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Sex with Neandertals Introduced Helpful and Harmful DNA into the Modern Human Genome

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Neandertal skull

Neandertal DNA survives in Asian and European people today. Image: 120, via Wikimedia Commons

Over the past few years a number of studies of ancient and contemporary genomes have reached the same stunning conclusion: early human species interbred, and people today carry DNA from archaic humans, including the Neandertals, as a result of those interspecies trysts. Now two new analyses of modern human genomes are providing insights into how the acquisition of Neandertal DNA affected anatomically modern Homo sapiens tens of thousands of years ago and how it continues to affect people today.

In the first study, Sriram Sankararaman and David Reich of Harvard University and their colleagues compared a complete Neandertal genome sequence with 1,004 modern human sequences to see which regions of the modern genome contain Neandertal DNA. Like other researchers before them, they observed that Asians and Europeans have DNA from Neandertals, whereas Africans have little or no Neandertal DNA. The pattern is consistent with a scenario in which early modern humans mated with Neandertals they encountered when they migrated out of Africa and into Eurasia, where Neandertals had lived for hundreds of thousands of years.

Moreover, the team determined that Neandertal DNA is not distributed evenly across the genome. Some genes have a high proportion of Neandertal ancestry (which is to say, many people today carry the Neandertal versions of these genes). Those genes with the highest Neandertal ancestry are associated with keratin, a protein found in skin and hair. The Neandertal variants of these genes may well have helped early modern humans adapt to the new environments they found themselves in as they spread into Eurasia. But the researchers also found that people today carry Neandertal genes that are associated with diseases including Crohn’s, type 2 diabetes and lupus.

Intriguingly, other regions of the modern human genome have no or very low Neandertal contribution, notably the X chromosome and genes related to the functioning of the testes. According to Sankararaman, Reich and their collaborators, the absence of Neandertal genetic material in these regions suggests that male hybrids who inherited a Neandertal X chromosome were infertile, and thus unable to pass their genes along to the next generation. The researchers detail their findings in a paper published in the December 30 Nature. (Scientific American is part of Nature Publishing Group.)

In the second study, published by Science, Benjamin Vernot and Joshua M. Akey of the University of Washington screened whole genome sequences from 665 living Europeans and Asians for telltale signs of Neandertal contributions. Their results show that although non-Africans individually inherited between 1 and 3 percent of their genomes from Neandertals, different people carry different bits of Neandertal genetic material. Together these sequences represent around 20 percent of the Neandertal genome.

Like the other team, Vernot and Akey found evidence that Neandertals passed along beneficial skin genes to modern humans, including some linked to pigmentation. And they, too, observed genome regions devoid of Neandertal contributions. One such region contains the gene FOXP2, which plays an important role in speech.

Vernot and Akey’s work is additionally interesting in that they were able to use statistical and computational methods to identify the Neandertal contributions in the genomes of modern-day people without using a Neandertal genome to guide their search. This work raises the possibility that simply by analyzing the genomes of people alive today, scientists will be able to discover and describe extinct human species that mated with early H. sapiens but that, unlike Neandertals, are unknown from the fossil record. Previous studies of genomes of living people have hinted at dalliances between early H. sapiens and unknown archaic humans in Africa. Perhaps this approach will shine a light on these mysterious skeletons in our closet.



Kate Wong About the Author: Kate Wong is an editor and writer at Scientific American covering paleontology, archaeology and life sciences. Follow on Twitter @katewong.

The views expressed are those of the author and are not necessarily those of Scientific American.

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  1. 1. jtdwyer 8:52 pm 01/30/2014

    Very interesting! As I began reading, I wondered if Northern skin pigmentation adaptations might have originated with Neanderthals – since they had several hundred thousand years to adapt to their rather restricted geographical range…

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  2. 2. Jerzy v. 3.0. 6:08 am 01/31/2014

    Which makes it odd that Homo sapiens and neanderthalensis are considered different species, not subspecies. Perhaps for the pure convenience of the shorter name.

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  3. 3. Devin2014 10:16 am 01/31/2014

    “One such region contains the gene FOXP2, which plays an important role in speech.”

    I wonder if this might suggest that Neanderthals could not speak? If they could not speak, I wonder how anatomically modern humans (AMH) and neanderthals communicated with one another, or if they did at all? I could imagine a scenario where both species fought and forwent diplomacy, which led to the cross-breeding (not to dehumanize anybody here).

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  4. 4. rkipling 11:21 am 01/31/2014

    The article below seems to be at odds with the studies discussed here. It indicates at least some Europeans were dark skinned, but blue eyed as recently as 7,000 years ago. At first I thought this was a different report on the same paper.

    Since the paper below is based on only one individual, the two studies above are likely more representative of what the reality was.

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  5. 5. Heteromeles 11:23 am 01/31/2014

    @Devin: Assuming there’s any difference at all between FOXP2 genes in different human lineages (and that’s a big assumption), it might be that the African FOXP2 was more versatile than the Neandertal FOXP2, rather than that Neandertals couldn’t speak at all. After all, when looking at the languages associated with the basal living lineages of Homo sapiens, people like the !Kung, they use a number of clicks and other phonemes that aren’t used in languages outside of Africa.

    However (checking Wikipedia), it looks like humans and chimps vary by only two amino acids (at most 6 bp) at FOXP2, and both Neandertal and Denisovan genomes contain the modern human version of FOXP2. The idea that the archaic human forms did not have a modern FOXP2 is based on modeling of the genome around FOXP2 that led one group of researchers to propose that the archaic sequence data reported was due to modern human contamination. If that’s so, then we know nothing about Neandertal (or Denisovan) DNA, because anything that’s not different from modern DNA could be blamed on contamination, and anything that’s different can be blamed on equipment errors. Given a choice between evidence and a model, I’d tend to go with the DNA evidence, especially since they have a complicated model to try to prove their point, and the rather nasty follow-on conclusion if they’re right.

    The other point is that FOXP2 is a protein, and there’s not much published about how its expression is controlled in different species. That might turn out to be more important than the shape of the protein itself.

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  6. 6. rshoff2 11:24 am 01/31/2014

    Can they piece together any off the circumstances of the mating? e.g. if it’s war/rape no communication necessary. If it’s a bonding relationship, the communication issue really comes into play. Perhaps interbreed sex and/or mating was a survival strategy -of both parties apparently.

    Do modern humans as a group harbor enough Neanderthal genes to sequence their genome? Finally, how do we know that the so called ‘Neanderthal’ genes are Neanderthal? What makes them ‘Neanderthal’? Could the Neanderthals have been walking around with ‘Human’ genes or could it have been a shared genetics from prior to a Neanderthal/Human split?

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  7. 7. rkipling 12:06 pm 01/31/2014

    Search for Neanderthal genome project. They completed a full genome last year.

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  8. 8. profbrown 12:47 pm 01/31/2014

    Over the past few years a number of studies of ancient and contemporary genomes have reached the same stunning conclusion: early human species interbred, and people today carry DNA from archaic humans, including the Neandertals, as a result of those interspecies trysts. Now two new analyses of modern human genomes are providing insights into how the acquisition of Neandertal DNA affected anatomically modern Homo sapiens tens of thousands of years ago and how it continues to affect people today.////////The definition of a species is reproductively isolated populations or groups of populations capable of interbreeding to produce fertile offspring. Therefore if “Neanderthals” had sex with homo sapiens that produced fertile offspring ( the only way their dna could be some of us today) , Neanderthals were the same species as homo sapiens. which is to say Neanderthals were just as “human” as you and I

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  9. 9. rshoff2 1:13 pm 01/31/2014

    rkipling – Thanks for the lead, my question was poorly written. I’m wondering what percentage of the Neanderthal genome we contain within ours. Not anyone individual, but the aggregate within all humans.

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  10. 10. rkipling 1:43 pm 01/31/2014

    I’ve read it is 1 to 4 % for non-Africans.

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  11. 11. rshoff2 1:43 pm 01/31/2014

    rkipling – Yep, all my questions answered, and more, with a web search for the neanderthal genome project. :\
    ~ NIH News, National Human Genome Research Institute

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  12. 12. Anna G. 1:53 pm 01/31/2014

    An analysis of a Neanderthal’s fossilised hyoid bone – a horseshoe-shaped structure in the neck – suggests the species had the ability to speak.

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  13. 13. Xialiang 2:34 pm 01/31/2014

    Not that odd Jerry. The genus is the same. Inter-species breeding does happen among various organisms, with varied success. For example, Ursus maritimus can breed with the various sub species of Ursus arctus. In some cases, the offspring is fertile, in others, it isn’t. If what they are positing is true, that there were some Neanderthal X Sapian offspring that were infertile, then that would fall in the spectrum of what you’d expect from inter-species, not inter sub species.
    Classification still has some grey areas, but I wouldn’t say Homo N. and Homo S. fall in those grey areas.

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  14. 14. harry77 3:34 pm 01/31/2014

    This helps to explain the Tea Party and Science Scoffers.

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  15. 15. wwdalitsch 4:06 pm 01/31/2014

    profbrown: Not entirely accurate description of “species.” Horses and donkeys are different species, but are interbred, preferably pairing an equine mare with a jack, resulting in a mule. (The opposite results in a hinny and hence the origin of the phrase, “Useless as a hinny.”) Although mules typically don’t interbreed, it is possible. While horses and donkeys are still distinct species, the mules and hinnies are hybrids.

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  16. 16. rkipling 4:07 pm 01/31/2014


    Off topic comment.

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  17. 17. ssm1959 5:19 pm 01/31/2014

    Regarding the question of species separation, the fact that there were non-fertile offspring suggests the Neandertal and modern humans were more separated that many have considered. There are many bird species that can crossbreed and produce fertile offspring. They are only considered species because their geographic distribution keeps them isolated. Clearly Modern humans and Neandertal were more separated that that.

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  18. 18. Heteromeles 6:14 pm 01/31/2014

    @17: What fact that they were non-fertile offspring? Remember, we may all be descended from “mitochondrial Eve.” She was not the first human, merely the one who got lucky enough that we all inherited her mitochondria and not those of all the other women of her time.

    If she existed and isn’t a statistical artifact, that is.

    We only have a model to suggest that male Neanderthal X Modern crossings were biologically infertile. They could have been fertile but unlucky (as with Mitochondrial Eve’s girl-friends), or we could have not sampled the people descended from them.

    I’d simply point out that mating barriers tend to be low in young, rapidly evolving species, ranging from Darwin’s Finches to bread wheat. Humans appear to be in the same situation, and probably Neanderthals, Denisovans, and moderns (along with, for all I know, Floresian Hobbits) could all have fertile biracial kids if they managed to get together.

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  19. 19. rshoff2 6:22 pm 01/31/2014

    “Species” is beginning to sound arbitrary, mostly based on whether members can reproduce (?). After all, it sounds like we share most genetics dating all the way back to, well, all the way back.

    I know this is off topic, but I would like to project this concept to abolish any delineation of ‘race’. Cultural heritage and coincidental genetics is as far as it goes. The category of Race does not exist because the greater category of Species barely does.

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  20. 20. PaulLev 7:06 pm 01/31/2014

    Fascinating! For speculation back in 1999 about Neanderthal-modern human relations, see The Silk Code, which “offers a startling hypothesis about modern-day humans and Neanderthals” -NY Times

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  21. 21. Heteromeles 11:53 am 02/1/2014

    @19: Species not existing? Not quite. There are dozens of definitions of species, and the ones that work for modern mammals don’t work as well for bacteria, fungi, or fossils.

    That said, the reproductive isolation definition works just fine for most animal and plant species. It doesn’t work at all for bacteria (which can share genes laterally), and it’s problematic for fungi, which have both sexual and asexual species names (for what were very important historical reasons). Fossils obviously don’t breed, so definitions of fossil species are based on differences in morphology

    Reproductive isolation also works great for defining modern humans as a species, because we’re all one huge, morphologically diverse, interbreeding species. Where we get into trouble is that we’re trying to deal with the intersection of fossil species definitions and modern species definitions, and the definitions don’t match each other.

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  22. 22. jcarlinsv 2:26 pm 02/1/2014

    Sorry guys. No Neanderthal X and no Neanderthal mtDNA means that the “interbreeding” was all Neanderthal males with Sapiens females. It seems that Sapiens males just couldn’t compete.

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  23. 23. Heteromeles 8:28 pm 02/1/2014

    @22: That’s what we’ve *found* so far. as I noted, the mitochondrial Eve story pretty comprehensively debunks this. Go reread it. There’s a gigantic difference between “No evidence survived for 30,000-70,000 years,” and “it didn’t happen.”

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  24. 24. greenhome123 5:53 pm 02/3/2014

    Neanderthals must have had giant penis that was irresistible to homo sapien women :-) Or, maybe the offspring of the male homo sapiens and female neanderthals were infertile. I have 3.1% neanderthal DNA according 23andme dna test (top 98% in humans), so I’m sticking with the giant Neanderthal penis theory.

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  25. 25. jonathanseer 6:38 pm 02/3/2014

    I’m glad to see the belief American researchers forced upon everyone is finally being overturned.

    It’s just one of many unsupported assumptions that have found their way into genetics, biology Etc., that stem not from any logical or scientific foundation, but from bias deeply rooted in the American psyche that originate in religious beliefs.

    Such bias is so fundamental now, that even if a born in and raised American researcher is a 100% unapologetic atheist most of the assumptions he or she makes regarding animals or our predecessors will reflect it.

    It’s only been in the last decade that Europeans mostly have finally found proof to confront the assumed facts of American researchers regarding neanderthals.

    Previously, with any such announcement contemptuous dismissals by researchers on this side of the Atlantic so shamed the less confident European researchers that the point was dropped as this ensured it would not pass peer review and get published.

    It’s taken time, but finally European and Asian science is realizing just how much of the facts (like Neanderthals did not contribute to the modern human genome) spoken as if proved by American researchers were nothing more than fanciful assumptions based on their own beliefs.

    Beliefs they thought just had to be true. They never asked themselves why, but if they did, many would realize that somewhere back our culture turned a lot of beliefs into facts because the bible told us it was so.

    The next false paradigm forced on the world of science is in regard to animal intelligence and their ability to feel emotion. Non-American researchers are increasingly dismissive of the American insistence that anthropomorphizing animal subjects is bad science, because they realize as animals we alone have the greatest ability to understand what they feel even if they can’t conceptualize this.

    It won’t fall easily though as already Australian and American researchers are trying to construct a firewall that strictly segregates things and how you can refer to them, and in that new paradigm, humans are not animals which by extension means you can’t learn anything about animals by looking in the mirror.

    If this notion takes over it will be the biggest triumph of religious thought in the history of mankind, for there is no rational basis to distinguish humans from animals just philosophical ones.

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  26. 26. arshagko 6:52 pm 02/3/2014

    to greenhome123: Maybe the Neandertal males didn’t consider rape an issue in reproduction with sapian females? Nothing about the record can point to consent as it stands.

    To jonathanseer: As far as religion and how they perceive other higher animals – good luck. As long as they take their selfish lead from a badly written book(s), they will find a way spread whatever dogma they see fit. At least this newer generation is asking more questions.

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  27. 27. timcliffe 9:40 pm 02/3/2014

    Jonathanseer and arshagko: Perhaps you didn’t notice that the two studies discussed in the article were done by faculty at Harvard and the University of Washington? Those are American institutions, so apparently not every American researcher is entirely the unconscious deist.
    Sweeping generalizations about entire nations or peoples are silly at best. Silly is the kindest word I can think of.

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  28. 28. Ehkzu 10:21 pm 02/3/2014

    re: abolishing concept of race, as one comment proposes, since the definition of “species” is necessarily fuzzy

    Persistent attempts by leftist ideologues to banish the concept of “race” mirrors persistent attempts by rightist ideologues to banish evolution, global warming, and statistics. All are based on ideology, not science.

    Race is a useful concept that’s never going away. It represents the first stage of genetic isolation (stemming from geography and/or ecological niche) that, if left unchecked, leads to speciation.

    Anyone involved in agronomy or animal husbandry uses race daily. So does medicine.

    For example, the Eskimo race responds differently to certain polio drugs than the Caucasian race does. Not knowing this produced an epidemic in the last century.

    Conversely, the belief that sickle cell anemia was race-linked has led to misdiagnosis of Caucasians with this genetic disorder.

    Evidently Neanderthals fall somewhere between a separate race and a separate species. Reality doesn’t feel any need to conform to our attempts at categorization, but if there is a differential in fertility–even if it isn’t complete, as is now obvious (I’m 3.1% Neanderthal myself)–I think it would be far to call them a separate species or at least a subspecies (intermediary between “race” and “species”).

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  29. 29. Ehkzu 10:32 pm 02/3/2014

    re: why human men may not have mated with Neanderthal females while Neanderthal males may have mated with human females.

    First, consider the context: small bands of humans were pushing into Neanderthal territory, where the Neanderthals were well established and present in greater numbers.

    In these circumstances a lone human might have emerged from some catastrophe that killed off the rest of his/her band. It’s very difficult for humans to survive by themselves, especially in what might have been for them a strange land with new things to learn about what to eat & to avoid eating & what weather signs means.

    Now imagine what would probably happen if a lone human approached a Neanderthal band. It is very, very unlikely that a male human would not be driven off by the Neanderthal alpha male and his beta warriors. OTOH he might be happy to add another female to his harem–even a human one.

    So there’s a hypothesis with substantiation in known facts about the behavior of ground-dwelling social primates.

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  30. 30. American Muse 10:34 pm 02/3/2014

    Why would the absence of Neanderthal genes in the X-chromosome of modern humans mean that male Human/Neanderthal hybrids were sterile? Don’t females also contribute X-chtomosomes? Did they mean Y-chromosome rather of X in the article? SEE EXCEPT BELOW:

    “the absence of Neandertal genetic material in these regions suggests that male hybrids who inherited a Neandertal X chromosome were infertile,”

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  31. 31. jameslouder 11:30 pm 02/3/2014

    Because there seem to be no Neanderthal contributions to the X chromosome, it is suggested that male Sapiens-Neanderthal hybrids may have been infertile. Yet clearly female S-N hybrids must have been fertile. So why one but not the other? Do we know of other mammalian hybrids that show the same sex-based difference in fertility?

    I would like to suggest another, and to my mind more likely explanation: that S-N hybridization was not a two-way affair. Rather, S-N hybrids were primarily, or even exclusively, the result of Sapiens men mating with Neanderthal women. This would be consistent with known models of warfare between rival human groups, where the vanquished males are killed or driven away, while their women are carried off as wives by the victors. Perhaps the Neanderthals won sometimes and absconded with Sapiens women. But the offspring of those unions and their descendents, remaining in the Neanderthal community, would have gone extinct and left no trace.

    There is the further possibility that a Sapiens woman might have had great difficulty passing an infant with strong Neanderthal characteristics through her birth canal; and that the difficulty would be greatest with a male infant, as male babies are, on average, larger in size. This is pure speculation on my part, for as far as I know, we have no fossils of Neanderthal neonates to show definitively how their skulls flexed during birth. Perhaps further discoveries may shed light on this possibility.

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  32. 32. jameslouder 11:39 pm 02/3/2014

    NOTE to my previous post: As American Muse has suggested, Ms. Wong’s allusion to “…the X chromosome and genes related to the functioning of the testes” is mistaken; that the Y chromosome is the one that was meant. I would like to correct my earlier post to reflect this.

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  33. 33. rshoff2 12:37 pm 02/4/2014

    @21 thank you for your comments and replies. One more question, if you’re of the mind to offer an insight. How much of the Neanderthal DNA exists in modern humanities aggregate genome? If I phrased the question right, I’m trying to imagine if the entirety of the Neanderthal DNA still exists within our species, just not within and one particular individual. I have read that it could be as high as 4% for anyone individual, but are those Neanderthal genes we share the same 4%?

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  34. 34. rshoff2 12:42 pm 02/4/2014

    Furthermore, I’m confused about the definition of Neanderthal DNA. It sounds like we already share(d) 99.7% of the DNA. That leaves .3% difference. Is the percentage of Neanderthal DNA we harbor a percentage of 100% of their DNA or a percentage of the .3% of their DNA that wasn’t already shared by humans?

    I know, this question is probably so deep in ignorance (positive sense of the word) that it’s unanswerable as asked. But your insight would be of interest.

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  35. 35. rshoff2 12:52 pm 02/4/2014

    The reason I ask is to gain perspective on whether the Neanderthal DNA is leftover junk that we happen to carry as a result of ancient history, or if the Neanderthal species is still a force that we can rely upon for future evolution depending upon our future mating behaviors. If Neanderthals were more adaptable to humanity’s future environment, will be be able to use those genes to evolve to a more Neanderthal state? Or are their evolutionary advantages to future environments lost to us forever?

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  36. 36. paleoneandertal 3:38 pm 02/4/2014

    Although I am very old, I feel I must draw attention to the prejudice against my ancestors displayed in the stories of ugly dwarfs and giants dwelling in caves, which I suggest were related by Sapiens mothers to their daughters, and handed down, century on century until collected and recorded by the Grimm brothers not so long ago. I always sensed that there must have been something behind these tales, and now I can see a possible reason. Clearly, Neandertal males were not considered by the Sapiens mothers as suitable mates for their daughters! But they must have exuded some charms.
    As a confirmed skeptic for over 80 years, I am only presenting this as a working hypothesis to be investigated. It would upset me if it were treated as some other working hypotheses such as gods, afterlife and heavens. “It’s all in the mind, you know.” (Goon Show)

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  37. 37. Jennie2 4:34 pm 02/4/2014

    I’m waiting for a complete description of what a Neanderthal person would have been like in behavior/personality/etc. We need more differentiation between Neanderthal & Homo Sapiens as far as practical matters are concerned. How exactly were they different?

    It would be interesting to find a person alive who has a majority Neanderthal genome.

    I also find it very interesting that Eurasians have Neanderthal genes while most Africans do not. What exactly did that confer on Eurasians?

    I’m also reminded of a statement by a teacher friend of mine who said the teachers at their school had observed that mixed-race children tended to be overall smarter than single-race children (on average). And incestuous inbreeding can cause Autism/Asperger’s traits of genius (and stupidity) which can often create people who have one area of extreme genius but are otherwise ‘average’. It makes me realize that we really don’t know what causes ‘genius’ or intelligence in general.

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  38. 38. MyLittleRadish 7:02 pm 02/4/2014

    Seems a cavalier waste of time comparing what and where we got our present day genetic materials…that could go back to the single-celled creatures and worms and fish and reptiles.

    What matters more to live humans is eliminating the damage done by DES and like-chemicals in the womb, endocrine disruptors, depression meds,nuclear waste,radioactive waste, etc.: Yes, that means moving forward.

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  39. 39. rshoff2 2:31 pm 02/5/2014

    monpetitechou – Not such a cavalier waste of time if you can use the past to help predict the future. And if you leverage that into helping to make more beneficial choices. Yes, that means using the information to best decide *how* to move forward!

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  40. 40. Leslie Fish 3:15 am 02/7/2014

    Oh, for heaven’s sake, shed the old prejudices! Neanderthal, Cro-Magnon, Java and Denisovan Man were not different species but different *races* — and Modern Man is, yes, the product of Race-Mixing. Oooh, oooh! Get over it.

    By the way, just how was Neanderthal DNA collected, and how completely was the Neanderthal genome analyzed? Without complete genome analysis, just how can Neanderthal DNA be adequately compared with Modern Man’s?

    –Leslie < Fish

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  41. 41. AndreaPMckinney 2:45 pm 02/11/2014

    greenhome 123

    You say that your percentage of Neanderthal genome puts you in the 98 percentile for humans – is that correct? Since I have an even higher percentage of Neanderthal genes I would like to find out where you got the info, and whether I could find out if mine puts me in the 99 percentile!

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  42. 42. Silkysmom 3:40 pm 08/22/2014

    “But the researchers also found that people today carry Neandertal genes that are associated with diseases including Crohn’s, type 2 diabetes and lupus.”

    “While not everyone with type 2 diabetes is overweight, obesity and lack of physical activity are two of the most common causes of this form of diabetes.”

    I highly doubt that Neandertals were overweight or lacked physical activity!!

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