Figure 1. Results of the ADMIXTURE analysis (k = 4) with North African populations.
ADMIXTURE was performed on a set of European, North African, Near Eastern and Sub-Saharan populations in order to account for the different admixture proportions in North Africa. Tunisians and Saharawi are the North African populations with highest proportion of autochthonous component, whereas the rest of the populations have greater amounts of admixture with neighboring populations. doi:10.1371/journal.pone.0047765.g001
Table 2. Estimates of Neandertal ancestry in North African populations, along with European, Asian and Sub-Saharan African groups. show more doi:10.1371/journal.pone.0047765.t002
Figure 3. Neandertal genetic introgression in North African populations as a fraction of that found in Europeans. show more Relative proportion of Neandertal ancestry for each population is presented as the dark blue section of the pies on a map of North Africa. Additionally, each population is also represented as a barplot of the different geographic genetic components; in red: North African, in blue: Sub-Saharan, in green: European, in yellow: Near East. Populations are shown as having Neandertal ancestry if the estimates are more than two standard errors from zero. Full name descriptions of these population labels are found in Table 2. doi:10.1371/journal.pone.0047765.g003
North African Populations Carry the Signature of Admixture with Neandertals
Federico Sánchez-Quinto equal contributor, Laura R. Botigué equal contributor, Sergi Civit, Conxita Arenas, María C. Ávila-Arcos, Carlos D. Bustamante, David Comas Carles Lalueza-Fox
Abstract
One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.
Introduction
Probably the most striking finding derived from the Neandertal genome project [1] was the evidence for admixture between Neandertals and a population of modern humans that left Africa between 80 Kya and 50 Kya subsequently expanding into the rest of the world. The study involved the sequencing and comparison of the Neandertal genome to five modern human genomes: two African (Yoruba and San) and three non-Africans (French, Chinese and Melanesian); all the non-African human genomes shared with Neandertals between 1–4% of their genome, in regions of low recombination placed along ten chromosomes [1]. Additional genomic region introgressions from Neandertals, Denisovans and also putative archaic African hominins have been recently described in Eurasian, Oceanic and even African populations, respectively [2]–[7].
However, an alternative scenario in which the ancestral population of today non-Africans was more closely related to Neandertals than the ancestral population of current Africans due to ancient substructure within the African continent, cannot be totally excluded with the present data [8], although it seems unlikely [9]. In light of this, it is unfortunate that North African individuals have not been included in these admixture analyses, since both the putative African substructure and the admixture are likely to differentially affect North African and sub-Saharan African populations.
The importance of North Africa in the emergence of modern Homo sapiens has been traditionally neglected. However, recent archaeological and paleontological evidence increasingly points to this area as a potential source of out-of-Africa migrations [10],[11]. Recent dating of the characteristic North African lithic industry, called Aterian, has provided much older dates than previously assumed, now ranging from 145 Kya to 40 Kya [12],[13]. These Aterian people made personal ornaments with shells, a sign of modern human symbolic behavior [14]. Morphometric analyses of the 80 Kya Dar es-Soltan skull (Morocco) and of Aterian hominin teeth show similarities with early modern humans from Qafzeh and Skhul (Israel) and with the later skull of Pestera cu Oase (Romania) [15],[16].
Recent genetic analysis of North African populations [17] have found that, despite the complex admixture genetic background, there is an autochthonous genomic component which is likely derived from “back-to-Africa” gene flow older than 12,000 years ago (ya) (i.e., prior to the Neolithic migrations). This local population substratum seems to represent a genetic discontinuity with the earliest modern human settlers of North Africa (those with the Aterian industry) given the estimated ancestry is younger than 40,000 years ago [17]. The estimated time of Neandertal admixture with modern human populations is between 37,000–86,000 years ago [18].
The aim of this work was to investigate if this autochthonous North African ancestry bares any traces of the introgression with Neandertals, by applying the f4 ancestry ratio statistic test, previously used to detect Denisovan admixture in Asia [3]. We show that North African populations, like all non-African humans [1], also carry the signature of admixture with Neandertals, and that the real geographical limit for Neandertal admixture is between sub-Saharan groups and the rest.
Materials and Methods
To ascertain whether or not current North African populations show any signs of Neandertal admixture, we analyzed recently published data of 125 North African individuals genotyped with the Affymetrix 6.0 chip and accounting for 780,000 SNPs were analyzed [17]. Individuals are representative of seven different North African locations (Table 1) spanning from west to east. To have a broader coverage of Eurasia and to allow comparison with Sub-Saharan populations, African and Eurasian populations were included in the analysis [1
In order to compare the human SNP data to the Neandertal, bam read files from all Neandertal samples from the UCSC ftp site (ftp://hgdownload.cse.ucsc.edu/gbdb/hg18/neandertal/seqAlis) were downloaded and merged. Base and mapping quality filters reported in previous studies were implemented in the analysis [2],[21]. To avoid any confusion with ancient DNA postmortem modifications, C-T and G-A human – ancient hominin nucleotide sites, were discarded. For all sequencing data, a single read was randomly sampled for each individual at positions overlapping the array SNPs coordinates. Furthermore all human and Neandertal data were merged with sequence data from chimpanzee (CGSC 2.1/Pantro), and data were further processed to control for strand misidentification [3], to conform a final data set of 142,720 SNPs.
North African populations have a complex genetic background. In addition to an autochthonous genetic component, they exhibit signals of European, sub-Saharan and Near Eastern admixture as previously described [17]. Moreover, the use of genotype data can suffer from potential biases that arise from discovering SNPs in a limited number of individuals, thus resulting in enrichment of common alleles, particularly in the populations from which the discovery panel was constructed [22],[23] (in the present case would be a bias towards European populations). Two challenges arise from these effects: first, patterns of gene flow detected between Neandertal and North Africans could be the consequence of subsequent admixture between North Africans and other modern human populations and second, the ascertainment bias towards European and East Asian populations could magnify differences in signals of Neandertal gene flow in individuals with high Sub-Saharan ancestry compared to individuals with high European ancestry.
In order to overcome these problems we initially assessed the different genetic components in North African populations using an unsupervised clustering algorithm, ADMIXTURE [24], on a sample set of around 50,000 SNPs that included all North African individuals, together with populations of European, Near Eastern and Sub-Saharan origin [17],[25],[26].
As a first approach to establish the relationship between North African populations and Neandertal, a projected Principal Component Analysis (PCA) was performed. In addition to the chimpanzee and the Neandertal genomes, data from the Denisova genome were downloaded and merged in this case resulting in 111,991 SNPs (after filtering for strand bias SNPs and ancient DNA miscoding lesions). Given that the ancient hominin and chimpanzee genomes have been originally sequenced at low coverage no SNP polymorphism data are available, and therefore individuals were considered at the haplotype level only. First, a PCA was generated using Neandertal, chimpanzee, and Denisova. Then, SNP loadings for the first two components were used to project the sample set of modern humans.
Next, we aimed at estimating the amount of Neandertal admixture in North African populations using the f4 ancestry ratio test [27]. Although a previous simulation study [28] suggested that the analysis of SNP data from arrays can provide biased results in admixture estimates, there is more recent evidence supporting that f4 ancestry ratio statistic is unaffected by those biases [3]. The f4 ancestry ratio test measures the proportion of archaic hominin genetic fraction in a modern human population as a fraction of the known amount of archaic introgression in another modern human population. Consequently, the f4 ancestry ratio test basically measures the correlation in allele frequency differences between two populations used as outgroups (e.g., chimpanzee and Neandertal), a Sub-Saharan African population (Yorubans) and the X-tested population, normalized by the correlation in allele frequency differences between chimpanzee, Neandertal, a Sub-Saharan African group (Yorubans) and a human population previously known to have experienced Neandertal admixture (in this case, CEU) [1]. If Yorubans and X descend from a single ancestral population without any subsequent admixture with Neandertals, then the allele frequency differences between Yorubans and X must have arisen solely after their separation from their common ancestor; the two frequency differences should be uncorrelated and thus the f4 ancestry ratio statistic should have an expected value of zero.
Finally, a block jackknife [29],[30] approach was used to estimate standard errors; blocks were separated by dropping each non-overlapping five cM stretch of the genome in turn, and studying the variance of each statistic of interest to obtain a approximately normal distributed standard error [25]. Further combinations (e.g. San instead of Yoruban and Chinese instead of CEU) were also calculated to test the consistency of the results (Table S1).
Results and Discussion
We ran ADMIXTURE for k equal 2 to 7 and obtained CV errors, and determined that the best k (the one with lowest cross-validation error) is k = 4. Results (Figure 1) are coincident with those previously published [17] and show that North Morocco, Libya and Egypt carry high proportions of European and Near Eastern ancestral components, whereas Tunisian Berbers and Saharawi are those populations with highest autochthonous North African component. Particularly, ten Tunisian individuals have more than 99% of their genome assigned to North African ancestry and therefore have been analyzed separately (subsequently referred to as N-TUN) from the overall Tunisian population.
In the PCA analysis (Figure 2) Eurasian populations are the closest to Neandertals among modern humans, which is in agreement with previous studies [1]. Sub-Saharan Africans are, as expected, more distant to Neandertal, whereas North African individuals are placed between these two groups. North African individuals with the highest Sub-Saharan African component (as detected by ADMIXTURE) are distant from Neandertal and closer to Sub-Saharan populations. It is interesting to notice that the North African populations closer to Neandertals are populations with a large known European or Near Eastern admixture, but also the Tunisians that have an almost complete autochthonous North African genetic component.
The results of the f4 ancestry ratio test (Table 2 and Table S1) show that North African populations vary in the percentage of Neandertal inferred admixture, primarily depending on the amount of European or Near Eastern ancestry they present (Table 1). Populations like North Morocco and Egypt, with the highest European and Near Eastern component (~40%), have also the highest amount of Neandertal ancestry (~60–70%) (Figure 3). On the contrary, South Morocco that exhibits the highest Sub-Saharan component (~60%), shows the lowest Neandertal signal (20%). Interestingly, the analysis of the Tunisian and N-TUN populations shows a higher Neandertal ancestry component than any other North African population and at least the same (or even higher) as other Eurasian populations (100–138%) (Figure 3).
Some results of the estimated ancestry in Table 2 are higher than 100%. Because the amount of Neandertal admixture provided by this statistic is in relation to the fraction found in another population, populations with more than 100% values, have more than the observed Neandertal admixture levels found in the “source population” used for comparison (i.e CEU). On the other hand, a negative f4 ancestry ratio value such as that one observed for the Luyha in Table 2 could have several explanations. One possibility is that it reflects an artifact of ascertainment bias on SNP arrays. Ascertainment bias is likely to affect the joint information from Europeans and East Asians, since SNP arrays are most commonly designed based on information from these populations. On the other hand it could also reflect a more complex demographic history (i.e population structure between the populations being compared) than previously assumed.
Subsequently, we aimed to compare the results revealed by ADMIXTURE and by the f4 ancestry ratio statistic in an attempt to corroborate that the signal of Neandertal admixture revealed in North African populations is not caused by Eurasian admixture. For this purpose, we performed a Pearson correlation test between the ancestry proportions estimated with ADMIXTURE and the proportions of Neandertal admixture estimated by the f4 ancestry ratio test. Specifically, we tested the correlation between a) both European and Near Eastern components and Neandertal admixture and b) European, Near Eastern and North African admixture components and Neandertal admixture. If signals of gene flow from Neandertals were due exclusively to the European and the Near Eastern components, we would expect that the correlation should significantly decrease in test b), when the North African component is included. On the contrary, the Pearson correlation test reaches significance only when the North African component is included, which is maintained even when Tunisians are removed from the analysis (Table 3).
Overall, the correlation analysis and the f4 ancestry ratio statistic show that the North African component actually contributes to the signal of gene flow from Neandertals. Given that the North African autochthonous ancestry seems to be 12,000–40,000 years old [17], our hypothesis is that this ancestral population was descendant from the populations that first interbreed with Neandertals about ~37,000–86,000 years ago [18] somewhere in the Middle East. Nonetheless further analyses in populations around the contact areas are needed to confirm this hypothesis.
A previous study [26] observed that the similarity to Neandertals increases with distance from Africa and suggested this could be explained by SNP ascertainment bias plus a strong genetic drift in East Asian populations. Nonetheless more complex, population-biased, ascertainment schemes might have additional effects (i.e bottlenecks), but these are not expected to significantly increase the rate of false positives in admixture tests [31]. The Tunisian population has been reported to be a genetic isolate [17] so it is plausible that part of the signal detected is actually due to genetic drift. However, this should not affect the other North African groups in our study. Finally, given that SNP arrays are based on common alleles and probably the relevant admixture information is encoded within the rare and very rare alleles, the potential bias, if anything, will underestimate ancient hominid admixture signals, as shown in previous studies [2],[3].
With the current data, however, it is not possible to discard the ancient African substructure hypothesis [8]. Although ours and some previous results [9] tend to favor the admixture hypothesis as the most plausible one, we think that a complete clarification of this issue can only be achieved with a Neandertal high coverage genome, such as this recently achieved for Denisova [32]. This, and sequencing data of North African populations, especially those with a high autochthonous component, may help elucidate more precisely the interbreeding process with Neandertals. In any case, our results show that Neandertal genomic traces do not mark a division between African and non-Africans but rather a division between Sub-Saharan Africans and the rest of modern human groups, including those from North
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xyyman what is your opinion on this article that North Africans have Neanderthal ancestry that is prehistoric? John Hawkes also claims to have found Neaderthal ancestry in some Yoruba although traces are much lower
On the one hand you have people like zarahan who subscribe to the idea that Neanderthal were savage vilolent brutes and that Euroepans are more aggressive and murder loving by nature because of it, due to their 1-4% Neanderthal admixture. Clyde on the other hand says that the neanderthals were black with afros and originated in Africa. When I then posted this North Africa article before in AE (I had forgotten about it-over 16000 posts) then zarahan pointed to articles suggesting that maybe Neanderthals never mixed with any humans. I think Explorer has brought that up before. All of the sudden zarahan did a 360 (you can predict this stuff) -and did humans kill them all?
On the third hand Mike also found a 2012 article stating
Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans
which is suprising since the Neanderthal sites cluster in Europe and a couple in the Mid East. Perhaps it is due to the fact that "While in skin color Europeans and Chinese are closer to each other than either is to Africans, the distribution of blood groups indicates that Europeans and Africans are closer to each other than either is to Chinese." -Loring Brace, An Antagonsist's Perspective
Theres the one denisova site, the only one found, which is a hominin a little different than Neanderthal in Siberia and they find this ancestry in Oceanic people, Papua etc.
So the topic is quite complex
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^It's not a fact they have "prehistoric" Neanderthal ancestry.
quote: Nonetheless further analyses in populations around the contact areas are needed to confirm this hypothesis.
--Federico Sánchez-Quinto equal contributor, North African Populations Carry the Signature of Admixture with Neandertals
It's speculation. And ignoring historic accounts of recent invasions and mixing which took place. Which is a FACT!
-- Anwar G. Chejne Islam and the West: The Moriscos, a Cultural and Social History(1993)
Quick reminder, only two days ago:
quote:Originally posted by alTakruri:
quote:Originally posted by the lioness,:
MITOCHONDRIAL DNA AND PHYLOGENETIC ANALYSIS OF PREHISTORIC NORTH AFRICAN POPULATIONS
Kefi et al 2004
. . .
With the aim to contribute to a better knowledge of the Iberomaurusian settlement we analysed the mitochondrial DNA (mtDNA) of skeletons exhumed from the prehistoric site of Taforalt in Morocco (23.000-10.800 years BP) and Afalou in Algeria (11.000 to 15.000 BP –Algeria).
Our results excluded the hypothesis of the sub-Saharan origin of Iberomaurusians populations and highlighted the genetic flow between Northern and Southern cost of Mediterranean since Epipaleolithic period.
Notice Kefi's so-called haplotypes are only either a single or no more than two mutations. It takes a string of mutations to make a haplotype. Since some of these mutations appear in more than one Haplogroup Kefi's assignment is willy-nilly subjected to a priori assumptions of an SSA free NA throughout time.
Yet pre or nascient Holocene SSA mtDNA is found in Iberia. However the great blind degree of anti-SSA prejudice imagines prehistoric SSA mtDNA is somehow in Iberia w/o ever having been in NW Afr.
For instance, in her PPt Kefi throws out TafVIII. Is it in order to deny an inner African component in epipaleolithic Taforalt? It is the only sample of possible L3, M, or N affiliation. There were only two U6 samples yet Kefi did not exclude them among originators of "Ibero-Maurusians."
Clearly if the L3/M/N individual was found at Taforalt then she was just as much an "Ibero-Maurusian" originator as the two U6 females were. 4% is as weighty as 8% when the true heavy weight ranks in at 50%.
Also, it is very significant that an L3/M/N female was living that far north so near the very shoreline of N Africa at that point in time with her other African mtDNA sisters of the U6 haplogroup.
Posts: 22235 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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According to 23andME I am 4% Neanderthal. Now isn't that a joke. But they are raking in the cash maybe I am Maasia ....He! He! He! and not a West African slave diasporan.
====
For those insisting on Neanderthal admixture....
A major Y-chromosome haplogroup R1b Holocene era
founder effect in Central and Western Europe
Richard Villems2,
Toomas Kivisild11 and Peter A Underhill*,3
....
combined heritage of initial upper Paleolithic colonization, secondary post-glacial mesolithic re-expansions and the Neolithic era demic diffusion of agriculturalists from the Near East.1 Regardless of possibly a minor autosomal contribution, as yet, there is no Y-chromosome evidence of hybridization between Neanderthals and modern human
quote:Originally posted by xyyman: [QB] I am confused....are they suggesting that since Europeans are admixed with a primitive ape and SSA are NOT then that makes Europeans...more "advanced" than SSA. The reasoning and premise defy logic.
why would that defy logic? Aren't you glad that they are admitting that Europeans and North Africans being more primitive than SSAs?
don't you realize the Europeans are sloppy, always have somebody snitch-leaking information on the side?
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Europeans are NOT admixed with Neanderthals neither are Africans. Europeans are a genetic subset of Africans.
It is hard to imagine Africans fugking an animal ...40kya This is a modern European sexual habit. Aficans don't fughk animals. They are in tune with nature.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: Europeans are NOT admixed with Neanderthals neither are Africans. Europeans are a genetic subset of Africans.
It is hard to imagine Africans fugking an animal ...40kya This is a modern European sexual habit. Aficans don't fughk animals. They are in tune with nature.
Neanderthals are an animal? Most anthropolgists think there may have been human/Neanderthal admixture markers showing in the human population today at up to 0-5.5% (average 1-4% in some pops) Some scientists think it didn't happen
quote:Originally posted by xyyman: Europeans are NOT admixed with Neanderthals neither are Africans. Europeans are a genetic subset of Africans.
It is hard to imagine Africans fugking an animal ...40kya This is a modern European sexual habit. Aficans don't fughk animals. They are in tune with nature.
I know of African American women who had done tests at several companies. And all these individuals all had several different outcomes. These women were of course disappointed and and became distrusted in these type of companies.
The coast of one sample is hundreds of dollars nowadays. In the early in the 90s it was about halve a million if not more. Early this century it still had a coast of many thousands of dollars to tens of thousands. This is why I take some of the early studies done on population genetics with a grain of salt. When they claimed 300 peeps etc. being tested.
Posts: 22235 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by xyyman: Europeans are NOT admixed with Neanderthals neither are Africans. Europeans are a genetic subset of Africans.
It is hard to imagine Africans fugking an animal ...40kya This is a modern European sexual habit. Aficans don't fughk animals. They are in tune with nature.
Neanderthals are an animal? Most anthropolgists think there may have been human/Neanderthal admixture markers showing in the human population today at up to 0-5.5% (average 1-4% in some pops) Some scientists think it didn't happen
quote: "The Qafzeh/Skhul sample is fundamentally modern, and in fact very similar to Cro-Magons.."
--Geoffrey A. Clark, Catherine M. Willermet. 1997. Conceptual Issues in Modern Human Origins Research. p111
Posts: 22235 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by xyyman: @ Lioness…dude I have to ask you. (1)Did you read the article? (2)Do you understand the article? I don’t understand why publishers such as PLOS One openingly support overtly racist article such as this…especially when it includes a conclusion such as QUOTE{{{{With the current data, however, it is not possible to discard the ancient African substructure hypothesis [8].}}}}” . Lioness do you know what the Ancient African Substructure Hypothesis is? It was posted here; I believe it was the TRex thread on the Neanderthal…one of many.
What is really despicable is when publishers publish papers with comments such as {{{{“IN ANY CASE, our results show that Neandertal genomic traces do not mark a division between African and non-Africans but rather a DIVISION between Sub-Saharan Africans and the rest of modern humangroups, including those from North Africa.”. }}}} Osunds like sour grapes. They did not get the results they wanted. Yet it was published. tsk! tsk!
The authors made their intentions clear. But what the ignorant readers don’t know is there is a genetic divide between ALL ethnic groups. As discussed with A-Ra Ultimate. With increasing K, divisions(sub-structures) will appear. As seen with Northern Europeans and Southern Europeans. Genetics is going to pop their bubble.
You will see at K=4 There is a clear geographic divide. At higher resolution, eg K=99?, there will be a lot more differences observed..
Lioness do you understand the methodology used by the researchers. They openingly admitted they can NOT discard the ancient African substructure hypothesis.
The paper is useless on Neanderthal admixture. BUT!!!!! The pro is….It confirms as I said before…my Tunisians and Beyokus Saharawis are the purest North Africans…whoever they are and whatever they look like. It also confirms Behar and Henn Hypothesis on demographic movements. So here we go again.
BTW – You do you realize that the Tunisians are the closest to the Neanderthals…even more than Europeans and East Asians. And yet Tunisians are the purest North Africans and the furthest genetically from Europeans. What does that tell you?….Tic! Toc!
Waste of time.!!!!
bytch dont call me dude
The article says North African populations have Neanderthal ancestry
That right there is enough to consider and you are a person who will call articles Eurocentric yets still extract information out of them you think is truthful
The article says that they believe the North African populations who have Neanderthal ancestry aquired it did so not recently
That is another thing to consider
quote:Originally posted by xyyman:
{{{{“IN ANY CASE, our results show that Neandertal genomic traces do not mark a division between African and non-Africans but rather a DIVISION between Sub-Saharan Africans and the rest of modern humangroups, including those from North Africa.”. }}}}
Vansertimavindicated and zarahan have argued that having Neanderthal ancestry is a mark of primitiveness so you can see this article as a mea culpa and makes Sub Saharans more civilized
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As usual you miss out on the underlying theme of the paper.
Quote: QUOTE{{{{With the current data, however, it is not possible to discard the ancient African substructure hypothesis [8].}}}}”
Do you know what the "ancient African substructure hypothesis " is? The authors concluded that the hypothesis still STANDS although they set out to debunk it.
Europeans, Asians and definitely not Africans are admixed with Neanderthal.
all they proved was that there are some genetic differences between SSA and NAians.
Same can be said for all populations throughout the world. Including North And South Europe.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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African substructure hypothesis, nobody's heard of that it's new it's a new term as per referring to Gokcumen but he didn't add the word "hypothesis" Obviously you dont know what it means either, you're just fronting
Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence 2013
Omer Gokcumen, Qihui Zhu, Lubbertus C. F. Mulder, Rebecca C. Iskow, Christian Austermann, Christopher D. Scharer, Towfique Raj, Jeremy M. Boss, Shamil Sunyaev, Alkes Price, Barbara Stranger,Viviana Simon, and Charles Lee.
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p less than 10-15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima’s D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations.
Discussion
Non-coding regulatory variation may be a major contributor to phenotypic variation [28] and are thought to be under strong selection among humans [48]. Only a handful of loci have been clearly shown to evolve under balancing selection [15]–[17]. In this study, we have identified a copy number variant, and its surrounding haplotype block, which shows highly atypical genetic structure within and among human populations and is likely under balancing selection.
There are two transcription factor binding site regions within the NE1 locus: TFBS-1 is upstream of the deletion polymorphism while TFBS-2, which is a target of SETDB1 and KAP1, is less than 1 kb downstream of the CNVR8163.1 deletion. KAP1 (also known as TRIM28) is a well-known transcriptional repressor that mediates its activity by recruiting a complex that also includes histone methyltransferase SETDB1 [49]. Of note is that KAP1 mediates silencing of both exogenous and endogenous retroviruses in embryonic stem cells [50]. Given that there are no known genes within the NE1 locus, it is unlikely that either region acts as a promoter. Instead, we speculate that these transcription factor binding sites may regulate transcription through long distance interactions. It is important to note that several of the SNPs that set apart the NE1 from nonNE1 haplotypes also change the sequence context of the transcription factor binding sites mentioned above. These SNP changes could explain the differential activity of active histone binding as measured by ChIP-qPCR. As such, it is attractive to speculate that these differences in regulatory activity may be the main target of the adaptive pressures acting on this locus but further functional characterization is required.
In cases of balancing selection, one usually finds an adaptive advantage of heterozygotes. Indeed, a considerable number of European populations show very high frequency of heterozygotes (>40%) and some populations, including Tuscans (TIS), Mexicans (MEX) and Puerto Ricans (PUR) show higher than 45% frequency of heterozygotes (Figure 3B). Moreover, the high FST values observed at this locus suggest that the strength of this force varies between different geographical regions.
Recent studies showed the existence of variation among modern humans that has persisted through ancient substructure [24]. Such substructure may account for some of the signals of the recently identified Eurasian hominin introgression [51]. The unusual nucleotide variation at the NE1 locus resembles signatures of Neandertal admixture to the modern Eurasian gene pool [e.g., 52]. If this variation were not detected among African populations, an argument would have been made for ancient hominin admixture to explain the observed variation. However, based on its presence in African population as well as previous theoretical insights [18], [19], we surmise that the NE1 and nonNE1 haplotypes were maintained by long-term balancing selection and most likely originated before the Human-Neandertal divergence. Future genome-wide scans for balancing selection, in genomic segments that were previously explained by admixture from archaic hominins, are warranted. The results of such studies will likely increase the number of known regions where balancing selection is acting and identify ancient variation that was previously attributed to archaic hominin admixture.
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xyyman you saw this term ""ancient African substructure hypothesis " you didn't know what it meant so you got parnoid. It sounded bad to you This nenaderthal stuff makes you nervous "what's inside of me,?"
below blog article a critique of the above Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence 2013
AN OUT-OF-AMERICA SIGNAL AS SEEN THROUGH HUMAN REGULATORY GENES
As the abstract indicates, Gokcumen et al. (2013) think they have advanced evidence for ancient African substructure that predates Human-Neandertal-Denisovan divergence and persists in Eurasian populations. The actual data is indeed interesting and deserves a broad discussion but the presentation of the data by Gokcumen et al. (2013) is biased against one continental population, namely American Indians. At the beginning, they do map out the worldwide distribution of the haplotypes in question (see below) and I will return to this data later.
But then American Indians are not featured in any of the subsequent calculations and interpretations and the worldwide conclusions are made on the basis of just YRI (Yoruba), CEU (European), CHB (Chinese) and JPT (Japanese) samples.
There seems to be a good reason for Gokcumen et al. (2013) to leave American Indian populations outside of their analysis – they would undermine their interpretation. As the above map of the distribution of the two haplotypes, NE1 and non-NE-1, demonstrates, American Indians show the world highest frequencies of homozygous NE1 haplotypes and the world highest frequencies of heterozygous (NE1/non-NE1) haplotypes. The NE1 haplotypes are precisely the ones that were detected in Neandertals and Denisovans.
This is not an aberrant finding. The two Neandertals tested for blood group alleles showed blood group O (Lalueza-Fox et al. 2008. “Genetic Characterization of the ABO Blood Group in Neandertals,” BMC Evolutionary Biology 8: 342), which is most frequent among American Indians. The least derived B006 haplotype in the X chromosome’s dystrophin gene (ds44) was observed in modern humans and in Neandertals. In modern humans the frequency of B006 was the highest among North American Indians followed by Europeans. Other examples of Neandertal-Denisovan-Amerindian genetic similarities are discussed here.
Interestingly, just like in the case of B006, NE1 is most frequent in Amerindians followed by Europeans and South Asians. From the point of view of the conventional theory of the origin of Amerindians from East Asia, this fact is unexpected. But it’s fully consistent with the autosomal and mtDNA studies that identified “Amerindian admixture” in European populations. The NE1 case study suggests that “Amerindian admixture” and “Neandertal admixture” are different labels for the same phenomenon.
Now, neither Neandertals nor Denisovans have ever been found in the New World. This undermines the theory that modern humans admixed with these hominin species because one would expect to find the highest frequencies of an introgressed haplotype in the geographical area in which admixture took place. But the world highest frequencies of Neandertal-Denisovan haplotypes among Amerindians are equally inconsistent with the African substructure hypothesis presented by Gokcumen et al. (2013). While they conclude that “the most parsimonious explanation for the observed variation at the NE1 locus is that the NE1/nonNE1 haplogroups arose after the human-chimpanzee common ancestor, but before the Human-Neandertal split in Africa. As such, the variation at the NE1 locus has persisted within ancient African substructure and later spread to non-African populations”
they are missing a key piece of the evidence – fossil DNA from Africa. NE1 haplotypes are ascertained in Eurasian hominins whose geographic range was likely adjacent to the New World, so if ancient substructure is at play here, it’s American and not African. The chimp-ascertained non-NE1 haplotype (the one without the deletion) is found in the New World, which suggests that this truly archaic genetic signature that predates the Neandertal-Denisovan-modern human split has survived there as well. It’s the more modern NE1 haplotype that shows a cline from the New World to Africa suggestive of a migration out-of-America leaving a clear trace on top of the undifferentiated chimp heritage.
Gokcumen et al. (2013) have identified a few interesting facts. First, contrary to the earlier accounts of “Neandertal admixture” in the human genome that failed to detect traces of it among African foragers, they found NE1 in 13% of their Mbuti Pygmy sample. This is precisely what out-of-America II predicts: modern humans with roots in a Eurasian hominin such as Neandertals or Denisovans colonized every remote corner of the world, including the African tropics. Second, they
“found that variation within African NE1 haplotypes is significantly higher than variation within Asian and European NE1 haplotypes (p<10−15)….”
But despite the higher variation within African NE1 haplotypes, the frequency of those haplotypes are the highest outside of Africa and, especially in America. This means that diversity is no indication of a population’s age. Plain simple. It’s likely that it shows the relaxation of a selective constraint in this region and the corresponding increase in mutation rate, which is something to be expected from a regulatory gene. Linkage disequilibrium (LD) metrics seem to support this interpretation (Amerindians again not represented):
“To understand the genomic composition upstream of the APOBEC3 locus, we first examined the phase I SNP data from the 1000 Genomes Project and identified an unusually strong linkage disequilibrium (LD) block spanning approximately 36 kb (NE1 locus, hg18 – chr22:37,600,063–37,636,026). This LD block is evident in Eurasian (CEU and CHB/JPT) populations but is absent in the Yoruban (YRI) population.”
The increase of genetic diversity as a result of the relaxation of selective constraints is something that is well described for some of modern humans’ companion species such as domesticated dogs and domesticated yaks following the domestication. A similar process must have affected their owners, too.
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Hang on to my coat tails. I will take you places....
As you can see Neanderthals and humans never admixed. Africans do not fukg animals. Maybe their subset do....(wink)
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The country is shocked at an emerging trend where people are caught having sex with animals. By Joab Apollo
First it was at the port city of Mombasa, famed for tourism, where eleven women, including two university students were found having sex with dogs. Then a famous businessman in Tigania was nabbed by police for raping a cow.
posted
Ha! Ha! the topic is not complex. For the smple minded raciaist ..it is.
Neanderthals are NOT AMH. They did not admixed wth modern humans. Light skin of East Asians and Europeans are derived from DIFFERENT Loci. Neaderthal supoosedly red hair also is at a completely diferet locus to AMH. Sources cited.
Post more interesting stuff and don't waste my time.
quote:Originally posted by the lioness,: xyyman what is your opinion on this article that North Africans have Neanderthal ancestry that is prehistoric?
So the topic is quite complex
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quote:Originally posted by xyyman: [QB] Ha! Ha! the topic is not complex. For the smple minded raciaist ..it is.
Neanderthals are NOT AMH. They did not admixed wth modern humans. Light skin of East Asians and Europeans are derived from DIFFERENT Loci. Neaderthal supoosedly red hair also is at a completely diferet locus to AMH. Sources cited.
You seesm to know very little about the topic. Skin color of the Nenaderthals is not known or even even mentioned in articles pertaining to their 1-4 % admixture with humans. And at that percentahe would ahve no effect on skin color anyway
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quote:Originally posted by xyyman: [QB] Ha! Ha! the topic is not complex. For the smple minded raciaist ..it is.
Neanderthals are NOT AMH. They did not admixed wth modern humans. Light skin of East Asians and Europeans are derived from DIFFERENT Loci. Neaderthal supoosedly red hair also is at a completely diferet locus to AMH. Sources cited.
You seesm to know very little about the topic. Skin color of the Nenaderthals is not known or even even mentioned in articles pertaining to their 1-4 % admixture with humans. And at that percentahe would ahve no effect on skin color anyway
You seem not to understand that xyyMan is saying that the locus is different. Unless you don't understand what he means.
Your question should have been which locus. What is the differences in the locus.
quote: DNA was extracted from the Neandertal-type specimen found in 1856 in western Germany. By sequencing clones from short overlapping PCR products, a hitherto unknown mitochondrial (mt) DNA sequence was determined. Multiple controls indicate that this sequence is endogenous to the fossil. Sequence comparisons with human mtDNA sequences, as well as phylogenetic analyses, show that the Neandertal sequence falls outside the variation of modern humans. Furthermore, the age of the common ancestor of the Neandertal and modern human mtDNAs is estimated to be four times greater than that of the common ancestor of human mtDNAs. This suggests that Neandertals went extinct without contributing mtDNA to modern humans.
Introduction
Neandertals are a group of extinct hominids that inhabited Europe and western Asia from about 300,000 to 30,000 years ago. During part of this time they coexisted with modern humans. Based on morphological comparisons, it has been variously claimed that Neandertals: (1) were the direct ancestors of modern Europeans; (2) contributed some genes to modern humans; or (3) were completely replaced by modern humans without contributing any genes (reviewed in; ; ). Analyses of molecular genetic variation in the mitochondrial and nuclear genomes of contemporary human populations have generally supported the third view, i.e., that Neandertals were a separate species that went extinct without contributing genes to modern humans (6, 50, 12, 2 and 47). However, these analyses rely on assumptions, such as the absence of selection and a clock-like rate of molecular evolution in the DNA sequences under study, whose validity has been questioned (; ). An additional and more direct way to address the question of the relationship between modern humans and Neandertals would be to analyze DNA sequences from the remains of Neandertals.
The reproducible retrieval of ancient DNA sequences became possible with the invention of the polymerase chain reaction (; ). However, theoretical considerations, (; ) as well as empirical studies (; ), show that DNA in fossil remains is highly affected by hydrolytic as well as oxidative damage. Therefore, the retrieval of DNA sequences older than about 100,000 years is expected to be difficult, if not impossible, to achieve (). Fortunately, Neandertal remains fall within the age range that in principle allows DNA sequences to survive. It is noteworthy, though, that even among remains that are younger than 100,000 years most fail to yield amplifiable DNA sequences (). In addition, contamination of ancient specimens and extracts with modern DNA poses a serious problem () that requires numerous precautions and controls. This is particularly the case when human remains are studied, since human DNA is the most common source of contamination. Therefore, a number of criteria need to be fulfilled before a DNA sequence determined from extracts of an ancient specimen can be taken to be genuine (; ; ; ).
Since 1991, the Neandertal-type specimen, found in 1856 near Düsseldorf, Germany, has been the subject of an interdisciplinary project of the Rheinisches Landesmuseum Bonn, initiated and led by R. W. S. (39 and 38). As a part of this project, a sample was removed from the Neandertal specimen for DNA analysis. Here, we present the sequence of a hypervariable part of the mtDNA control region derived from this sample. We describe the evidence in support of its authenticity and analyze the relationship of this sequence to the contemporary human mtDNA gene pool.
Results
Amino Acid Racemization
A 3.5 g section of the right humerus was removed from the Neandertal fossil (). It has previously been shown that ancient specimens exhibiting high levels of amino acid racemization do not contain sufficient DNA for analysis (). To investigate whether the state of preservation of the fossil is compatible with DNA retrieval, we therefore analyzed the extent of amino acid racemization. Samples of 10 mg were removed from the periostal surface of the bone, from the compact cortical bone, and from the endostal surface of the marrow cavity. Samples were also removed from remnants of a varnish, with which the specimen has been treated at least twice. The samples were hydrolyzed under acid conditions, and the released amino acids were analyzed using high performance liquid chromatography and fluorescent detection (). shows that the total amounts of the amino acids detected in the Neandertal bone are 20%–73% of those in modern bone and more than two orders of magnitude higher than in the varnish, indicating that the results do not reflect the amino acid content of the varnish. Furthermore, the absolute and relative amounts of the amino acids analyzed (e.g., the ratio of glycine to aspartic acid) are similar in the three Neandertal samples and comparable to those of a contemporary bone. Most importantly, the ratio of the D to the L enantiomers of aspartic acid in the three Neandertal samples varies between 0.11 and 0.12, which is in the range compatible with DNA survival (). Thus, the extent of amino acid racemization in the Neandertal fossil suggests that it may contain amplifiable DNA.
Figure 1. Sample Removed from the Right Humerus of the Neandertal-Type Specimen
code:
Table 1. Racemization Results for Three Neandertal Bone Samples, Varnish from the Neandertal Fossil, and Modern Bone
Neandertal DNA Sequences and the Origin of Modern Humans
Matthias Krings1, Anne Stone2, Ralf W Schmitz3, Heike Krainitzki4, Mark Stoneking2 and Svante Pääbo1, *
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DNA was extracted from 0.4 g of the cortical compact bone. Previous experience shows that ancient DNA tends to be degraded and damaged to an extent that makes amplification of segments of mtDNA longer than 100–200 bp difficult (). Therefore, two primer (L16,209, H16,271) that amplify a 105-bp-segment of the human mtDNA control region (including primer) were used to perform amplifications from the bone extract as well as from an extraction control. An amplification product was obtained in the bone extract but not in the control (data not shown). In a subsequent experiment, this was repeated and the same results were obtained.
Sequence Variation of the Amplification Product
The two amplification products were cloned in a plasmid vector and 18 and 12 clones, respectively, were sequenced (, extract A). Twenty-two of the 30 clones contained seven nucleotide substitutions and one insertion of an adenine residue, when compared to the standard human reference sequence (). Three of these eight differences to the reference sequence were individually lacking in a total of five of the clones. In addition, among the 27 clones were nine differences that each occurred in one clone, three differences that occurred in two clones and one that occurred in three clones, respectively. Such changes that are present in only a few clones are likely to be due to misincorporations by the DNA polymerase during PCR, possibly compounded by damage in the template DNA. In addition, some of these could be due to mitochondrial heteroplasmy, which may be more common in humans than often assumed (8 and 22) and is abundant in some mammalian species (). Of the remaining three clones, two were identical to the reference sequence, and the third clone differed from the reference sequence at one position.
Figure 2. The DNA Sequences of Clones Derived from Four Amplifications of the Mitochondrial Control Region from the Neandertal FossilDots indicate identity to a human reference sequence () given above. The clone designations consist of a letter (A, B, C) indicating the DNA extract followed by a number indicating the amplification reaction, as well as a number after the period identifying the particular clone. Extracts A and B were performed at the University of Munich; extract C, at Penn State University. Clones derived from different amplifications are separated by a blank line. Asterisks identify sequence positions where more than one clone differs from the majority of sequences. For the three upper amplifications (performed at the University of Munich) primer L16,209 (5′-CCC CAT GCT TAC AAG CAA GT-3′) and H16,271 (5′-GTG GGT AGG TTT GTT GGT ATC CTA-3′) were used. For the bottom amplification (performed at Penn State University) the primer NL16,230 (5′-GCA CAG CAA TCA ACC TTC AAC TG-3′) and NH16,262 (5′-GTA GAT TTG TTG ATA TCC TAG TGG GTG TAA-3′) were used. Thus, the amplification product was composed of two classes of sequences, a minor class represented by three clones that is similar to the human reference sequence, and another class represented by 27 clones that exhibits substantial differences from it. The former class of molecules probably reflects contamination of the specimen, which is likely to have occurred during handling and treatment of the specimen during the 140 years since its discovery. The other class of sequences is not obviously of modern origin. Further experiments were therefore performed to determine if this class is endogenous to the Neandertal fossil.
Quantitation of Putative Neandertal DNA
Amplifications that start from more than 1000 ancient template molecules tend to yield reproducible results, while amplifications starting from fewer molecules tend to yield results that vary between experiments, due to misincorporations during the early cycles of the PCR as well as due to sporadic contamination (). Therefore, the number of template molecules representing the putative Neandertal sequence in the extract was determined by quantitative PCR. To this end, a molecule representing the putative Neandertal sequence but carrying a 12 bp deletion was constructed. To each step in a dilution series of this construct, a constant amount of extract was added and amplifications were performed using primer that are specific for a 104 bp product of the putative Neandertal sequence and that do not amplify contemporary human sequences. The results () show that on the order of 10 putative Neandertal molecules exist per microliter of extract and thus that amplifications starting from 5 μl of extract are initiated from approximately 50 template molecules. However, due to variation in the efficiency of individual primer pairs, and stochastic variation in the number of template molecules added to an individual amplification, some amplifications may start from fewer (or even single) molecules. This makes nucleotide misincorporations in early cycles of the amplification reaction likely to affect a large proportion of the molecules in the final amplification product. Such misincorporations may be frequent since the template molecules are likely to carry miscoding base modifications (). To detect this type of sequence change, amplifications were performed such that each sequence position to be determined was covered by at least two independent PCR reactions. The products of each PCR reaction were independently cloned and the sequences determined from multiple clones.
Figure 3. Quantitation of the Putative Neandertal mtDNAA dilution series of a competitor construct carrying the putative Neandertal sequence with a 12 bp deletion was added to 2.5 μl of extract A from the fossil. Primer used were specific for the putative Neandertal sequence. Above the lanes, the approximate numbers of cd LWcompetitor molecules added are indicated. The control amplification (C) contained neither competitor nor Neandertal extract.
--Neandertal DNA Sequences and the Origin of Modern Humans Matthias Krings1, Anne Stone2, Ralf W Schmitz3, Heike Krainitzki4, Mark Stoneking2, Svante Pääbo1,
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Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany Abstract
quote:
The origin, history, and singularity of our species has fascinated storytellers, philosophers and scientists throughout, and doubtless before, recorded history. Anthropology, the modern-era discipline that deals with these issues, is a notoriously contentious field, perhaps because the topic at hand – the nature of our own species – is one that is difficult or impossible to approach in an unbiased way. Recently, molecular genetics has increasingly contributed to this field. Here, I briefly discuss three areas where I believe molecular studies are likely to be of decisive importance in the future. These concern the questions of where and when our species originated, what the genetic background for characters that differ between us and apes is, and how the phenotypic traits that vary among human groups have evolved. Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany Abstract
The origin, history, and singularity of our species has fascinated storytellers, philosophers and scientists throughout, and doubtless before, recorded history. Anthropology, the modern-era discipline that deals with these issues, is a notoriously contentious field, perhaps because the topic at hand – the nature of our own species – is one that is difficult or impossible to approach in an unbiased way. Recently, molecular genetics has increasingly contributed to this field. Here, I briefly discuss three areas where I believe molecular studies are likely to be of decisive importance in the future. These concern the questions of where and when our species originated, what the genetic background for characters that differ between us and apes is, and how the phenotypic traits that vary among human groups have evolved.
FIGURE 1. (a) Diagram showing how the mitochondrial DNA (mtDNA) sequences detected in Neanderthals and humans are related. The possibility of gene flow between Neanderthals and humans is not illustrated because it has not affected the current human mitochondrial gene pool. (b) The putative relationship of a nuclear DNA sequence where the variation is older than the putative population split between Neanderthals and humans (about 500 000 years ago). Note that, even in the absence of gene flow, some contemporary human sequences are more closely related to some Neanderthal sequences than they are to other human sequences. Table 1. Some loci for which DNA sequence variation in humans has been studied
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The fag Paabo and his buddies have being trying for over a decade to infer Europeans somehow decended from Neanderthals...and not from Africans. At least they(Europeans) are part Neanderthal. GTFOH!! They have failed at every attempt. That article is one of many ...each attempt has been subsequently debunked by other researchers.
Even this one, OP, admitted they are just BSing. Read the article Lioness. Give me a call when you have something. Bye!
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If I have to explain everything to you...you should stick to pic spamming and leaving the cerebral stuff to other posters.
About 4-5ya the biggest thing on the racialist web was the red hair gene of Neanderthal. Again Paabo was behind it. He/She has a monopoly(monoploy! lol!) on Neanderthal genome.
It was later discovered that red-hair of AMH was a completely different gene cf to Neanderthal. So, No, AMH did not get their red hair from Neanderthal. And like most everything else, Blue, green eyes, light skin and red/blond hair came from their African fathers and mothers. Who's your daddy! Get It! and that will NEVER change. Sorry.
As I said Africans has a 150,000y head start. That is why biologically they are superior. You should be happy and proud you are black. And the stronger of the two sexes. You are batting 1000. Send me your pic..I need to see if you have baby making hips. Wink!
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quote:Originally posted by xyyman: [QB] If I have to explain everything to you...you should stick to pic spamming and leaving the cerebral stuff to other posters.
quote:Originally posted by xyyman: [QB] The fag Paabo and his buddies have being trying for over a decade to infer Europeans somehow decended from Neanderthals...and not from Africans.
Ok if you claiming Paabo said something he didn't say is cererbral
re-check your cortex, only 1-4% admixture
In case you hadn't noticed I didn't post a Paabo article.
and I also added your African substructure hypothesis and you still haven't digested what it meant
quote:Originally posted by xyyman:
As I said Africans has a 150,000y head start. That is why biologically they are superior.
you said Europeans descend from Africans not Neanderthals. That is correct
That means they had the same start
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For Newbies... Article(April 2013) (ancient African substructure hypothesis )
Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence
ABSTRACT
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and REFUTING recent Neandertal admixture.
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You are welcome. I hope some of you brothas familiar with continent can shed some light on the Luyha, Hema and other groups from the African Great Lakes. I can't authenticate Google images or Bing.
They seem to be the most ancient group. ..similar to San.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
Blah blah blah. If I coulda woulda shoulda....what if what if what if.
I own you. .you know that?
quote:Originally posted by the lioness,:
quote:Originally posted by xyyman: [QB] If I have to explain everything to you...you should stick to pic spamming and leaving the cerebral stuff to other posters.
quote:Originally posted by xyyman: [QB] The fag Paabo and his buddies have being trying for over a decade to infer Europeans somehow decended from Neanderthals...and not from Africans.
Ok if you claiming Paabo said something he didn't say is cererbral
re-check your cortex, only 1-4% admixture
In case you hadn't noticed I didn't post a Paabo article.
and I also added your African substructure hypothesis and you still haven't digested what it meant
quote:Originally posted by xyyman:
As I said Africans has a 150,000y head start. That is why biologically they are superior.
you said Europeans descend from Africans not Neanderthals. That is correct
That means they had the same start
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Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence
ABSTRACT
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and REFUTING recent Neandertal admixture.
You are right about this paper it's a refutation of Neanderthal ancestry in humans, But it's just another opinion other articles say there was admixture and most science outlets support that point of view more.
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quote:Originally posted by xyyman: For Newbies... Article(April 2013) (ancient African substructure hypothesis )
Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence
ABSTRACT
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and REFUTING recent Neandertal admixture.
Great paper,
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The Tech Museum of Innovation. Department of Genetics, Stanford School of Medicine.
Understanding Genetics
-A curious adult from California
October 14, 2009
Back in 2001, some researchers speculated that the "red hair" gene of Europeans came in too many varieties to have come from human stock. They reasoned that it must have come from somewhere else. The most likely candidate was the folks living in Europe when humans got there -- the Neanderthals.
Since then, most of the evidence has not supported humans and Neanderthals regularly having babies together. Most likely, we were fighters and not lovers and wiped the poor species out. What this all means is that Europeans probably aren't Neanderthal-human hybrids.
Scientists did recently show that at least some Neanderthals had red hair. But this turned out to be evidence against interbreeding. Why? Because Neanderthals end up with red hair in a way not yet seen in people.
Now I don't mean they had red hair because they used a different gene than Europeans do. Both Neanderthals and Europeans use the same gene to get red hair -- MC1R. The difference is that they both use the gene a bit differently.
So for right now it looks like humans got their red hair from their own genes. But keep in mind that scientists haven't looked at the DNA from a lot of different Neanderthals yet.
It might be that Neanderthals had lots of ways to end up with red hair and we happened to find one way that we don't share. If scientists do find some human versions of the MC1R gene in Neanderthals, then that would support the idea that the two interbred.
(Although remember this would just be one piece of evidence against a whole lot of evidence against interbreeding.)
I thought what I'd do next is go into a bit more detail about all of this. Even though it looks like red hair didn't come from Neanderthals, we still don't have a good explanation for why there are so many different versions of the MC1R gene in Europeans.
MC1R and Red Hair
As I said before, red hair happens because of the MC1R gene. Well, it actually happens when this gene can't do its job quite right.
See, each gene is really just the recipe for a specific protein. And each protein has a specific role in the cell.
The MC1R gene has the instructions for making the MC1R protein. And one role of this protein is to get rid of the pigment that gives red hair, pheomelanin.
Some people have versions of the gene that can't do this job very well. The end result is that they get a build up of red pigment and have red hair.
Now this isn't what made people think that red hair came from Neanderthals. For example, blue eyes (and most every other trait) happen in the same way and no one is claiming that we inherited blue eyes from Neanderthals.
What makes red hair different is that there are so many different versions of the MC1R gene. And that there has been so little time for them to happen.
Gene Changes and Time
As humans, we all share nearly the exact set of genes. What makes us each different is we have different versions of these same genes.
For example, some people have red hair versions of the MC1R gene and have red hair. Other people have different MC1R gene versions and don't have red hair.
The same sort of thing goes for eye color and the HERC2 gene. Or skin color and the SLC24A5 gene. Or most any other trait you can think of and its associated gene(s).
All of these different gene versions are there because of DNA changes that happened at some point in our history. People tend to think of DNA as stable and written in stone and for the most part it is. But even stones can get chips once in a while.
DNA can and does change over time. But very slowly. And it seems like humans were in Europe for too short a time for there to be so many different versions of the MC1R gene.
Out of Africa
The evidence so far supports the idea that all humans started out in Africa. Around 40,000 years ago, a small group arrived in Europe. These original settlers almost certainly looked more like modern Africans than modern Europeans.
Modern Africans are by far the most genetically diverse group on Earth. Except when it comes to most skin, hair, and eye color genes. These genes are very similar within the population (to protect them from the sun).
Remember, this is the group that settled Europe 40,000 years ago. And the situation is very different there now. Europeans have the widest range of skin, hair, and eye color of any group on Earth. So where did that diversity come from?
One possibility is that there were a few Africans who already had these changes and when the conditions were right, these gene versions became common. The other possibility is that these DNA changes happened in the last 40,000 years.
Traits like lighter skin and different eye colors could have happened either way. A single difference in a single gene explains a good part of the skin color difference between Africans and Europeans. Same thing with lighter colored eyes.
But red hair is different. So far over 80 different versions of the MC1R gene have been found in Europeans. And this gene is one of the least diverse in Africans (because of the light skin that happens when the gene isn't working). This is an awful lot of change for 40,000 years.
This is why some people thought that red hair must have come from Neanderthals. The idea was that Neanderthals didn't need protection from Europe's weak sunlight and so the MC1R gene was free to build up DNA changes over the hundreds of thousands of years they lived there.
This is an interesting theory but there just isn't that much support for it. The consensus right now is that Europeans are not a mix of Neanderthals and humans.
Of course with more evidence that could change. As scientists figure out Neanderthal MC1R genes from many different individuals, they may find that we did interbreed.
But if we didn't, then why the wide variety in the MC1R gene in Europeans? There are lots of possibilities but I'll just discuss one.
It could be that the MC1R gene happens to be a place in our DNA that changes a lot. There are "hotspots" like this scattered throughout our DNA.
The reason it didn't show up in Africans is that light skin was such a disadvantage that anyone who had it did not do very well at all. They ended up sunburned, with skin cancer and, maybe even with babies that had numerous birth defects.
There isn't any evidence yet to support this idea. But scientists will keep looking at the MC1R gene to try to figure out why it is so diverse in Europeans. Maybe my great, great, etc. grandpa was a Neanderthal after all.
posted
OK so we are all on the same page with Neanderthal.
Now, why is MC1R so diverse in Europeans? That has been answered already by Kittles and Co. More specifically Heather Norton. Lioness can you pull that paper? Norton has the ownership on pigmentation...not Jablonski. Rees has some very good papers on it also.
Lioness - some people believe Obama was born in Kenya.
This is an interesting theory but there just isn't that much support for it. The consensus right now is that Europeans are not a mix of Neanderthals and humans.
Of course with more evidence that could change. As scientists figure out Neanderthal MC1R genes from many different individuals, they may find that we did interbreed.
But if we didn't, then why the wide variety in the MC1R gene in Europeans? There are lots of possibilities but I'll just discuss one.
It could be that the MC1R gene happens to be a place in our DNA that changes a lot. There are "hotspots" like this scattered throughout our DNA.
The reason it didn't show up in Africans is that light skin was such a disadvantage that anyone who had it did not do very well at all. They ended up sunburned, with skin cancer and, maybe even with babies that had numerous birth defects.
****There isn't any evidence yet to support this idea.***( THE AUTHOR IS LYING OR THE PAPER IS VERY OLD). But scientists will keep looking at the MC1R gene to try to figure out why it is so diverse in Europeans. Maybe my great, great, etc. grandpa was a Neanderthal after all.
I read recently that Neanderthals and humans interbred and some of their genes are still in our DNA. Have these genes been shown to have any benefit? Did this interbreeding matter for the survival of our species?
-A curious adult from California
ans: For the most part it is too early to know if Neanderthal DNA has had much of an effect on our biology. After all, Neanderthal DNA has only been known in detail for a very short time. And we've only known about the interbreeding for about a year.
____________________________________
so yes, your quote is too old a year prior to 2011 is 2010 when the nenderthal genome was mapped, your quote 2009 is form before that
another 2010 article from your source, the same Stanford site:
Yo Daddy Was a Neanderthal
This Insult May Have Some Truth in it for Europeans and Asians
A new study out has figured out about 60% of the letters of DNA from three different Neanderthal bones. It is amazing how much a scientist can learn from a long extinct relative.
[ A Draft Sequence of the Neandertal Genome 2010]
First off, it looks like there was some interbreeding between species at some point. By comparing human and Neanderthal DNA, scientists can tell that around 1-4% of European and Asian DNA came from Neanderthals. And it looks like Africans have no Neanderthal DNA at all.
Anthropologists believe that the progenitors of the Luhya were part of the great Bantu expansion out of Western-Central Africa around 1000 BC.[clarification needed]. In sharp contrast with anthropologists, the Luhya history records that they migrated into what is now Kenya, from North Africa in a kingdom they call Misri.[5][6] Today Misri is Egypt. The current inhabitants of Egypt call it Masr. ====
Who is correct? What is their lineage Haplogroup? Looks like indeed E1b1a in line with AEians
Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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posted
This is like an obsession...too early in the morning.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: For Newbies... Article(April 2013) (ancient African substructure hypothesis )
Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence
ABSTRACT
Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and REFUTING recent Neandertal admixture.
Posts: 22235 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by xyyman: OK so we are all on the same page with Neanderthal.
Now, why is MC1R so diverse in Europeans? That has been answered already by Kittles and Co. More specifically Heather Norton. Lioness can you pull that paper? Norton has the ownership on pigmentation...not Jablonski. Rees has some very good papers on it also.
Molecular genetics of human pigmentation diversity
Next Section Abstract
quote: Next Section Abstract
The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between and within human populations. A combination of approaches have been used including comparative genomics of candidate genes and the identification of regions of the human genome under positive selection, together with genome-wide and specific allele association studies. Independent selection for different pigmentation gene sets has been found between Asian, European and African populations. Several genome-wide association studies for pigmentation have now been conducted and identified single nucleotide polymorphism (SNP) markers in known, TYR, TYRP1, OCA2, SLC45A2, SLC24A5, MC1R, ASIP, KITLG and previously unknown SLC24A4, IRF4, TPCN2, candidate genes. The contribution of SNP polymorphisms present in populations from South Asia have been tested and alleles found at TYR, SLC45A2 and SLC24A5 can largely account for differences between those of darkest and lightest skin reflectance using a simple additive model. Skin and hair colour associations in Europeans are found within a range of pigmentation gene alleles, whereas blue-brown eye colour can be explained by a single SNP proposed to regulate OCA2 expression. Functional testing of variant alleles has begun to connect phenotype correlations with biological differences. Variant MC1R alleles show direct correlations between the biochemical signalling properties of the encoded receptor and the red-hair fair skin pigmentation phenotype. Direct testing of a range of clonal melanocyte cultures derived from donor skin tissue characterized for three causal SNPs within SLC45A2, SLC24A5 and OCA2 has assessed their impact on melanin content and tyrosinase enzyme activity. From a culmination of genetic and functional studies, it is apparent that a number of genes impacting melanosome biogenesis or the melanin biosynthetic pathway are candidates to explain the diversity seen in human pigmentation.
Previous Section Next Section INTRODUCTION
It is astonishing that in a few short years, our understanding of the molecular genetics of human pigmentation has progressed from asking simple questions about what type and how many genes underlie the diversity of skin, hair and eye colour (1) to the identification of several of the major loci and polymorphisms responsible. There is a high degree of variation in colour (amount and type of melanin pigment) and skin type (responsiveness to UV exposure) apparent between and within human populations (Fig. 1), though only those with European ancestry show a large range of hair (2) and eye colours (3). This recent exponential rate of discovery of important pigmentation determining genes has been made through a combination of genetic, biochemical and cellular approaches, but undoubtedly it has been the ready access to the complete human genome sequence and documentation of a vast number of single nucleotide polymorphisms (SNPs: www.hapmap.org; genome.perlegen.com) in several populations (4,5) that is responsible for this expanding knowledge. The methods include comparative genomics of candidate genes such as those identified through studies of mouse coat colours (6) or fish pigmentation patterns (7,8), looking for regions under positive selection between human populations (9–12) that a priori include loci for pigmentation traits, together with genome-wide (13) and specific allele association studies (14) in individuals of defined phenotype. These genetic approaches and the insight they have provided into the pigmentary process will be the focus of this review; however, determination of the molecular mechanism of action, gene interaction and functional protein assays need to be considered to understand how allelic variation in pigmentation genes results in such a diversity of phenotypes in human populations.
posted
well you had thanked xyy, but he came at me buthen I back flipped what he came at me with, dont take it too serious
Posts: 42935 | From: , | Registered: Jan 2010
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quote: A high-quality Neandertal genome sequence The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.
The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.
quote: Use of the genome sequence data
All data is made freely available. However, we ask users to observe the Ft. Lauderdale principles, which entitles the data producers to make the first presentation and publish the first genome-wide analysis of the data. The data can be used freely for studies of individual genes or other individual features of the genome.
Alignments for all Neandertal sequences to the human genome are available in BAM format.
quote:Originally posted by the lioness,: well you had thanked xyy, but he came at me buthen I back flipped what he came at me with, dont take it too serious
Don't worry, I don't take anything involving back flipping seriously.
Posts: 2981 | Registered: Jan 2012
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The lyinass just can't give up can she? I'm thinking the moderators should delete her threads that are a repeat of older threads. Posts: 26267 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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posted
The first thing Djehuti does is when he gets back is insults three people. That is the definition of a Troll. Someone who makes useless comments trying to provoke emotional response and conflict. The one who does that the most currently is the troll Djehuti.
Total facetiousness> "I'm thinking the moderators should delete her threads that are a repeat of older threads." at the same time bumping up this thread which had been dead for a month and sinking down the page, That is what trolls do. The revive old threads for the sole purpose of starting a childish insult war. It's a deep need for attention
Posts: 42935 | From: , | Registered: Jan 2010
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posted
Lying ass said: When I then posted this North Africa article before in AE (I had forgotten about it-over 16000 posts) then zarahan pointed to articles suggesting that maybe Neanderthals never mixed with any humans. I think Explorer has brought that up before. All of the sudden zarahan did a 360
Don't you ever quit lying? I said that using "HBD" and "biodiversity" models and themes, then said Neanderthals would, according to their own claims and models, be classified as "white"- including their cold adaptation, red hair etc etc..
As for actual science, rather than dubious "HBD" models, Neanderthal admixture is one theory, but another approach is that rather than admixture, the seeming commonalities between NEanderthals and modern humans is based on a common hominid ancestor.
RE-QUOTE from elsewhere:
Abstract "Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization.
To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure." --Anders Eriksson, Andrea Manica (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. PNAS 201
and
"Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10-15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence."
Gokcumen et al 2012. Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence. PLoS Genet 9(4):
SO stuff your bogus claims..
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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posted
^^^^ useless remark from cheerleader who keeps bumping my threads up in lieu of have no threads of his own
Posts: 42935 | From: , | Registered: Jan 2010
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Genome Biol Evol. 2013 Oct 25. [Epub ahead of print]
Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations.
Wang S, Lachance J, Tishkoff S, Hey J, Xing J.
Abstract
Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and the modern humans descended from the Out-of-Africa (OOA) migration. Here we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression while others do not. To test this alternative model we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like SNP alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern human and Neanderthal-like hominid within Africa.
Posts: 42935 | From: , | Registered: Jan 2010
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