [snippets]
We hypothesize that the unusual haplotype descends from an archaic DNA segment that entered the AMH population via admixture.
. . . .
... the Mbuti represent the only population in our survey that carries the introgressive variant at all three candidate loci, despite the fact that no Mbuti were represented in our initial sequencing survey.
Given that the Mbuti population is known to be relatively isolated from other Pygmy and neighboring non-Pygmy populations, this suggests that central Africa may have been the homeland of a now-extinct archaic form that hybridized with modern humans.
... the results point to relatively recent genetic exchange with an unknown archaic hominin that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene and remained isolated for several hundred thousand years.
. . . .
Interestingly, recent studies attest to the existence of Late Stone Age human remains with archaic features in Nigeria (Iwo Eleru) and the Democratic Republic of Congo (Ishango). The observation that populations from many parts of the world, including Africa, show evidence of introgression of archaic variants suggests that genetic exchange between morphologically divergent forms may be a common feature of human evolution.
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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posted
I think we discussed this before in a couple of other threads. The problem is scientists don't have yet a total grasp of the African gene pool and all its subtleties. Thus any particular feature found in one segment of the African population such as Pygmies, and they jump to the conclusion that it is the result of some archaic species. Remember how one study claimed East Africans like Maasai had genetic influence from Neanderthals [sic]?! LOLPosts: 26243 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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Speaking of archaic admixture, given the population geneticists' recent fixation on Neanderthals, does anyone wonder if they'll look for Neanderthal elements in the Egyptian mummies' STR profiles? I would love to see some newspaper headline ask whether King Tut et al had Neanderthal ancestry (which I seriously doubt they did). Come to think of it, if they fail to find Neanderthal affinity in the AE genetic data, that could give the mainstream scientific establishment a good clue...
posted
^ It's funny you mention this considering that studies on modern North African populations show alleged Neanderthal admixture as was presented here and then again here. Of course that is with modern populations of heavy European and north Southwest Asian extraction. I too seriously doubt such affinities in more ancient samples such as the pharaohs, especially since studies show them to be very disparate in affinity with modern North Africans and approximate closer with modern Sub-Saharans.
Posts: 26243 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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In all seriousness, it would cool if they would compare King Tut and co.'s genetic data with that of Neanderthals and African archaics (think Iwo Eleru), and try to figure out which archaics show the greatest affinity with the mummies. Come to think of it, it might make for a good grad or even undergrad project...
posted
^ Yet before geneticists can even talk about 'archaics' they need to first compare ancient populations with modern ones and most of all try to understand the subtleties of the human gene pool at large. I even question whether such genetic features are really the result of archaic species or genuinely evolved in humans!
Posts: 26243 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Before I broached the thread I was on a page listing a few studies or articles on archaic admixture in Africans but after going to Hammer's study I lost the others.
quote:Joseph Lachance, Benjamin Vernot, Clara C. Elbers, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, Godfrey Lema, Wenqing Fu, Thomas B. Nyambo, Timothy R. Rebbeck, Kun Zhang, Joshua M. Akey, Sarah A. Tishkoff
Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers [snippets]
Cell, Volume 150, Issue 3, 457-469, 26 July 2012
Summary
To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60 coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.
Hunter-Gatherer Genomes Possess Signatures of Archaic Admixture
Gene flow between anatomically modern humans and archaic species has been described for European, Melanesian, and African populations (Hammer et al., 2011; Plagnol and Wall, 2006; Wall et al., 2009; Reich et al., 2010). To detect putatively introgressed regions in the Pygmy, Hadza, and Sandawe hunter- gatherer populations, we modified the summary statistic S*, which searches for clusters of population-specific SNPs in near complete LD, to be suitable for genome-scale analyses. S* has previously been used to detect archaic admixture in individuals of European and African descent (Hammer et al., 2011; Plagnol and Wall, 2006; Wall et al., 2009).
...non-African genomic regions with high values of S* were significantly enriched for Neanderthal-specific SNPs (p < 1016, Figure 3B). Thus, S* can robustly detect genomic regions inherited from archaic ancestors.
We next used S* to identify putatively introgressed regions in the African hunter-gatherer samples. In all three African hunter gatherer samples, we found evidence of introgression from at least one archaic population. Strikingly, the median TMRCA for putatively introgressed haplotypes in the hunter-gatherer samples is similar to the median TMRCA for introgressed haplotypes in Europeans --1.2–1.3 Mya versus 1.1–1.2 Mya, respectively; Figure 2A--, suggesting that the archaic African population diverged from anatomically modern humans in the same time frame as Neanderthals --simulations suggest that relative time of split with archaic populations can be recovered via TMRCA; Figure 3C--.
If candidate regions identified by unusually large values of S* are enriched for genuine introgressed sequence, then we would expect STRUCTURE to identify two populations, as introgressed regions primarily consist of individuals carrying one archaic and one anatomically modern haplotype.
... this is precisely what we find --Figures 2B and 2C--, further demonstrating that top-ranked S* regions are enriched for putatively introgressed sequence.
... introgressed regions in extant human populations represent neutrally evolving vestiges of archaic sequences. In short, we find that low levels of introgression from an unknown archaic population or populations occurred in the three African hunter- gatherer samples examined, consistent with findings of archaic admixture in non-Africans --Reich et al., 2010--.
One thing I don't get is the association with hunter gatherers for archaic admix in Africans but non-Africans supposedly admixed with archaics are of various economies.
Another thing, it seems geneticist want/need Africans to match non-Africans in both the time and scale of admixture.
These simulations seem a bit too neat but at least Tishkoff recognizes its a computerized model and has shortcomings.
Rapid decay of African fossils notwithstanding we have beaucoup archaic African fossil men. Why invent ones that simply don't exist outside of computer simulation?
On the up side, several Africans and two African institutions were involved with the research work.
Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011
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posted
^ There is nothing to get. It's typical Eurocentrism. The theory is that isolated populations tend to preserve so-called archaic traits yet not all isolated populations are hunter-gatherers and this is true in Africa as well as in Eurasia.
By the way, your mailbox is full.
Posts: 26243 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
You know what? I want to see introgression levels for Neanderthal into Denisovan and vice versa and then with the invented African archaics vs real existing archaic Africans.
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