Razib Khan One-stop-shopping for all of my content

September 17, 2012

The feathery Neandertal

Filed under: Evolution,Neandertal — Razib Khan @ 10:11 pm

Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids:

The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham’s, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We ...

August 15, 2012

Ötzi – more Neandertal than the average bear

Neandertal ancestry “Iced”:

Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman

Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Ne- andertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequi- libria in successive populations.

August 14, 2012

Neanderthal admixture & the ecology of academe

Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here’s what Reich said:

…But Reich believes that the discussion would have been different if it had happened in the open. The PNAS paper questioning the Neanderthal admixture addresses issues swirling around two years ago, but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now, “it’s kind of an obsolete paper,” he says.

Here’s what Nick Patterson, Reich’s colleague told me via email:

Ancient structure in Africa was considered when we wrote the Green et al. paper, and we were aware that this could explain D-statistics. But the hypothesis is no longer viable as the major explanation of Neandertal genetics in Eurasia. This was discussed in the recent paper of Yang et al. (MBE, 2012). (Not referenced by the PNAS paper).

A very simple argument, that convinces me, is that the allelic frequency spectrum of Neandertal alleles in Eurasia falls off very quickly. A bottleneck flattens out the ...

August 12, 2012

Human-on-human sex

Filed under: Human Evolution,Neandertal — Razib Khan @ 11:27 pm

Dienekes tips me off to the fact that the long-awaited Reich lab paper on Neandertal admixture dating has finally been put on arXiv! The date of interbreeding between Neandertals and modern humans:

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000-86,000 years before the present (BP), and most likely 47,000-65,000 years ago. This supports the recent interbreeding hypothesis, and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

This isn’t the only group working on the Neandertal genomic admixture story. From reading his blog you probably know that John Hawks is working in this area, but there are other ...

July 17, 2012

Is resurrecting Neandertals unethical?

Filed under: Bioethics,Neandertal,Neandertal genomics — Razib Khan @ 8:34 am

An interview with paleoanthropologist Chris Stringer:

This raises one more question: Could we ever clone these extinct people?

Science is moving on so fast. The first bit of Neanderthal mitochondrial DNA was recovered in 1997. No one then could have believed that 10 years later we might have most of the genome. And a few years after that, we’d have whole Denisovan and Neanderthal genomes available. So no one would have thought cloning was a possibility. Now, at least theoretically, if someone had enough money, and I’d say stupidity, to do it, you could cut and paste those Denisovan mutations into a modern human genome, and then implant that into an egg and then grow a Denisovan.

I think it would be completely unethical to do anything like that, but unfortunately someone with enough money, and vanity and arrogance, might attempt it one day. These creatures lived in the past in their own environments, in their own social groups. Bringing isolated individuals back, for our own curiosity or arrogant purposes, would be completely wrong.


I do find it curious that Chris used the term “creatures.” This probably not intentional, or with serious conscious intent, but Neadertals and Denisovans are creatures I think the ...

December 15, 2011

Are you a caveman?

Filed under: Anthroplogy,Neandertal,Personal genomics — Razib Khan @ 8:53 pm

23andMe finally unveiled a Neanderthal Ancestry estimation feature. I’m at ~2.4 percent. What I’m curious about is the fact that out of the 45 “friends and family” who are surveyed, only two are at 3 percent. One of my them is my sibling who I found seems to have the Neandertal copy of a dystrophin variant! I have hypothesized that this may be the reason for his relatively robust build (he looks a lot like me, except kind of Neandertaloid).  Also of curiosity, I’m the least Neandertal in my family, including my parents!

August 1, 2011

Non-zero sum transitions in the human past

A few people have pointed me to the recent paper in Science, Tenfold Population Increase in Western Europe at the Neandertal–to–Modern Human Transition. The basic result is obvious, and not totally revolutionary: anatomically modern humans may simply have demographically absorbed the Neandertals (the word “absorbed” has many connotations here obviously). The results are clear in this figure:

This is not surprising, even though I have only a glancing familiarity with the guts of paleontology I was aware that there’s a lot of inferential evidence that Neandertals were not as efficient at extracting resources from any given piece of territory as modern humans. In The Dawn of Human Culture the paleoanthropologist Richard Klein offered a straightforward biological explanation for why and how the neo-African populations so rapidly marginalized Neandertals: some sort of macromutation which allowed for language and so the protean flexibility of human culture.

Implicitly this was the conventional wisdom until the likelihood of Neandertal admixture was discovered, and earlier the fact that Neandertals seemed to share the derived FOXP2 variant (the “language gene”). The earlier inferences of human demography using mtDNA, and later ancient ...

July 19, 2011

What did red-haired Neanderthals look like?

So asks a commenter below in relation to the question above. First, why would one even presume that they were red-haired, see my 2007 post, or the paper in Science: A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals. In humans loss of pigmentation can usually be thought of as loss of function on genes. That’s probably one reason that there are several different genetic architectures for light skin, but only one for very dark skin. There might be only one way for an engine to operate as designed, but there are many different ways you can tweak a part and render it broken.

The reason that scientists have posited that Neanderthals were red-haired is that they examined the region around a melanocortin receptor gene which serves as something of a master regulator in terms of melanin production. Their sample was of two Neanderthals, one from Italy and one from Spain, and both exhibited signs of loss of function within this region. An N = 2 is small, but one must recall the fact that they are independent draws as they were sampled from different regions. Also, since then from what I ...

July 18, 2011

Neanderthal-human mating, months later….

Image credit:ICHTO

Recently something popped up into my Google news feed in regards to “Neanderthal-human mating.” If you are a regular reader you know that I’m wild for this particular combination of the “wild thing.” But a quick perusal of the press release told me that this was a paper I had already reviewed when it was published online in January. I even used the results in the paper to confirm Neanderthal admixture in my own family (we’ve all been genotyped). One of my siblings is in fact a hemizygote for the Neanderthal alleles on the locus in question! I guess it shows the power of press releases upon the media. I would offer up the explanation that this just shows that the more respectable press doesn’t want to touch papers which aren’t in print, but that’s not a good explanation when they are willing to hype up stuff which is presented at conferences at even an earlier stage.

A second aspect I noted is that except for Ron Bailey at Reason all the articles which use a color headshot use a ...

March 21, 2011

Different Neandertal strokes

Filed under: Evolution,Neandertal — Razib Khan @ 10:38 pm

John Hawks, Europe and China have different Neandertal genes:

This is very striking. China and Europe by and large have different Neandertal-derived haplotypes. Haplotypes from Neandertals that are common in Europe — say, with more than two or three copies — are mostly rare in China. And vice-versa; haplotypes that are common in CHB are rare in CEU.

Why should this be? Green and colleagues…hypothesized an early population mixture of Africans and Neandertals in West Asia, before that population dispersed throughout the rest of Eurasia. This hypothesis was meant to explain why China and Europe have the same proportion of Neandertal genes.

I think that is also consistent with the fact that China and Europe have different Neandertal genes. If the population mixture was followed by substantial genetic drift as the West Asian population dispersed in different geographic directions, drift would randomly increase the frequency of some haplotypes in one direction, others in the other direction. Europe and China would end up with the same proportion of Neandertal ancestry, but it would be distributed very differently among loci.

Next, we’ll examine whether this pattern is the same for the rest of the chromosomes. Or maybe something even more interesting…

Guesses? I’m assuming it has ...

February 1, 2011

My family’s Neandertal genes, ii

Last week I reported that it turns out that one of my siblings carry a possible Neandertal haplotype on the dystrophin gene. To review, it seems likely that ~3% of the average non-African’s genome is derived from Neandertal populations. But by and large this ancestral quantum seems broadly dispersed through the genome of individuals, so that there isn’t a particular set of loci which are Neandertal, as such. As an analogy, about ~20-25% of the genome of an average black American is derived from Europe because of white American ancestry. But you can’t usually predict from that on which locus the “white” alleles will be found. The main exception to this will be loci where you might suspect selection will be operative, such as those implicated in malaria defense (some of them have negative consequences).

The dystrophin haplotype though has higher frequencies in some populations than expectation. ~9% in non-Africans as a whole, and higher in some groups. So there was a reasonable expectation that people might find that they carried it snooping through their genomes. Now that my parents (RF and RM) have come through, as well as sibling #2 (RS2), I can show you this:

SNPs rs1456740 rs6628685 rs331370 rs2854965 rs6653863 rs331369 rs331368 rs331367 rs331366 RF A A T G A A T T T RS1 A/G A/A C/T G/G A/G A/C T/T T/T G/T Razib G A C G (not typed) C T T G RM A/G A/A C/T G/G A/G A/C T/T T/T G/T RS2 A A (no ...

January 26, 2011

Neandertal admixture, revisiting results after shaken priors

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 ...

November 9, 2010

Size doesn’t always matter

Filed under: Human Evolution,Neandertal — Razib Khan @ 12:26 am

Neandertals famously had larger cranial capacities than modern humans, and, have gone through multiple phases of de- and re-humanization. A few weeks ago there was a revision of the idea that Neandertals in France ~30,000 years ago adopted some aspects of modern human culture through diffusion. This was a support for the Neandertal “ooga-booga” thesis. In contrast last spring we were treated to the possibility that most human beings have trace but non-trivial Neandertal ancestry. This naturally made Neandertals seem a little less primitive, since we don’t like to perceive ourselves as primitive.

A new article in Current Biology supports the position for the primitive Neanderal, Brain development after birth differs between Neanderthals and modern humans:

Neanderthals had brain sizes comparable to modern humans, but their brain cases were elongated and not globular as in Homo sapiens…It has, therefore, been suggested that modern humans and Neanderthals reached large brain sizes along different evolutionary pathways…Here, we assess when during development these adult differences emerge. This is critical for understanding whether differences in the pattern of brain development might underlie potential cognitive differences between these two closely related groups. Previous comparisons of Neanderthal and modern human cranial development have shown that many morphological characteristics separating these two groups are already established at the time of birth…and that the subsequent developmental patterns of the face are similar, though not identical…Here, we show that a globularization phase seen in the neurocranial development of modern humans after birth is absent from Neanderthals.

In other words there are developmental differences between Neandertals and modern humans. They’re a little less circumspect in the text, “We find that the modern human pattern of brain development is derived compared to Neanderthals.” The implication here is that the Neandertals exhibit the ancestral pattern, in common with chimpanzees. Below is figure 1, which summarizes their results:


(link acknowledge, Dienekes)

May 7, 2010

The three layers of the Neandertal cake

I assume by now that everyone has read A Draft Sequence of the Neandertal Genome. It’s free to all, so you should. At least look at the figures. Also, if you haven’t at least skimmed the supplement, you should do that as well. It’s nearly 200 pages, and basically feels more like a collection of minimally edited papers than anything else. There’s no point in me reviewing the paper, since you can read it, and plenty of others have hit the relevant ground already.

Since there seem to be three main segments of the paper, here are a few minimal thoughts on each.

First, the draft genome. What would you have said if someone came up to you ten years ago and told you that you’d live to to see this? Svante Paabo himself admitted he didn’t think he’d see something like this in his lifetime. There was a lot of hard work that went into figuring out how to get at the genetic material, purify it, and confirm that it was actually from the samples in question and not handler contamination and such (remember that there was a problem with contamination a few years back). To a great extent the focus on the results, instead of the methods, is like critiquing a set of landscape photographs taken from a very high peak. We can’t forget the effort and energy that went into scaling the peak itself. A lot of labor input obviously went into this, but additionally we can thank the fact that we live in a technological society where progress is not only expected, but often can’t be accounted for in our projections of future possibilities. I think that’s a very hopeful thing which makes me a little less pessimistic about the possibility of the magic carpet economy.

Second, the are the comparisons between Neandertals, modern humans, and chimpanzees. As Carl Zimmer noted there are an alphabet soup of genes thrown at you in the results. It is hard to make sense of it all, though I did note that genes involved in skin function and phenotype seem to have been the subject of differential evolution between Neandertals and modern humans (i.e., SNP differences in regards to substitutions in the lineages). We already know that there are suggestive signs that Neandertals lost function on pigmentation independently from modern humans. That shouldn’t be too surprising, given that it seems that West and East Eurasians evolved light skin independently. There are some uncertainties about the timing of this, but the different genetic architecture implies that it was unlikely to have occurred immediately after the Out-of-Africa event, and in fact some of the loci imply that depigmentation may have occurred in the Holocene. Skin is famously our biggest organ, so it shouldn’t be that shocking that it is possibly a target of selection, but curious nonetheless (recall that it seems that humans evolved darker skin from a paler ancestor as we lost our fur in the tropics).

Additionally, I think the finding that Neandertals and modern humans seem to share most of the same HARs, regions of the genome where our human lineage seems to differ from other mammals in exhibiting a lot of evolutionary change, is of great interest, though not necessarily surprising. When pointing to Luke Jostins’ post on rates of encephalization, I observed that in some ways it seems like there was a very powerful and consistent lineage specific trend toward greater cranial capacity which had incredible time depth. In The Dawn of Human Culture Richard Klein puts the emphasis on the sharp break between those populations before ~50 thousand years ago, and after. This period is marked by the shift toward behavioral, as opposed to just anatomical, modernity (there were anatomically modern humans in Africa ~200 thousand years ago). Klein’s thesis is that some mutation triggered a radical biocultural change, and was responsible for the Great Leap Forward, the efflorescence of creative symbolic culture which we truly consider the sin qua non of culture. The sharing of HARs between Neandertals and pure humans, and the consistent trend toward encephalization (aside from the post-Ice Age reversal), makes me shift the priors a touch more toward inevitable continuity and away from contingency. I find much of the politics of Robert J. Sawyer’s Neanderthal Parallax series a bit heavy-handed, but his depiction of Neandertals as fundamentally intelligent creatures who differ only on the margins seems a lot more plausible to me now than it was when I first read it in the early to mid-aughts.

Third, and finally, there’s the story of admixture and sex. This is getting all the press, but of course this is the most uncertain, inferential, and speculative aspect of the paper. It’s impressive, but it should open to skepticism, especially after the Out-of-Africa totalism which was ascendant until recently. John Hawks accepts the thrust of the findings, but obviously has his own ideas as to modifications, extensions and qualifications. Dienekes Pontikos favors an alternative interpretation of the data, which the authors point to in the text but dismiss as less parsimonious. My own inclination is to favor the authors in their interpretation of parsimony, but I will admit that this assertion is disputable. Dienekes and others would suggest that it is just as, or more, plausible that the shared variants between non-Africans and Neandertals arise from their common northeast African ancestral population (or some ancestral population of non-Africans and Neandertals). He rightly points out that there may be ancient population substructure within Africa, and using a particular African group as a “reference” for the whole continent may lead to false inferences. The main issue is that the probability of retrieving ancient DNA from northeast African samples in the near future seems low because the conditions for preservation are not optimal  (tropical climates famously degrade and recycle biological material more efficiently than temperate or boreal climates). Additionally, using modern northeast African populations is somewhat problematic because there has clearly been some back-migration from the nearby Arabian populations into this area in the medium-term past (the languages of the Ethiopian highlands are Semitic). One supposes that one could differentiate between the African and Arabian components of the genome of Ethiopians and Somalis, but if the admixture event was two to three thousand years ago I presume it would be technically more challenging than an African American, where very few generations have passed since admixture for recombination to fragment long genomic regions attributable to one ancestral population. In other words, how do you distinguish Neandertal variants which arrived back from Eurasia from ancient African ones? (I suppose that the haplotypes would differ so that the genuinely African ones would be more diverse)

But even if you reject the top-line finding, that most of us are not pure human, I think the paper is a game-changer in terms of shifting your priors in relation to evaluating the plausibility of a result which suggests admixture from an ancient non-African population. I found out about the high likelihood of this paper just before the UNM results were presented at the American Anthropological Society meeting, and it is clear in hindsight with the large author list that many people knew what was coming down the pipepline and had recalibrated their assessment of results which indicated admixture. It is perhaps time to go back and take a second look at papers which you skipped over before because it seemed that they may have been spurious or reporting a statistical quirk because they lay outside of the orthodox paradigm. This is clearly a case where it is good to live in interesting times.

Citation: Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

No scientists had to die for this paradigm shift!

Filed under: Genetics,Genomics,Human Evolution,Neandertal,Neandertal Genome — Razib Khan @ 12:17 am

In Science Ann Gibbons has a very long reported piece, Close Encounters of the Prehistoric Kind. It’s well worth reading, but behind a pay wall. If you don’t have access though, I want to spotlight one particular section:

The discovery of interbreeding in the nuclear genome surprised the team members. Neandertals did coexist with modern humans in Europe from 30,000 to 45,000 years ago, and perhaps in the Middle East as early as 80,000 years ago (see map, p. 681). But there was no sign of admixture in the complete Neandertal mitochondrial (mtDNA) genome or in earlier studies of other gene lineages…And many researchers had decided that there was no interbreeding that led to viable offspring. “We started with a very strong bias against mixture,” says co-author David Reich of Harvard Medical School in Boston. Indeed, when Pääbo first learned that the Neandertal DNA tended to be more similar to European DNA than to African DNA, he thought, “Ah, it’s probably just a statistical fluke.” When the link persisted, he thought it was a bias in the data. So the researchers used different methods in different labs to confirm the result. “I feel confident now because three different ways of analyzing the data all come to this conclusion of admixture,” says Pääbo.

The finding of interbreeding refutes the narrowest form of a long-standing model that predicts that all living humans can trace their ancestry back to a small African population that expanded and completely replaced archaic human species without any interbreeding. “It’s not a pure Out-of-Africa replacement model—2% interbreeding is not trivial,” says paleoanthropologist Chris Stringer of the Natural History Museum in London, one of the chief architects of a similar model. But it’s not wholesale mixing, either: “This isn’t like trading wives from cave to cave; the amount of admixture is tiny,” says molecular anthropologist Todd Disotell of New York University in New York City. “It’s replacement with leakage.”

The power of data to overwhelm human prejudice is sometimes very awesome. And the bias which Reich and Pääbo exhibited was not unfounded; Pääbo was involved in the sequencing of the Neandertal mtDNA, and found no evidence of admixture there. These data were strong, and I believe they should now shift our assessment of probabilities in relation to earlier papers which claimed some admixture between the population which derives from the Out-of-Africa expansion, and the Others.

In the second section it is notable that Chris Stringer has discarded replacement as not viable. He uses the term “not trivial,” which means that it’s a significant finding of note which one can’t simply ignore when generating inferences from a set of facts which one takes as axiomatic. Disotell’s attempt to minimize the finding is more a matter of rhetoric. He does not dismiss the admixture, he simply consigns it to the undefined category “tiny.” To some extent this reminds me of the neutralist vs. selectionist arguments of the 1970s, and more recently of the Out-of-Africa vs. Multi-regionalism disputes in human evolutionary origins. An argument over the meaning of words is a matter of law, an argument grounded in empirical data and quantitative estimates is an argument about science. No one holds to the extreme caricatures of any four of the models at this point; we’ve established that all these paradigms are unchaste, now we’re just haggling over price. We know that humans and the Others did the deed, we’re now mapping out the what, where, and how often.

But this is not the closing of the gate of itjihad. Dienekes presents an alternative model which may explain the data:

There is an alternative explanation. It involves the emergence of Homo sapiens and Homo neanderthalensis from a common ancestor and the subsequent admixture of Homo sapiens with populations that have branched out before this divergence. This would account for increased similarity between Eurasians and Neandertals, but without the problem of explaining how “Neandertal” ancestry is so similar in Europeans and East Asians.

What about Africans? Why do they stand further away from Neandertals? The answer is simple: low-level of admixture with archaic humans in Africa itself. It is fairly clear to me that the sapiens line whose earliest examples are in East/South Africa must have been an offshoot of an older African set of populations. We are lucky that Neandertals lived in a climate conducive to bone (or even DNA) preservation, while the African populations inhabiting the tropics left no traces of their existence.

In conclusion: I am not at all convinced that the authors have uncovered evidence of Neanderthal admixture in Eurasians; the alternative explanation is that modern humans and Neandertals were related, modern humans spread from East Africa/West Asia and as they entered deeper into Africa, they interacted with archaic human populations there.

In his magisterial post John Hawks has hinted at more wheels within wheels. From a Kate Wong story in Scientific American:

Intermixing does not surprise paleoanthropologists who have long argued on the basis of fossils that archaic humans, such as the Neandertals in Eurasia and Homo erectus in East Asia, mated with early moderns and can be counted among our ancestors—the so-called multiregional evolution theory of modern human origins. The detection of Neandertal DNA in present-day people thus comes as welcome news to these scientists. “It is important evidence for multiregional evolution,” comments Milford H. Wolpoff of the University of Michigan, the leading proponent of the theory.

The new finding shows that “gene flow across taxonomic boundaries happens,” observes geneticist Michael F. Hammer of the University of Arizona. Hammer is among the minority of geneticists who have espoused the idea of gene flow between archaic and modern populations. His own studies of the DNA of people living today have uncovered, for example, a stretch of DNA that seems to have come from encounters between moderns and H. erectus.

I assume Wolpoff is exultant. I do not personally think that this finding necessarily is going to result in a renaissance in Multi-regionalism, but Wolpoff has been the subject of a rising tide of skepticism and dismissal these past few decades. But rather than a more robust discussion between a revived Multi-regionaism and Out-of-Africa, I think these findings, and those that are likely to follow, will force us to move past simplistic typologies and accept that human evolutionary history works itself out through the principles of population genetics, and so can only roughly be modeled in words. The devil is in the parameters.

May 6, 2010

Neandertal online

Filed under: Anthroplogy,Evolution,Genetics,Genomics,Neandertal — Razib Khan @ 10:19 pm

Here’s the UCSC Genome Browser page for the Neandertal genome. Ensembl is supposed to have something up soon, but I don’t see it. Here’s the Anfo Short Read Aligner/Mapper; you can download it on that page. Page 21 of the online supplement has some configuration file code on it which might be useful. Also, make sure to check out the supplements.

The Neandertal Genome & Us

Filed under: Admixture,Evolution,Genetics,Genomics,Neandertal — Razib Khan @ 11:23 am

I’m still digesting the papers on the Neandertals which just came out. You can find them here. If you have questions, please read the papers first. They’re open access, so free to all. There’s a lot to mull over, and I don’t know what I can add right now, but I will note:

1) There’s a lot of stuff that doesn’t have to do with admixture, but focuses on genes where Neandertals and modern humans differ. There is for example an enrichment of differences in genes which relate to skin morphology. But my friends who think that modern human uniqueness can’t be pinned down to changes in SNPs will probably feel even more validated by this paper.

2) The fact that non-Africans as a whole, including Papuans, have Neandertal admixture, presumably from interactions in the Middle East, seem close to falsifying the “two-wave” model of expansion “Out of Africa” which came to prominence in the early aughts. That is, one group of Africans went north through the Middle East, and another swept along the Indian ocean fringe and onto southeast Asia. If there were two waves then they interacted a lot because they both received the same proportion of Neandertal alleles, which makes the idea of two genetically distinct waves a bit useless.

Breaking: there’s a little bit of Neandertal in all of us

Filed under: Anthroplogy,Evolution,Human Evolution,Neandertal,Neanderthal — Razib Khan @ 10:00 am

We’re all a bit of a Neanderthal:

As a result, between 1pc [percent] and 4pc of the DNA of non-African people alive today is Neanderthal, according to the research. The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree. Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

Prof Svante Paabo, of the Institute for Evolutionary Anthropology in Leipzig, Germany, said: “Those of us who live outside Africa carry a little Neanderthal DNA in us.”

eva-green-picture-1I will have a thorough write-up when I get a hold of the paper, which should be soon. As I said, this is a story of genomics, not just genetics. 1-4% is not trivial. The Daily Telegraph has more:

They were surprised to find that Neanderthals were more closely related to modern humans from outside Africa than to Africans.

Even more mysteriously, the relationship extended to people from eastern Asia and the western Pacific – even though no Neanderthal remains have been found outside Europe and western Asia.

The most likely explanation is that Neanderthals and Homo sapiens interbred before early modern humans struck out east, taking traces of Neanderthal with them in their genes.

Professor Svante Paabo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the international project, said: “Since we see this pattern in all people outside Africa, not just the region where Neanderthals existed, we speculate that this happened in some population of modern humans that then became the ancestors of all present-day non-Africans.

“The most plausible region is in the Middle East, where the first modern humans appeared before 100,000 years ago and where there were Neanderthals until at least 60,000 years ago.

“Modern humans that came out of Africa to colonise the rest of the world had to pass through that region.”

Several genes were discovered that differed between Neanderthals and Homo sapiens and may have played important roles in the evolution of modern humans.

They included genes involved in mental functions, metabolism, and development of the skull, collar bone and rib cage.

Image Credit: United Press International

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