The Science of Sustainability

Knowing Neanderthals

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Some of my ancestors (and maybe yours) before we wiped them out.
Image courtesy of Victuallers, Wikimedia Commons.

One of the more interesting things to come out of all the cheaper, more robust DNA sequencing technology has been our deeper understanding of human history. Now that we can get a pretty good read from 30,000 year old Neanderthal DNA, we can tell that humans and Neanderthals had babies together. The key to figuring this out was the fact that some human ancestors had more opportunity to hook up with Neanderthals than did others.

See, around one million or so years ago, there wasn’t a lot of difference between a human and a Neanderthal. We were one big happy species living in Africa. Then, maybe 800,000-900,000 years ago, two of these groups became separated from one another. Each group built up changes in their DNA so that they gradually became two separate species. One group stayed in Africa and became our ancestors while the other group, who became Neanderthals, left Africa through the Middle East and spread across Europe and Asia.

Now at this point these two groups still shared a lot of the same DNA. After all, they started from the same pool of DNA in the relatively recent past. If they all came back together and started having kids together, we wouldn’t be able to easily tell there had been interbreeding. We would see a lot of Neanderthal DNA in human DNA, but it would be very tricky to distinguish DNA that we originally shared from recently reintroduced Neanderthal DNA.

The reason we can more easily see that there was interbreeding is because of another group of Africans that decided to leave Africa via the Middle East. These folks left somewhere between 120,000 and 60,000 years ago and stumbled across the Neanderthals already out there in the world. This group of Africans eventually supplanted the Neanderthals and went on to become Europeans, Asians, Native Americans and everyone else out there (except for the Africans who stayed behind).

A couple of years back, scientists were able to get a good read of a few Neanderthals’ DNA. They then compared this DNA to lots of other people’s DNA. What they found was that Africans and Neanderthals shared less DNA than did Neanderthals and everyone else. They interpret this result to mean that Africans and Neanderthals never had the chance to breed while the ancestors of the rest of humanity and Neanderthals did.

What this all means is that we can see the Neanderthal in some of us because only some of our ancestors had kids with Neanderthals. If this weren’t the case, then we wouldn’t be able to easily tell that interbreeding had happened.

Of course now that we have good evidence for this, people are trying to link weird, mostly European traits with Neanderthals. For example, there is a whole lot of chatter out on the web that Rh negative blood comes from Neanderthals. While this may be true, there isn’t any real evidence to support it. That part of Neanderthal DNA has yet to be sequenced. (Although we do know that at least some of them had O type blood which isn’t surprising since it probably arose at least one million years ago when we were all still one big happy species.)

Another idea is that red hair came from Neanderthals. Again, maybe, but there isn’t any evidence yet to support it. At least one Neanderthal did have red hair but he got it from a DNA difference not seen in people. In other words, there is evidence to support that Neanderthals had red hair too but not that we got it from them.

What our ancestors apparently got from Neanderthals (besides a good time) was immunity genes to help them survive. When our ancestors burst out of Africa, they encountered germs they had never seen before (think Native Americans and smallpox). The Neanderthals had adapted to these germs and so were more resistant to them. The human-Neanderthal hybrids (Humanderthals?) would have survived better than the humans meaning they were more likely to survive. The rest is the history of people living outside of Africa.

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Dr. Barry Starr

About the Author ()

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the Stanford Department of Genetics and The Tech Museum of Innovation. Together these two partners created the Genetics: Technology with a Twist exhibition. Read his previous contributions to QUEST, a project dedicated to exploring the Science of Sustainability.
  • John Fiorentino

    I was very surprised to have read this coming from Barry.

    Much of what is presented here is dated. More recent studies have shown that it is extremely doubtful that Neanderthals inter-bred with humans.

    What Barry is using here as a basis for his thesis is what is best termed "ancient DNA."

    One of the main drawbacks of working with ancient DNA is that these studies are working with what is considered "low quality DNA."

    Degradation of the DNA molecules caused by various factors which create upper limits beyond which no DNA is likely to survive.(1)

    (1) (See ^ Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos RF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M (2012). "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils". Proc. R. Soc. B 279: 4724-33. doi:10.1098/rspb.2012.1745.

    It wasn't until 2007 that a process called Single primer extension (abr. SPEX) amplification was introduced to address post mortem DNA modification damage.(2)

    (2) Brotherton, P; Endicott, P; Sanchez, Jj; Beaumont, M; Barnett, R; Austin, J; Cooper, A (2007). "Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post-mortem miscoding lesions" (Free full text). Nucleic Acids Research 35 (17): 5717–28. doi:10.1093/nar/gkm588. ISSN 0305-1048. PMC 2034480. PMID 17715147.

    Some examples of errors include "Dinosaur DNA" which turned out to be Human Y-chromosome (3)

    (3) ^ Zischler H, Höss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J (May 1995). "Detecting dinosaur DNA". Science 268 (5214): 1192–3; author reply 1194. doi:10.1126/science.7605504. PMID 7605504.

    Also various bacterial DNA samples which are in fact probably not from ancient times.(4)

    (4) Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, Brand T, Gilbert MT, Zuber MT, Bunce M, Rønn R, Gilichinsky D, Froese D, Willerslev E (September 2007). "Ancient bacteria show evidence of DNA repair". PNAS 104 (36): 14401-5. doi:10.1073/pnas.0706787104.
    PMID 17728401.

    I'd also like to point you to a very recent study from Aug. of 2012 the headline of which is "Neanderthals did not interbreed with humans, scientists find" which everyone here can read about here:

    http://www.telegraph.co.uk/science/science-news/9474109/Neanderthals-did-not-interbreed-with-humans-scientists-find.html

    It's my opinion, hopefully without offending anyone, that there seems an over-abundance of conjecture and inference in today's "science." presentations.

    Most notably in the made for television series' which seem to permeate the cable channels. Unproven, non peer-reviewed, and generally poorly presented scenarios are offered as fact in many cases without the slightest shred of valid scientific evidence to back them up.

    The average citizen has little concept of the use of inference in science and oftentimes accepts poorly construed theories and conjecture as fact.

    And, (to my dismay at least) even some "experts" have a poor understanding of scientific principles.

    I think entertaining television programming is a great outlet for many people. But I do think it should be conspicuously labeled as such.

    Frankly, when I hear someone start to talk about what some dinosaur did 200 million years ago, my first inclination is to reach for the remote. Unless I happen to be in the mood for some sci-fi.

  • Alicia Martin

    While there have been two sides of the Neandertal and human interbreeding story supported by scientists, I think there are a few issues with Fiorentino's argument that need clarification.

    The quality control on the samples used to generate the draft of the Neandertal genome is extensive (including a 170 pg supplement on the original paper). This research is not dated. It is from 2010. Of the citations that Fiorentino's response contributes, only the first one is newer than the Green et al paper where the human Neandertal interbreeding argument stems from. The paper that the response cites is simply about dating bones, and so is irrelevant to the argument at hand.

    The original Neanderthal draft genome paper is from 2010 (Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H., et al. (2010). A draft sequence of the Neandertal genome. Science (New York, N.Y.) 328, 710–722.), and the paper documenting the dating of the interbreeding is from this year (Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012) The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genet 8(10): e1002947. doi:10.1371/journal.pgen.1002947). The Reich and Pääbo labs are some of the leading groups in the world working on ancient DNA right now, and they've made great strides to avoid contamination. In my opinion, their greatest QC step so far has been genotyping all of the field workers that handle bones so they can mask out contamination from the genome. This portion of Fiorentino's argument is rather misleading:

    "It wasn't until 2007 that a process called Single primer extension (abr. SPEX) amplification was introduced to address post mortem DNA modification damage"

    The project was done after this. This is also confusing:

    "Degradation of the DNA molecules caused by various factors which create upper limits beyond which no DNA is likely to survive."

    The cited study states that DNA degrades 400 times slower than previously predicted. Additionally, it gives a half life, which is exponential. It would take a very long time for 100% of the DNA in Neandertal bones to decay (much longer than the split time between humans and Neandertals).

    The crux of the interbreeding argument lies in fact that Neandertals are genetically more similar to Asians and Europeans than Africans. It wouldn't make sense for Neandertals to be less like African groups only if their genome was low quality or contaminated (especially after controlling for the field workers' genotype data). In fact, because African DNA is more heterozygous generally, Neandertal DNA might resemble it more if it were low quality and contained many errors.

    As a scientist, this opinion is somewhat disappointing to me:

    "It's my opinion, hopefully without offending anyone, that there seems an over-abundance of conjecture and inference in today's "science." presentations.

    Most notably in the made for television series' which seem to permeate the cable channels. Unproven, non peer-reviewed, and generally poorly presented scenarios are offered as fact in many cases without the slightest shred of valid scientific evidence to back them up."

    The interbreeding argument is based on a peer-reviewed Science article, which is one of the most prestigious journals in science. This argument did not stem from TV. I agree that media often misconveys science, but I would encourage the general public to read the articles that academic arguments stem from before claiming that scientific research generally is flawed.

    Finally, the researchers that argued against interbreeding relied on the Neadertal genome to generate their argument. This means they reanalyzed the ancient DNA and took a statistical argument rather than a contamination or decay argument to try to poke holes in the interbreeding theory.

    • John Fiorentino

      Ms Martin asserts that: Of the citations that Fiorentino's response contributes, only the first one is newer than the Green et al paper where the human Neandertal interbreeding argument stems from.

      She further states the research upon which her argument is based is from 2010.

      While she is correct that my first citation is newer (2012) she ignores my other reference here: which is also from 2012:

      http://www.telegraph.co.uk/science/science-news/9474109/Neanderthals-did-not-interbreed-with-humans-scientists-find.html

      That reference points to a rather readable article, the title and subtitle of which are:

      Neanderthals did not interbreed with humans, scientists find

      The genetic traits between humans and Neanderthals are more likely from a shared ancestry rather than interbreeding, a British study has suggested.

      The first paragraph of that article reads: Cambridge University researchers concluded that the DNA similarities were unlikely to be the result of human-Neanderthal sex during their 15,000-year coexistence in Europe.

      Their analysis, published in the journal Proceedings of the National Academy of Sciences (PNAS), contradicts recent studies that found inter-species mating, known as hybridisation, probably occurred.

      The actual study to which the article refers is titled:

      Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

      Anders Eriksson1 and
      Andrea Manica1

      Edited by Francisco Mauro Salzano, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, and approved July 20, 2012 (received for review January 19, 2012)

      and can be referenced here: http://www.pnas.org/content/109/35/13956

      So "statistically speaking" Ms. Martin is off the mark to a rather large degree.

      Ms. Martin also says: As a scientist, this opinion is somewhat disappointing to me:

      "It's my opinion, hopefully without offending anyone, that there seems an over-abundance of conjecture and inference in today's "science." presentations."

      I will say it's also disappointing to me, but that doesn't have any relationship to the issue.

      I will, if I might provide a quote from a scientist long dead, who apparently held that opinion YEARS before ( at my advanced age) even I did:

      In this piece the writer is making reference to "Darwinism"

      "In recent years there has been a disturbing trend toward scientific dogmatism in certain areas of science — Pronouncements by notable scientists and scientific organizations about "only one scientifically acceptable explanation" for events which are clearly outside the domain of science — like all origins are — can only destroy the curiosity of those who must carry on the future work of science."

      "Humility, a seeming natural product of studying nature appears to have largely disappeared. At least its visibility is clouded from the public viewpoint. Extrapolation backwards in time until there are no physical artifacts of certainty that can be examined requires sophisticated guessing, which scientists prefer to refer to as inference. Since hypotheses, the product of scientific inference are virtually the stuff that comprises the cutting edge of scientific progress, inference must constantly be nurtured. However, the enthusiasm that encourages inference must be matched in degree with the caution that clearly differentiates inference from what the public so readily accepts as scientific fact. Failure to keep these two factors in balance can lead to sterile or seduced science."

      The writers' name was Dr. Wernher von Braun

      • Alicia Martin

        I think the bottom line is that there is a high quality Neandertal genome that has undergone substantial quality control to avoid contamination, and that scientists have used statistical models to argue for Neandertal interbreeding with some opposition via alternative statistical models. Both sides of peer-reviewed literature should be carefully read, and the full analysis should shape your opinion.

        A few more clarifying points…

        Fiorentino states that: "While she is correct that my first citation is newer (2012) she ignores my other reference here: which is also from 2012: http://www.telegraph.co.uk/sci…" The first sentence of my response stated that, "While there have been two sides of the Neandertal and human interbreeding story supported by scientists…" I openly acknowledged this reference here. I was referring to Fiorentino's literature citations as dated, rather than his media references.

        As we both mentioned, media often misconvey science, so rather than referring to the news release, I was referring to journal articles and research itself rather than second hand information throughout my response. I was referring to the Eriksson & Manica paper when I said: "This means they reanalyzed the ancient DNA and took a statistical argument rather than a contamination or decay argument to try to poke holes in the interbreeding theory."

        Indeed, the paper referred to by the link Fiorentino presents (Eriksson A, Manica A (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proc Natl Acad Sci USA, 10.1073/pnas.1200567109.) states that, "To be able to directly compare our model to the real data and simulations in Green et al. (22), we closely followed the analyses described in SOM 17 of that paper." Additionally, the authors state that they used approximate Bayesian computation (ABC) generalized linear models to assess a variety of demographic parameters. This means they used statistical models as a basis for their argument. I think Fiorentino misunderstood me in this pedantic remark: "So "statistically speaking" Ms. Martin is off the mark to a rather large degree."

        • John Fiorentino

          It is not my intent nor my desire to bicker with Ms. Martin, whose formal qualifications in this area I am quite sure would trump mine.

          However, when a "scientist" such as Ms. Martin accuses me (essentially a layman) of making a "pedantic" remark, I'm afraid I really must chuckle.

          One definition of "pedantic" is thus: "Characterized by a narrow, often ostentatious concern for book learning and formal rules." There are other worded slightly differently definitions of course, but I think everyone gets the picture.

          I'll make the assumption that Ms. Martin has a degree of some type in the life sciences, perhaps a Doctorate. Unless Ms. Martin's Degree is "honorary" you can probably assume that she herself held a "concern for book learning and formal rules." (Maybe she was even "ostentatious" about it.) (Maybe she still is?)

          Just to be fair, Dr. Manica also made the following statement, which I'm not so sure needed to be said, but was said anyway……."hybridisation between Neanderthals and humans can never be disproved entirely."

          Ms. Martin in her first response also stated: "I agree that media often misconveys science, but I would encourage the general public to read the articles that academic arguments stem from before claiming that scientific research generally is flawed."

          The problem here of course is that the "general public" for the most part lacks the ability to access MOST articles published in scholarly journals. Many also lack the ability to really understand what they are reading, provided they could get access.

          That is why it is the job of science to provide forums (such as this one) for what might be defined as "open science."

          Ms. Martin says…."This means they used statistical models as a basis for their argument. I think Fiorentino misunderstood me………"

          No, I didn't misunderstand anything, I believe it is you who misunderstood, I was referring to the difference between 1 and 2 re: the references I provided.

          I'm quite familiar with Bayesian statistical models and I will say that if Manica relied too heavily on the good Presbyterian minister Bayes, then perhaps her study should be scrutinized more closely, being the frequentist that I am. (That doesn't mean I think "Neanderthals" and humans interbred)

          Just as an aside the link to the Telegraph article which you posted in your last response goes nowhere http://www.telegraph.co.uk/sci%E2%80%A6/

          so I will repost it correctly for those who might wish to read it.

          http://www.telegraph.co.uk/science/science-news/9474109/Neanderthals-did-not-interbreed-with-humans-scientists-find.html

          Regards,

          JF

  • Barry

    Good discussion so far! What I conclude is that earlier technical difficulties with looking at ancient DNA have for the most part been overcome and that we have a solid genome for Neanderthals. This is what I remembered but it would have been very time consuming to dredge up the articles myself so thanks Alicia! I probably should have mentioned the competing theory that there was no inbreeding or at least put in a few weasel words to indicate that it isn't a done deal.

    John brings up an excellent point in his last comment where he asks how a nonscientist is supposed to figure out the validity of the science behind some of the discoveries out there. While I had appreciated that wading through the jargon is beyond most people, I had forgotten about the lack of access to a lot of the studies because they are published in a journals that make you pay to see them. (As a Stanford employee I have access to a whole lot of them.) This is starting to change with all of the PLOS journals but there is still a whole lot hidden away unless you pay.

    • John Fiorentino

      I think a great idea might be a site where scientific questions are submitted by the public to a (perhaps committee) of editors, and 1 question is chosen every week for comments from the scientific community.

      The details could be worked out fairly easily I should think.

      I believe it would prove to be a great asset to all involved.

      Happy Holidays!!

      JF

    • John Fiorentino

      I recently e-mailed the authors of the article

      The Date of Interbreeding between Neandertals and
      Modern Humans

      referring to interbreeding between Neandertals and Humans. I will post any response I get.

  • John Fiorentino

    I recently corresponded with the authors of the article:

    The Date of Interbreeding between Neandertals and
    Modern Humans

    I will post any response I get.

    • John Fiorentino

      No response on two tries from any of the three authors. Seems nobody wants to answer any questions?

      I wonder why?

  • Barry

    This might be worth a watch: http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html PBS usually does a great job on this stuff.