Neandertal admixture, revisiting results after shaken priors

By Razib Khan | January 26, 2011 9:14 am

After 2010’s world-shaking revolutions in our understanding of modern human origins, the admixture of Eurasian hominins with neo-Africans, I assumed there was going to be a revisionist look at results which seemed to point to mixing between different human lineages over the past decade. Dienekes links to a case in point, a new paper in Molecular Biology and Evolution,  An X-linked haplotype of Neandertal origin is present among all non-African populations. The authors revisit a genetic locus where there have been earlier suggestions of hominin admixture dating back 15 years. In particular, they focus on an intronic segment spanning exon 44 of the dystrophin gene, termed dys44. Of the haplotypes in this they suggested one, B006, introgressed from a different genetic background than that of neo-Africans. The map of B006 shows the distribution of the putative “archaic” haplotype from a previous paper cited in the current one from 2003. As you can see there’s a pattern of non-African preponderance of this haplotype. So what’s dystrophin‘s deal? From Wikipedia:

Dystrophin is a rod-shaped cytoplasmic protein, and a vital part of a protein complex that connects the cytoskeleton of a muscle fiber to the surrounding extracellular matrix through the cell membrane. This complex is variously known as the costamere or the dystrophin-associated protein complex. Many muscle proteins, such as α-dystrobrevin, syncoilin, synemin, sarcoglycan, dystroglycan, and sarcospan, colocalize with dystrophin at the costamere.

Dystrophin is the longest gene known on DNA level, covering 2.4 megabases (0.08% of the human genome) at locus Xp21. However, it does not encode the longest protein known in humans. The primary transcript measures about 2,400 kilobases and takes 16 hours to transcribe; the mature mRNA measures 14.0 kilobases….

Dystrophin deficiency has been definitively established as one of the root causes of the general class of myopathies collectively referred to as muscular dystrophy. The large cytosolic protein was first identified in 1987 by Louis M. Kunkel…after the 1986 discovery of the mutated gene that causes Duchenne muscular dystrophy (DMD) ….

OK, so we’ve established that this is not an obscure gene. Here’s the abstract of the new paper:

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of H. sapiens who left Africa between 80 Kya and 50 Kya to colonize the rest of the world. Here we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

The authors do consider the possibility that the B006 haplotype is derived from a common haplotype spanning Eurasian hominins and northeast Africans. They reject this on the grounds that the only African populations where such sharing with Eurasians occurs occurs are known to have been subject to recent back-migration (this presumably includes the Maasai). Additionally, they assert that “oldest lineages tend to be found in South rather than North-Eastern Africa.” I’m not totally sure about the context of this assertion. Oldest lineages overall? Or for this particular locus?

In any case, here’s a table from the 2003 paper:

The peculiarity of B006 is its restriction to non-Africans, and its variance. Remember that the null hypothesis presumes and “Out of Africa,” where non-African distinctiveness should be relatively shallow. The current paper illustrates the model for how the B006 haplotype slipped into the non-African genetic background. Interestingly the authors note the presence of B006 in “a remote community of isolated indigenous Australians living in Central Australia.” Naturally the big difference between now and 2003 is the ability to compare with the Neandertal draft reference genome. They note that “In the Neandertal sequence, no information is available for 28 of these sites, 36 sites represent ancestral alleles and 13 derived alleles. Importantly, three of the derived alleles (rs17243319, rs1456729 and rs11796299 in Table S2) are absent from the African chromosomes, as in the case of the derived G of rs11795471 from within B006. Moreover, all derived alleles shared with Neandertals occur at high frequencies (0.75 and more) on a background of the extended B006 haplotype (Figure 3 and Table S2) as expected in a segment of recent Neandertal origin.”

Overall this paper illustrates two trends. First, the general one whereby research groups are going to revisit loci which exhibit signatures of admixture with Neandertals and other assorted Eurasian hominins. Prior to 2010 these results were peculiarities, published, but generally not integrated into a bigger theoretical framework (by this, I mean the scientific community did not pay much attention to the authors’ attempts to integrate their research into a counter-narrative to “Out of Africa”). Second, there will be the specific focus on particular genes with an interest in ascertaining functional significance, and possible adaptation. This is hinted at in the last sentence of the discussion: “Considering such early encounter of H.sapiens with Neandertals, a question may be raised: was this encounter coincidental and without important evolutionary consequences or…did it facilitate adaptations to novel environmental conditions that actually contributed to the successful expansion of human migrants from Africa to other continents?” Indeed.

Citation: Vania Yotova, Jean-Francois Lefebvre, Claudia Moreau, Elias Gbeha, Kristine Hovhannesyan, Stephane Bourgeois, Sandra Bédarida, Luisa Azevedo, Antonio Amorim, Tamara Sarkisian, Patrice Avogbe, Nicodeme Chabi, Mamoudou Hama Dicko, Emile Sabiba Kou’ Santa Amouzou, Ambaliou Sanni, June Roberts-Thomson, Barry Boettcher, Rodney J. Scott, & Damian Labuda (2011). An X-linked haplotype of Neandertal origin is present among all non-African populations Mol Biol Evol : 10.1093/molbev/msr024

  • Insightful

    German Dziebel raised some intriguing points from this study on Dienekes’ blog:

    1. “Needless to say, they didn’t find B0006 in Neanderthals. They simply attribute it to Neanderthals.”

    2. “What is most interesting is that, according to the map, B0006 is much more frequent in the Americas, where there are no Neanderthals.”

    Razib, what are your thoughts concerning these 2 points raised by German Dziebel?..

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    i haven’t read german’s comment, so no context. but, i don’t know what #1 is supposed to mean. this is a historical science of inference, so yeah, there’s no neandertals running around. #2, i don’t find a strong objection. the paper tacitly endorses an early admixture model, out-of-africa-with-a-pause. the higher frequency in the americas then has two (not exclusive) explanations

    1) selection, particularly in siberia

    2) surfing the wave of advance, so that it stochastically rose in frequency through bottlenecks.

  • http://www.kinshipstudies.org German Dziebel

    Selection is very unlikely because, if the introgression occurred all the way down in West Asia (where Neanderthals were found) and wasn’t immediately selected against (even further south in East Africa where B006 is found), the new gene can hardly be positively selected for in a Subarctic/Arctic environment, which your Siberians had to traverse in order to get to the New World.

    Surfing the wave of advance is a popular theory but if a “stochastic” process affects the least common gene in a population (why didn’t instead B001 end up at 100% frequencies in the new World?) and drives it despite bottlenecks all around the globe, then it looks like selection. But the selection argument is equally unlikely. So we end up having two very unlikely explanations. The most parsimonious one is that B006 is most frequent in the New World because it arose there. But there are no Neanderthals to be found in the New World. Hence, what’s called “Neanderthal admixture” is better explained as the common descent of non-Africans and Neanderthals (with speciation into “us” taking place somewhere in or close to America), with Africans eventually deriving from early non-Africans (with chimp-like homoplasies affecting Sub-Saharan Africans). We just have a huge fossil gap in the New World and Asia, but time will fill it in.
    In the meantime, linguistics and kinship studies attest to greater diversity in the new World than in the Old World (especially in Africa), which is consistent with B006 divergence.

    B007 is strictly African-specific lineage. If humans expanded out of Africa, we would have found it outside of Africa at decreasing frequencies. This is not the case. B007 could only arise in Africa AFTER B006 and B001 had evolved.

  • gcochran

    Point 1 is simply false: they did find the unique SNP of this haplotype in the Neanderthal genome, and although not all the other SNPs were available due to the not-great data quality, those that were available matched. There is of course no huge fossil gap in the Americas, because (North America in particular) the place is full of literate farmers, quarries, and people using backhoes. There are no > 15k year old hominid fossils in the Americas, nor are there any old stone tools. Tools are _much_ more common than fossils – there must be 10,000 acheulean tools found for every human fossil -and when nobody has found a single one in the Americas, there’s a simple explanation. There were no humans in North America back then.

    Note that although Australia is a far less fertile continent that would have had low population density for hunter-gatherers. with maybe a tenth as many people around today to stumble onto fossils, they have found a fair number of skeletons older than 15k years, going as far back as ~45k years old. And lots of old stone tools as well.

  • gcochran

    Hint: a quote from Adventures in the Bone Trade: “We’ve probably seen 100,000 handaxes this morning.” That happens in Africa at a favorable site. . The total number in the US: zero.

  • http://www.kinshipstudies.org German Dziebel

    “Point 1 is simply false: they did find the unique SNP of this haplotype in the Neanderthal genome, and although not all the other SNPs were available due to the not-great data quality, those that were available matched.”

    I agree that point 1 was confusing. I posted in-between other things. But, in any case, the “Neanderthal admixture” story postulates a unique event leading to a systematic pattern in the phylogeny. B006 is found all over the globe and its the most divergent lineage. To attribute something like this to a unique historical accident: Neanderthals contributing a lineage in a one-way gene exchange with modern humans at a periphery of Neanderthal distribution (West Asia) is a rather unlikely occurrence. To use it to interpret modern data requires some factual attestation, which is of course impossible.

    “There is of course no huge fossil gap in the Americas, because (North America in particular) the place is full of literate farmers, quarries, and people using backhoes.”

    This is unclear. How can backhoes predict the age of human arrival?

    “Tools are _much_ more common than fossils – there must be 10,000 acheulean tools found for every human fossil -and when nobody has found a single one in the Americas, there’s a simple explanation. There were no humans in North America back then.”

    Illogical, gcochran, illogical. A more parsimonious explanation is that WE haven’t found them. The rest is speculation. The age of oldest tools and fossils is growing on all continents, including the New World. It’s just in the New World the rate of archaeological and paleontological recovery is slower than in Africa and Europe. But this again has nothing to do with the date of human arrival. It has to do with 1) low Pleistocene population size and density (low levels of genetic diversity in the New World) support that; 2) an adaptation that relies on soft technologies and perishables; 3) politics in American archaeology that make systematic exploration of pre-Clovis layers potentially career-damaging; 4) lack of funds to recover a demographically sparse ancient population.

    BTW, I just came back from Argentina, where I visited a Guarani village. They showed me their traditional toolkit. It didn’t have lithics at all.

    A couple of other observations: until 2005 we had no fossil remains of chimps. Did you use to believe that they derive from Pygmies in the past 15,000 years? Charles Darwin didn’t base his Origins on any fossil finds. He predicted them. We haven’t moved past Darwin that much in the New World. That’s all. It’s our problem, not the problem of “the first man in the New World.”

    There’re no shortcuts in doing science, gcochran. You need to take a big-picture view.

    “Note that although Australia is a far less fertile continent that would have had low population density for hunter-gatherers. with maybe a tenth as many people around today to stumble onto fossils, they have found a fair number of skeletons older than 15k years, going as far back as ~45k years old.”

    Good point. But up until early 1980s there were no finds earlier than 10,000 years in Australia. And all archaeologists claimed that Australia was peopled only then. Future proved them wrong. Let’s not repeat their mistakes.

  • http://www.kinshipstudies.org German Dziebel

    ““We’ve probably seen 100,000 handaxes this morning.” That happens in Africa at a favorable site. . The total number in the US: zero.”

    I know this. And I know archaeologists who “defected” to the Clovis I camp after having experienced the sheer number of tools in Europe and Africa. But to claim that humans were absent in the Americas is a non-sequitur. Just leave this fact as it is. Don’t force an interpretation on it. Archaeology is a moving target. Time will sort it out. For comparison: there are 140 (!) unique language families in America and only 20 in Africa (on a good day!) This won’t change. Every language has tens of thousands of words. It takes time and isolation for these words to differentiate beyond the recognition of a professional linguist. Prior to 40-45K (and in some places even later), we don’t even know what species ultimately manufactured what tools. But language is a uniquely human product. You can’t miss here.

    Plus, read the first published mtDNA study. It’s Johnson, M.J., D.C. Wallace, S.D. Ferris, M.C. Rattazzi, and L.L. Cavalli-Sforza. 1983. Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns. J Mol Evol 19:255–271. You’ll see that the basal haplotype was found at highest frequencies in the Americas? Exactly what X chromosome shows us.

  • gcochran

    I have no real expectation of changing your mind, because you’re nuts. Even nuttier than the average bear, which is saying something. In fact, floridly crazy, although not crazy enough to set a record: you see, I already have _Out of Antarctica_ on my bookshelf. I think you’d have to claim that humans originated in Atlantis or Lemuria to top that.

    Reminds me of another book I once read about humans originating in the Americas. I remember that the author (a Ph.D. in anthropology, natch) had the site locations for his digs appear to him in dreams – nice touch.

    However, some people read this blog, and it wouldn’t do to let them think that you could be trusted to give a correct account of existing evidence, calculate anything, make a correct logical inference, or indeed think your way out of a paper bag. So I occasionally bother to point out what a fool you are.

  • http://entitledtoanopinion.wordpress.com TGGP
  • http://www.kinshipstudies.org German Dziebel

    “However, some people read this blog, and it wouldn’t do to let them think that you could be trusted to give a correct account of existing evidence, calculate anything, make a correct logical inference, or indeed think your way out of a paper bag. So I occasionally bother to point out what a fool you are.”

    There’s an amateur crackpot out here on the web, who also turns mainstream science into a fanatical belief. He also tries to correct me for the sake of other people. The problem with people like you and him is that you take pride in having very elementary skills (like calculating or reading textbooks) but you just can’t take it a notch up. You can’t do the thing called “thinking.” It’s not going to take much effort for me to recite the out of Africa theory and all the data points that went to prove it. I just think it hinges on cultural beliefs and not on science.

    “Reminds me of another book I once read about humans originating in the Americas. I remember that the author (a Ph.D. in anthropology, natch) had the site locations for his digs appear to him in dreams – nice touch. ”

    You’re talking about Jeffrey Goodman, the author of “American Genesis.” He claims to have a Ph.D. in psychic archaeology. What does it have to do with me? I have two doctorates in respectable fields from elite universities.

    “I have no real expectation of changing your mind, because you’re nuts.”

    Nuts? You believe that humans originated in Africa and then somehow crossed the Bering Strait to the Americas. I believe that humans originated in America (from an Old World hominid ancestor but you need isolation to speciate, don’t you?), crossed the Bering Strait and ended up in Africa. How am I more nuts than you?

  • onur

    There’s an amateur crackpot out here on the web, who also turns mainstream science into a fanatical belief. He also tries to correct me for the sake of other people. The problem with people like you and him is that you take pride in having very elementary skills (like calculating or reading textbooks) but you just can’t take it a notch up. You can’t do the thing called “thinking.”

    German, is that “amateur crackpot” me? I am asking this because I am a self-avowed amateur in genetics and human origins related stuff and you and I had previously discussed Out of Africa and Out of America theories on this blog and Dienekes’ blog; though our discussions had been in a pretty polite and non-fanatical manner.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    onur, it’s not always about you. german is obviously talking about greg.

  • gcochran

    With ‘you and him’, it would seem that Dziebel was talking about me and someone else, although I couldn’t say who. Sounds like a fine fellow, though. Of course, in this case, ‘ him’ might mean my invisible six-foot rabbit.

  • Justin Giancola

    I like you guys. This place is certainly not stuffy. It can certainly bring “teh funneh” like a bored and disgruntled hipster messageboard.

  • onur

    German was obviously talking about Greg and someone else.

  • http://www.kinshipstudies.org German Dziebel

    “German was obviously talking about Greg and someone else.”

    No, onur, it’s not you. Our conversations were indeed polite and not ad hominem. Also, gcochran is not an “amateur crackpot.” But the other fellow is. Gcochran just considers amateur crackpots “fine fellows” and sports the same unpolished manners and wits.

  • onur

    Also, gcochran is not an “amateur crackpot. But the other fellow is.”

    I already know that you used the expression “amateur crackpot” only for that someone else and not for Gregory Cochran.

  • dave chamberlin

    I would just like to add that I wish that the world had more German Dziebels and Greg Cochrans in it. You two are absolutely unique, and while I may suspect one of the you two of you as off base, so what, it is a great read.

    Anyway you look at it, I think we are all looking forward to the truth remaining far stranger than fiction as new genetic results continue to pour in revealing our heretofore lost past. There will be many more days here when new results are revealed, and all the bigwigs weigh in with their excited opinions, and insignificant others like myself are just fascinated flies on the wall, grateful to be alive in such interesting times.

  • Pingback: After the evolutionary revolution | Gene Expression | Discover Magazine()

  • http://washparkprophet.blogspot.com ohwilleke

    The most notable thing about B006 is that it has a 9% frequency, compared to 1%-4% for Neanderthal autosomal DNA as a whole.

    While this could be a product of natural selection, an alternative is Haldane’s law, which states that hybrids are generally homozygotic (i.e. XX rather than XY in the hominin case). If Haldane’s law applies to human-Neanderthal hybrids then it follows that hybrid children will be daughters rather than sons.

    This elevates the expected amount of X linked chromosome introgression to 50% greater than for the genome as a whole, and more if Haldane’s law has some effect in the second generation.

  • Pingback: Neandertal (haplotype) in the family! | Gene Expression | Discover Magazine()

  • http://abugblog.blogspot.com Blackbird

    Mmm, changing topic from the comment thread, and into the subject of the post, I wonder if somebody is testing this in Denisovans, which has much better coverage than the Nearderthals. It would shed some light into the direction of the introgression I guess.

  • http://www.kinshipstudies.org German Dziebel

    I forgot to mention another intriguing connection between Neanderthals and Amerindians. The 2 Neanderthals tested for blood groups turned out to be type O. This suggests that blood group may have been prevalent among Neanderthals. Admixture between humans and Neanderthals is not likely here. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629777/

    And type O is, again, most prevalent in Amerindians reaching 100% frequencies in South America. And it’s the least frequent in Africa. There’s a long standing contention that type O, being the universal donor blood, predated other blood types, specifically A and B.

  • BoNo

    gcochran wrote;

    “We’ve probably seen 100,000 handaxes this morning.” That happens in Africa at a favorable site. . The total number in the US: zero.”

    Ever wondered why?!

    Handaxes found in the Americas have consequently been dismissed as geofacts
    If you want to understand why thee are no handaxes on the official records in the US you may remember the official mantra from the last 50 years; “There are no handaxes in North America. Period”.

    May I remind you that a eventhough professionals have repported a number of paleolitic artefact from America they have always been disregarded as “geofacts” and/or “anomalies”.
    Perhaps you have heard about highly regarded professionals standing by their analysis of 120+ thousand year old artefacts – just to ruin their careers?

    Virginnia Steen-McIntyre – once a very promising geologist – for one. Her repport from Hueyatlaco, Mexico of 1962 (!) about a 250.000 year old handaxe became an “embarrasment” – and it still is. Not to her though, but to the text-book authorities. And you, it may seem:
    http://pleistocenecoalition.com/

    Here you may see some american handaxes too – from Calico:
    http://calicochoppers.earthmeasure.com/Choppers1/

  • BoNo
  • BoNo

    Back in the 30-ties, when George F. Carter was a young archaeologist, he had learned that the arrival of the first Americans happened NO more than 5000 years ago. During his first years of practice though, Carter came to discoveri tools and artefacts that says otherwise.

    Already in the 1950-ies Carter could present an enigmatic discovery of tools from the Middle and Lower Paleolithic stages, principally from his own work at Southern California sites. Though, with his own, solid experience at hand he could evaluate other repports of similar findings – ranging as far afield as Canada, New York, and Trans-Pecos Texas.

    For some cracky reason Carters presentations were debunked, placing him att odds with collegues and mainstream institutions. Most unfortunate for the progress of the archaeological sciences in both America and Europe, of course. Luckily Carter was strong enogh to stick to his collection of evidences – and develop his work to present various environmental attributes of the sites in question. Moreover he was the first to profile how lowered sea levels in what is now the Bering Straits, could present a route to be followed by humans entering the Americas. Today we know that the 120 meters lower ocean-level would also allow a possible island-hopping across the North Atlantic.

    Whatever the origin and migration-routes Carter could focus on the sites at hand – and by time present how the various paleolithic populations showed varying types of physical traits and cultural styles and characteristiscs – where a clear ‘Neanderthaloid component’ was found in some of the earlier populations.

    In the days of hos emiritus Carter could evolve his comprehensive material to finalize his discoveries in the book. Although his results would still ‘have to’ be disputed, the quality of his professional attitude and work was reviewed as nothing but excellent – by his former peers and collueges.

    Earlier than You Think: A Personal View of Man in America.
    By George F. Carter. College Station: Texas A&M Press, 1981.

    Review of the book by Professor of anthropology, Paul Ezell, is found here:
    http://www.sandiegohistory.org/journal/81summer/br-earlier.htm

    Today, 30 years after Carters book, its time to reconsider the paleolithic cultures, in terms of skills and abilities. Check what Chris Stringer & Co have been pondering over the last months;
    http://www.nhm.ac.uk/about-us/news/2011/january/ancient-denisovans-and-the-human-family-tree93500.html

    Moreover, the last five years have presented what we may comprehend as candidates for archaic migrations – one way or the other (!) – across the North-Atlantic:

    700.000 yrs old populations – at the Atlantic rim:
    http://www.nature.com/nature/journal/v438/n7070/abs/nature04227.html

    900.000 yrs old ., tool-making populations – in an arctic climate – at the Atlantic rim;
    http://www.guardian.co.uk/science/2010/jul/07/first-humans-britain-stone-tools

    Have a nice week-end!

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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