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Thread: Neanderthal Contribution to European Genome is 5%

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    Neanderthal Contribution to European Genome is 5%

    New evidence based on the total genome, not mtDNA or Y-chromosome shows that Neanderthals did contribute to modern Europeans and that West Africans had genetic input from another non-sapiens source.

    http://dienekes.blogspot.com/2006/06...ern-human.html

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    AW: Neanderthal Contribution to European Genome is 5%

    Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p ~ 10^{-7}), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe,
    I wouldnt go that far, its not sure now, after just this study and even if (froma genetic standpoint) archaic admixture was present, Neandertals being just a candidate so far.
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    Re: AW: Neanderthal Contribution to European Genome is 5%

    Quote Originally Posted by Agrippa
    I wouldnt go that far, its not sure now, after just this study and even if (froma genetic standpoint) archaic admixture was present, Neandertals being just a candidate so far.
    This is a good point and one which is true using the data we have so far, strict logic and the scientific method. Nevertheless, there are not many other candidates other than Neanderthal in Europe so unless the non-sapiens genetic material can be somehow dated prior to 50,000 years ago.....

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    AW: Neanderthal Contribution to European Genome is 5%

    By the way, this is the aforementioned survey, though only a preliminary release:
    http://genetics.plosjournals.org/arc...020105.eor.pdf
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    Re: AW: Neanderthal Contribution to European Genome is 5%

    Quote Originally Posted by Q.
    By the way, this is the aforementioned survey, though only a preliminary release:
    http://genetics.plosjournals.org/arc...020105.eor.pdf
    Great work Q, I downloaded this for future reading at a more sober time.

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    5% seems a little high, as some studies would suggest that Neanderthals are more closely related to chimpanzees than modern humans.

    Neanderthals not at all related to modern humans
    Friday, 7 March 2003

    Neanderthals may not have interbred or shared culture with modern humans (Pic: Natural History Museum, UK)
    The famous prehistoric Neanderthal people made little or no contribution to the gene pool or culture of modern humans, according to a re-evaluation of their part in evolution.

    A wide range of recent research into Neanderthal bones, tools, artefacts, archaeological sites and genetics now suggest that they were "a fascinating but extinct side branch of humanity" said the report, published today in the journal Science.

    "The longest continuous debate in palaeoanthropology is nearing resolution," wrote Professor Richard Klein of Stanford University in California, in his review of the evidence. "Modern humans replaced the Neanderthals with little or no gene exchange. Almost certainly, the Neanderthals succumbed because they wielded culture less effectively."

    Neanderthals are an extinct hominid species closely related to modern humans. They were tool-makers who lived throughout Europe, parts of Asia and northern Africa from the Pleistocene (about 350,000 years ago) until they disappeared about 30,000 years ago.
    Retrieved From:http://www.abc.net.au/science/news/stories/s800914.htm

    Sleep with Neanderthals? Apparently we (homo Sapiens) did
    By Faye Flam


    The Philadelphia Inquirer

    Though it's been 150 years since mysteriously humanlike bones first turned up in Germany's Neander Valley, the find continues to shake our collective sense of human identity.

    Neanderthals are humanity's closest relatives, with brains at least as big as ours, and yet we don't know whether we should include them as members of our own species.

    No longer does science consider them our direct ancestors but some suspect Neanderthals and modern homo Sapiens interbred during the 20,000 some-odd years we co-existed in Europe. The archaeological record doesn't tell us one way or another, but earlier, researchers announced they would seek more clues by scraping DNA from Neanderthal bones and teeth.

    The question of sex with Neanderthals speaks to our understanding of ourselves, our origins and our uniqueness. If this other type of human being wasn't like us, what was he like?

    As I started researching this issue, I found myself staring at a picture of a nude Neanderthal man — a forensic sculpture created by Duke University paleoanthropologist Steve Churchill that was published last year in the journal Science. The model, based on a skeleton found at La Ferrassie in France, is mesmerizing in its combination of familiarity and alienness.
    Retrieved From:http://seattletimes.nwsource.com/htm...owledge13.html

    NEANDERTHAL: NO RELATION
    By Sean Henahan, Access Excellence

    University Park, Pa. (10 July 1997) New evidence from mitochondrial DNA analyses indicates that the Neanderthal hominid was not related to human ancestors.
    Using refined and expensive genetic techniques, U.S. and German researchers extracted mitochondrial DNA from Neanderthal bone. These studies showed that the Neanderthal DNA sequence falls outside the normal variation of modern humans.

    "These results indicate that Neandertals did not contribute mitochondrial DNA to modern humans," says Dr. Mark Stoneking, associate professor of anthropology at Penn State. "Neandertals are not our ancestors."

    The findings will cause of reconsideration of the current consensus that Neandertals became extinct only 30,000 years ago and co- existed for some time with modern humans in Europe. The new research indicated that Neandertals and modern humans diverged genetically 500,000 to 600,000 years ago. While the two species may have lived at the same time, Neandertals did not contribute genetic material to modern humans, the researchers report.

    The team analyzed bone from a Neanderthal specimen found in the eponymous valley. This is the first time researchers have been able to extract useful DNA fragments from such a specimen.

    "The ability to extract DNA from ancient bone is dependent on many factors, including preservation, temperature and humidity," says Stoneking, a faculty member in Penn State's College of the Liberal Arts.
    Retrieved From:http://www.accessexcellence.org/WN/SUA10/neander797.php

    Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are.

    Shi Huang,Ph.D.

    The Burnham Institute for Medical Research
    10901 North Torrey Pines Roads
    La Jolla, CA 92037


    Of the 11 independent sequences of hyper-variable region I, 9 showed more similarity between modern humans and chimpanzees than between Neanderthals and chimpanzees and 2 (both of 31 bp in length) showed equal similarity (Table 2). The observation of 9 cases of more similarity between humans and chimpanzees against 0 case of more similarity between Neanderthals and chimpanzees is highly significant by Chi square test (Chi-square = 6, P<0.025, one degree of freedom). In addition, the two published hyper-variable region II sequences of Neanderthals are also more distant to chimpanzees than modern humans are. The data suggests that significantly more human samples than Neanderthals show higher similarity with chimpanzees. A randomly chosen human mtDNA is almost certain to be more related to chimpanzees than a randomly chosen Neanderthal mt DNA is. Therefore, modern humans are significantly more related to chimpanzees than the Neanderthals are.
    Another way to test the statistical significance of this finding is to randomly select a number of human sequences and see how many of them are more or less related to chimpanzees than a randomly selected Neanderthal sequence is. If humans and Neanderthals are equally related to chimpanzees, then the number of human sequences that are more related to chimpanzees than the Neanderthals are should be similar to the number of human sequences that are less related to chimpanzees than the Neanderthals are. I randomly selected 20 human mitochondrial sequences from Genbank and determined whether their similarity to chimpanzees is greater or less than the similarity between the Neanderthal sequence AF011222 (379bp) and chimpanzees. The Neanderthal sequence AF011222 was used to BLAST or retrieve all the human mitochondrial sequences from Genbank (about 14000 sequences) that show significant similarity with the Neanderthal sequence, ranging in identity between 94% and 90%. From this list of 14000 human sequences ordered by their degree of similarity with the Neanderthal sequence, every 700 th sequence was selected for analysis and a total of 20 was selected. All 20 sequences showed greater similarity with chimpanzees than the similarity between the Neanderthal sequence AF011222 and chimpanzees. This is highly significant by Chi square test (Chi-square = 13.33, P<0.001, one degree of freedom).
    To confirm this result using only independently verified or conserved Neanderthal sequences, I next identified a region of 186 bp that is completely shared by 4 independent Neanderthal samples, DQ859014 (303 bp, sample from Spain), AF011222 (379bp, sample from Feldhofer, Germany), AY149291 (357 bp, sample from Feldhofer 2, Germany), and AF282971 (357 bp, sample from Vindija Cave, Croatia). This conserved 186 bp region is from position 118 to 303 of DQ859014. I next analyzed the corresponding 186 bp region from the 20 randomly selected human sequences that were used in the above analysis. All of these human sequences show more similarity between human and chimpanzee than between Neanderthal and chimpanzees (P<0.001). The Neanderthal 186 bp region is also more distant to chimpanzees than the human Cambridge Reference sequence. Thus, even when I only used conserved Neanderthal sequences that have been verified by independent sequencing analysis of 4 independent samples from 3 vastly separate locations, I still found that Neanderthals are significantly more distant to chimpanzees than modern humans are. The analysis suggests that the greater distance between Neanderthals and chimpanzees as observed here is not a result of sequencing errors or artifacts.

    Neanderthals are more distant to gorillas than modern humans and chimpanzees are
    I next examined whether Neanderthals are also more distant to gorillas than chimpanzees and modern humans are. If Neanderthals were alive today, they would be equidistant to gorillas as chimpanzees and humans are. If the molecular clock hypothesis is true, ancient Neanderthals cannot be more distant to gorillas than extant chimpanzees or modern humans are.
    I first made sure that my method of analysis using mtDNA is able to reveal or confirm that humans and chimpanzees are indeed equidistant to gorillas. I randomly selected 30 hyper-variable region I sequences from a list of 1000 chimpanzee sequences from Genbank that were retrieved by BLAST using the Neanderthal DQ859014 (303 bp) sequence (every 33 th sequence from this list was selected). Each of these sequences was used to identify a most closely related human sequence. Next, each chimpanzee sequence and its corresponding human sequence of equal length were used to obtain a best BLAST similarity score with gorilla non-nuclear mitochondrial sequences in the Genbank. These scores were used to determine whether the distance between a chimpanzee sequence and gorillas is greater or not than that between a corresponding human sequence and gorillas. Among the 30 comparisons, 13 showed greater similarity between chimpanzees and gorillas than between humans and gorillas
    Retrieved From:http://precedings.nature.com/documen...20081676-2.doc

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