With all the crazy talk about George Church and an adventurous young woman conspiring to bring back Neandertals, I do think it is important to keep in mind that we can bring back an individual with a predominantly Neandertal genome in a very old fashioned manner: controlled breeding. The most humane and viable manner in which you might do this is simply start a religion in a Bene Gesserit fashion where the prophesied Kwisatz Haderach is a Neandertal. Over the generations by selecting individuals within the population (which could draw in converts) enriched for Neandertal ancestry to mate assortatively one could slowly increase the proportion of that ancestral component. The population would become more and more “Neandertal,” probably to the point of being phenotypically distinctive in a dozen generations (even a minority of non-modern human ancestry is probably significant, just as many individuals who are 3/4 European and 1/4 African still exhibit features of their minority heritage). One could apply the same logic to the Denisovans.
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 also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.
Not to be too skeptical, but has anyone done an analysis of a possible change in the nature of publications about the cognitive capacities of Neandertals since it was established that there is a high likelihood of admixture between that lineage and ours (i.e., that that lineage is to some extent ours)? This is where I have to point to Luke Jostins’ loess curve illustrating the increase in cranial capacity of hominins over the past few million years. As Luke notes “brain size increases gradually in all lineages.”
This isn’t to deny that there seem some qualitative differences between the descendants of anatomically modern humans and other hominins. Neandertals, Denisovans, etc., never made it to the New World or Oceania. But there are differences, and there are differences. One model which was rather popular, and which I tacitly accepted, is that modern humans, the “descendants of Eve,” are sui generis. Somehow, somewhere, ~50-100,000 years ago a lineage of geniuses came upon the scene and swept all others away. I don’t accept this proposition anymore. Rather, it may be that 1-2 million years ago the hominin lineages took some irreversible step, and all the parallel and reticulate branches were hurtling toward a new evolutionary equilibrium.
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.
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 spectrum, and it turns out that the Neandertal gene flow has to be placed after the out of Africa bottleneck or the spectrum is much too flat.
The paper on the arXiv from the Reich lab (Sankararaman et al.) is trying to do something much more subtle than this and date the flow. I personally am no longer interested in explaining the introgression as ancient structure. That ship has sailed.
Of course the question of what was the genetic structure of Ancient Africa is quite open, and remains very interesting.
If Nick’s explanation is a bit cryptic for you (he was a cryptographer!), figure 2 from the Yang et al. paper lays it out quite clearly:
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 labs too. I’m hoping that the Reich lab pushing their stuff on arXiv will prompt the other groups to also start moving (instead of just presenting preliminary results to a narrow group of researchers).
As for these results, I’m still amazed that LD based methods can work this far into the deep past. Second, it is nice that the low bound estimate can plausibly predate the arrival of anatomically modern humans to Australia. Also, this admixture date is well after anatomical modern humanity, and well before the classical “Great Leap Forward” of behavioral modernity. Though I think that over the next few years we may start to discard the idea of any such punctuated leap.
And again, it’s on arXiv. As they used to say, read the whole thing!
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.
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!
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.
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.
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 brunette reconstruction, like the one here which is from the Smithsonian. But the most recent research (dating to 2007) seems to suggest that the Neanderthals may have been highly depigmented. This shouldn’t be too surprising when one considers that they were resident in northern climes for hundreds of thousands of years.
But there are some new tidbits, from researchers in the field of study:
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 something to do with adaptation.
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:
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:
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:
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.
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.
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.
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.
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.”
I 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