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Post by djoser-xyyman on Feb 28, 2014 19:52:17 GMT -5
I am beginning to like this Barbujani guy. He is methodology and use of simple logic to tests controversial hypothesis is straight-forward . Here he is trying to confirm whether Neandertal and modern humans did actually admixed. His conclusion is …no!
His approach is very simple and logical. The “yea-sayers” only compare autosomal markers of modern humans and Neandertals. However here Barbujani et al took a logical approach. That is , Compare the mtDNA of the three groups. Neandertals, Paleolithic AMH Humans(European version) and Extant Europeans. With the simple expectation that Paleothic Europeans should carry Neandertal DNA if admixture did occur which would subsequently be passed on to modern Europeans. The Result!!!! Absolute not!!! Infact Paleolithic Europeans carry NONE of the so called Neandertal genetic marker. NADA!, Zilch!. So obviously the so called Neandertal markers found in Euroepans warrants a different explanation. Keeping in mind Paleolithic Europeans should be the group with the largest Neandertal admixture since they are the closest chronological to Neandertals in Europe. The result also confirms the CONTINOUS REPLACEMENT MODEL since the genetic diversity of Paleolithic Europeans are lower than both Neandertals and Modern Europeans. Proving yet again that modern Europeans are recent migrants to the area. Read on..
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Post by djoser-xyyman on Feb 28, 2014 19:53:51 GMT -5
========
No Evidence of Neanderthal Admixture in the Mitochondrial Genomes of Early European Modern Humans and Contemporary Europeans
Guido Barbujani - 2011
We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neanderthals, and Upper Palaeolithic European early modern humans (EEMH), who coexisted with Neanderthals for millennia. We compared by Approximate Bayesian Computations the simulation results with mitochondrial diversity in 7 Neanderthals, 3 EEMH, and 150 opportunely chosen modern Europeans.
A model of genealogical continuity between EEMH and contemporary Europeans, with no Neanderthal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but
However, most morphological and genetic evidence seems to agree with the predictions of a model in which anatomically-modern people and archaic humans DID NOT hybridize.
Neandertal mitochondrial DNA (mtDNA) sequences FALL OUT OF THE RANGE of current European variation (Krings et al., 1997; Briggs et al., 2009), so that even a small mitochondrial contribution of Neanderthals to the modern human gene pool appeared unlikely (Currat and Excoffier, 2004; Belle et al., 2009). By contrast, in the first survey of the whole Neandertal nuclear genome, patterns of allele sharing with modern humans have been interpreted as suggesting gene flow from Neanderthals into the ancestors of modern non-Africans, before the Eurasian populations separated (Green et al., 2010).
between Neandertal and modern mtDNA variation does not imply that there was no admixture, because, at the low Palaeolithic population sizes, drift could have eliminated rare, and even not-so-rare, haplotypes. The question, then, became how rare a haplotype should be, and how small the population, to produce the observed absence of Neandertal haplotypes in modern subjects, despite admixture having actually occurred.
. Belle et al. (2009) incorporated EEMH sequences in their analyses, but still failed to find evidence for any appreciable degree of Neandertal admixture in the European mtDNA pool. For methodological reasons, in both studies mutation rates and population sizes had to be fixed at the start of the simulation.
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Post by djoser-xyyman on Feb 28, 2014 19:54:37 GMT -5
We found that the best estimate by far of mitochondrial admixture between Neanderthals and the ancestors of modern Europeans is zero. Even at very low population sizes and with high mutation rates, the patterns of diversity observed in ancient and modern samples appear incompatible with a Neandertal contribution to the mitochondrial genealogy of EEMH and modern Europeans.
Only one complete Neandertal genome has been studied so far, and, given the rigid standards established to guarantee the quality of the data, sample size is not going to increase any time soon. A second problem is that the admixture model between Neandertal and anatomically modern populations proposed by Green et al. (2010) implies that the ancestors of ALL modern humans who left Africa had contacts with Neanderthals, including those from Papua New Guinea. On the contrary, it is possible that ancestral modern humans also dispersed from Africa via a Southern route, through the Arab peninsula, the Indian subcontinent and Melanesia. This hypothesis was proposed to account for temporal and spatial patterns of cranial diversity (Lahr and Foley, 1994), has been supported by analyses of mtDNA variation (Quintana-Murci et al., 1999; Maca- Meyer et al., 2001; Macaulay et al., 2005) and, recently, by the analysis of [100,000 nuclear single-nucleotide polymorphisms (Ghirotto et al., 2011). If some modern populations of Southern Asia and Papua New Guinea are descended from people who left Africa without crossing Palestine, we see no way that their ancestors could have met, and hybridized with, Neanderthals.
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Post by djoser-xyyman on Feb 28, 2014 19:55:16 GMT -5
Therefore, their genetic affinities with Neanderthals must have a different origin. It is thus necessary to find another explanation for the discrepancy between the apparent implications of the mitochondrial and nuclear analyses. In principle, two possibilities, neither simple to support empirically, would be sex-biased gene flow and hybrid selection. The former means that maybe Neandertal males, but not females, admixed with early anatomically modern Europeans. This is in contrast with studies of sex-biased admixture in modern communities, suggesting that the invading population tends to incorporate females more than males (Abe-Sandes et al., 2004; Goncalves et al., 2008; Gonzalez-Andrade et al., 2007; Stefflova et al., 2009; Quintana-Murci et al., 2010); to what extent this might also apply to prehistoric populations, nobody knows. Hybrid selection could account for the observed differences between admixture estimates if Neandertal mtDNAs had lower fitness in combination with a hybrid nuclear genome. Once again, we see no way to test empirically whether that was actually the case. Moving on to testable hypotheses, a simple process of genetic drift after admixture is not the explanation we seek (see Fig. 3). In addition, in a simple admixture model, alleles passed from a resident to an invading population
are expected to often surf to high frequencies if the invading populations also undergoes demographic growth (Currat et al., 2008). Because the incoming EEMH doubtless increased in numbers, even small Neandertal contributions should be detectable in the gene pool of their descendants, which is not the case for the European mtDNAs (Currat and Excoffier, 2004; this study). To reconcile findings based on nuclear and mitochondrial variation we thus need a more articulate model, of which genetic drift is only a component. Many studies of modern DNA data have suggested that the common ancestors of Neanderthals and modern humans might have been geographically structured (Falush et al., 2003;
These figures come with a large standard error, but imply that if the lineages leading to Neanderthals and modern humans separated between 175,000 and 700,000 years ago, one would expect exactly what has been observed, namely independent mtDNA genealogies, and a certain degree of allele sharing at the autosomal level (see Fig. 5).
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Post by djoser-xyyman on Feb 28, 2014 19:55:42 GMT -5
Therefore, the Replacement model with structured ancestral population is in reasonable agreement with fossil, nuclear DNA and mtDNA evidence, whereas the model of admixture fails to account for the observed relationships between ancient and modern mtDNAs.
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Post by djoser-xyyman on Feb 28, 2014 19:56:08 GMT -5
and now the pictures...Red circle=essential zero admixture between Neandertals and Paleolithic Europeans. Green Circle shows high diversity of modern Europeans and Neandertals. Notice Paleolithic Europeans is extremely comparatively low. Again proof that modern Europeans are "recent" migrants to Europe. Of course African diversity is "off the charts". And Paleolithic Humans may represent a dead end. And is therefore insignificantly related to modern Europeans.
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Post by azrur on Feb 28, 2014 21:08:08 GMT -5
it is said that a lot of other people are from neanderthal too is that true or false like the european one
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Post by djoser-xyyman on Mar 1, 2014 14:49:11 GMT -5
There is a benefit to READING and understanding. Your questions are answered.... That is the basis of the entire study. That is why they analyzed Paleolithic Europeans, which showed NO Neandertal admixture. So obviously the admixture hypothesis is wrong. And the so called Neandertal admixture gene in Europeans (and other groups) are NOT from Neandertal but a different source. ie possible "sub-structure" as many OTHER studies have shown!! Also the Neandertal admixture hypothesis is based upon the assumption that AMH left Africa through the Levant and NOT the Horn into Arabia. Why? Neanderthals never ventured into Arabia. Also keep in mind the so called Neanderthal gene is found in the ....Luyha, Maasai etc and North African. I have always speculated that the lasts wave came from the Great Lakes. it is said that a lot of other people are from neanderthal too is that true or false like the european one QUOTE: Only one complete Neandertal genome has been studied so far, and, given the rigid standards established to guarantee the quality of the data, sample size is not going to increase any time soon. A second problem is that the admixture model between Neandertal and anatomically modern populations proposed by Green et al. (2010) implies that the ancestors of ALL modern humans who left Africa had contacts with Neanderthals, including those from Papua New Guinea. On the contrary, it is possible that ancestral modern humans also dispersed from Africa via a Southern route, through the Arab peninsula, the Indian subcontinent and Melanesia. This hypothesis was proposed to account for temporal and spatial patterns of cranial diversity (Lahr and Foley, 1994), has been supported by analyses of mtDNA variation (Quintana-Murci et al., 1999; Maca- Meyer et al., 2001; Macaulay et al., 2005) and, recently, by the analysis of [100,000 nuclear single-nucleotide polymorphisms (Ghirotto et al., 2011). If some modern populations of Southern Asia and Papua New Guinea are descended from people who left Africa without crossing Palestine, we see no way that their ancestors could have met, and hybridized with, Neanderthals.
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Post by herodotus on Mar 2, 2014 16:55:10 GMT -5
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Post by herodotus on Mar 2, 2014 17:07:19 GMT -5
There is a benefit to READING and understanding. Your questions are answered.... That is the basis of the entire study. That is why they analyzed Paleolithic Europeans, which showed NO Neandertal admixture. So obviously the admixture hypothesis is wrong. And the so called Neandertal admixture gene in Europeans (and other groups) are NOT from Neandertal but a different source. ie possible "sub-structure" as many OTHER studies have shown!! Also the Neandertal admixture hypothesis is based upon the assumption that AMH left Africa through the Levant and NOT the Horn into Arabia. Why? Neanderthals never ventured into Arabia. Also keep in mind the so called Neanderthal gene is found in the ....Luyha, Maasai etc and North African. I have always speculated that the lasts wave came from the Great Lakes. it is said that a lot of other people are from neanderthal too is that true or false like the european one QUOTE: Only one complete Neandertal genome has been studied so far, and, given the rigid standards established to guarantee the quality of the data, sample size is not going to increase any time soon. A second problem is that the admixture model between Neandertal and anatomically modern populations proposed by Green et al. (2010) implies that the ancestors of ALL modern humans who left Africa had contacts with Neanderthals, including those from Papua New Guinea. On the contrary, it is possible that ancestral modern humans also dispersed from Africa via a Southern route, through the Arab peninsula, the Indian subcontinent and Melanesia. This hypothesis was proposed to account for temporal and spatial patterns of cranial diversity (Lahr and Foley, 1994), has been supported by analyses of mtDNA variation (Quintana-Murci et al., 1999; Maca- Meyer et al., 2001; Macaulay et al., 2005) and, recently, by the analysis of [100,000 nuclear single-nucleotide polymorphisms (Ghirotto et al., 2011). If some modern populations of Southern Asia and Papua New Guinea are descended from people who left Africa without crossing Palestine, we see no way that their ancestors could have met, and hybridized with, Neanderthals. There is no "Neandertal admixture hypothesis" its now been proven Neandertals and the Denisovan Asians account for at least 8% of the gene-pool of living non-Africans (Reich et al. 2010). Skoglund and Jakobsson (2011): "In addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia (“Denisovans”) and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome... These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asian." There is wide agreement that not all humans share a single unique ancestry in a recent African (or any other) population. Does this upset you?
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Post by djoser-xyyman on Mar 2, 2014 20:31:47 GMT -5
Listen. This is not RR forum. I am not about rabid dogma. If you can't follow the argument then just read and DON'T comment. Get you thoughts straight before you respond.
Do you understand WHY Paleothic Europeans were used?
Answer; to test the genetic drift or selective sweep hypothesis. All the points are bolded for easy reading.
If you dont have a argument..please shut up.
BTW: Are you a multi-regionalist? It sounds that way.
I am always open to a counter argument but no hypotheticals ..there are no winners. Read, understand , then make your point. Admit when you are wrong and we can move on.
So I repeat....why were Paleolithic Europeans used in the study?
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Post by herodotus on Mar 2, 2014 21:39:31 GMT -5
"The recent finding that significant interbreeding occurred between Neanderthals and modern populations refutes the long-standing model that proposes all living humans trace their ancestry exclusively back to a small African population that expanded and completely replaced archaic human species, without any interbreeding." (d’Errico & Stringer, 2011)
The model you subscribe to has been discredited. Yes you are about "dogma". You are a complete nut whose dogma is the "everyone and everything is African" nonsense. You simply cannot accept the reality not all humans share a single unique recent ancestry from Africa - a model that has been falsified. Read the Stringer quote.
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Post by herodotus on Mar 2, 2014 21:49:00 GMT -5
Do you even read what you are quoting from? Many of your quotes which you missed to bold refute your own thread:
Barbujani (2011) does not rule out mixture at all.
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Post by herodotus on Mar 2, 2014 21:51:59 GMT -5
Barbujani's (2011) study even estimates 1.5% admixture. Something you failed to quote in bold lolol.
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Post by herodotus on Mar 2, 2014 22:06:58 GMT -5
You're also not up to date with the latest finds. From Harvati 2012 - Barbujani (2011) didn't have access to the latest studies on Neanderthal nuclear DNA. There are no studies post-2011 that deny interbreeding occurred. Skip forward to 2013: www.edge.org/conversation/rethinking-out-of-africaGame over sir.
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