Skull Caps and Genomes

By Carl Zimmer | May 6, 2010 2:02 pm

Winner of the 2010 Strange Quark!

neanderthal 440The skull cap is thick and flat. It looks distinctively human, and yet its massive brow ridge, hanging over the eyes like a boney pair of goggles, is impossible to ignore. In 1857, an anatomist named Hermann Schaafhausen stared at the skull cap in his laboratory at the University of Bonn and tried to make sense of it. Quarry workers had found it the year before in a cave in a valley called Neander. A schoolteacher had saved the skull cap, along with a few other bones, from destruction and brought it to Schaafhausen to examine. And now Schaafhausen had to make the call. Was it human? Or was it some human-like ape?

Schaafhausen did not have much help to fall back on. At the time, archaeologists had only found faint hints that humans had coexisted with fossil animals, such as spears buried in caves near the bones of hyenas. Charles Darwin was still two years away from publishing the Origin of Species and providing a theory to make sense of human evolution. Naturalists tended to look at humanity as a collection of races arranged in a rank from savagery to civilization. The most savage races barely ranked above apes, while the naturalists themselves, of course, belonged to the race at the top of the ladder. When anatomists looked at human bodies, they found what they thought was a validation of this hierarchy: differences in the size of skulls, the slopes of brows, the width of noses. Yet all their attempts to neatly sort humanity were bedeviled by the tremendous variation in our species. Within a single so-called race, people varied in color, height, facial features–even in their brow ridges. Schaafhausen knew, for example, about a skull dug up from an ancient grave in Germany that “resembled that of a Negro,” as he later wrote.

To make sense of the “Neanderthal cranium,” as he called it, Schaafhausen tried to fit it into this confusing landscape of human variation. As peculiar as the bone was, he decided it must belong to a human. It was very much unlike the cranium of living Europeans, but Schaafhausen speculated that it belonged to an ancient forerunner. Yet for naturalists of Schaafhausen’s age, such a heavy brow ridge implied not the advanced refinement of European civilization, but wild savagery.

Well, Schaafhausen thought, Europeans were pretty savage back in the day. “Even of the Germans,” Schaafhausen wrote in his report on the Neanderthal cranium, “Caesar remarks that the Roman soldiers were unable to withstand their aspect and the flashing of their eyes, and that a sudden panic seized his army.” Schaafhausen found many other passages in classical history that suggested to him a pracitically monstrous past for Europe. “The Irish were voracious cannibals, and considered it praiseworthy to eat the bodies of their parents,” he wrote. Even in the 1200s, ancient tribes in Scandinavia still lived in the mountains and forests, wearing animal skins, “uttering sounds more like the cries of wild beasts than human speech.”

Surely this heavy-browed Neanderthal would have fit right in.

Some 150 years later, pieces of that original Neanderthal cranium now sit in another laboratory in Leipzig, just 230 miles away from Schaafhausen’s lab. Instead of calipers, it is filled with a different set of measuring tools: ones that can read out sequences of DNA that have been hiding in Neanderthal fossils for 50,000 years or more. And today a team of scientists based at the Max Planck Institute of Evolutionary Anthropology published a rough draft of the entire Neanderthal genome.

It is an historic day, but it reminds us, once again, that the publication of a genome does not automatically answer all the questions scientists have about the organism to whom the genome belongs. In fact, a careful look at the new report is a humbling experience. We gaze at the Neanderthal genome today as Schaafhausen gazed at the Neanderthal skull cap that first introduced us to these ambiguous humans.

Since Schaafhausen’s day, paleoanthropologists have discovered Neanderthals across a huge range stretching from Spain to Israel to Siberia. Their fossils range from about 400,000 years ago to about 28,000 years ago. Instead of a lone skull cap, scientists now have just about every bone from its skeleton. Neanderthals were stocky and strong, with a brain about the size of our own. The isotopes in their bones suggest a diet rich in meat, and their fractured bones suggest a rough time getting that food. There’s no evidence that Neanderthals could paint spectacular images of rhinos and deer on cave walls like humans did. But they still left behind many traces of very sophisticated behavior, from intricate tools to painted jewelry.

Ideas about our own kinship to Neanderthals have swung dramatically over the years. For many decades after their initial discovery, paleoanthropologists only found Neanderthal bones in Europe. Many researchers decided, like Schaafhausen, that Neanderthals were the ancestors of living Europeans. But they were also part of a much larger lineage of humans that spanned the Old World. Their peculiar features, like the heavy brow, were just a local variation. Over the past million years, the linked populations of humans in Africa, Europe, and Asia all evolved together into modern humans.

In the 1980s, a different view emerged. All living humans could trace their ancestry to a small population in Africa perhaps 150,000 years ago. They spread out across all of Africa, and then moved into Europe and Asia about 50,000 years ago. If they encountered other hominins in their way, such as the Neanderthals, they did not interbreed. Eventually, only our own species, the African-originating Homo sapiens, was left.

The evidence scientists marshalled for this “Out of Africa” view of human evolution took the form of both fossils and genes. The stocky, heavy browed Neanderthals did not evolve smoothly into slender, flat-faced Europeans, scientists argued. Instead, modern-looking Europeans just popped up about 40,000 years ago. What’s more, they argued, those modern-looking Europeans resembled older humans from Africa.

At the time, geneticists were learning how to sequence genes and compare different versions of the same genes among individuals. Some of the first genes that scientists sequenced were in the mitochondria, little blobs in our cells that generate energy. Mitochondria also carry DNA, and they have the added attraction of being passed down only from mothers to their children. The mitochondrial DNA of Europeans was much closer to that of Asians than either was to Africans. What’s more, the diversity of mitochondrial DNA among Africans was huge compared to the rest of the world. These sorts of results suggested that living humans shared a common ancestor in Africa. And the amount of mutations in each branch of the human tree suggested that that common ancestor lived about 150,000 years ago, not a million years ago.

Over the past 30 years, scientists have battled over which of these views–multi-regionalism versus Out of Africa–is right. And along the way, they’ve also developed more complex variations that fall in between the two extremes. Some have suggested, for example, that modern humans emerged out of Africa in a series of waves. Some have suggested that modern humans and other hominins interbred, leaving us with a mix of genetic material.

Reconstructing this history is important for many reasons, not the least of which is that scientists can use it to plot out the rise of the human mind. If Neanderthals could make their own jewelry 50,000 years ago, for example, they might well have had brains capable of recognizing themselves as both individuals and as members of a group. Humans are the only living animals with that package of cognitive skills. Perhaps that package had already evolved in the common ancestor of humans and Neanderthals. Or perhaps it evolved independently in both lineages.

In the 1990s, the geneticist Svante Pääbo led a team of scientists in search of a new kind of evidence to test these ideas: ancient DNA. They were able to extract bits of DNA from bones that were found along with Schaafhausen’s skull cap in the Neander valley cave. Despite being 42,000 years old, the fossils still retained some genetic material. But reading that DNA proved to be a collossal challenge. Over thousands of years, DNA breaks into tiny pieces, and some of the individual “letters” (or nucleotides) in the Neanderthal genes become damaged, effectively turning parts of its genome into gibberish. It’s also hard to isolate Neanderthal DNA from the far more abundant DNA of microbes that live in the fossils today. And the scientists themselves can contaminate the samples with their own DNA as well.

Over the years,Pääbo and his colleagues have found ways to overcome a lot of these problems. They’ve also taken advantage of the awesome leaps that genome-sequencing technology has taken since they started the project. They have been able to reconstruct bigger and bigger stretches of DNA. They’ve been able to fish them out of a number of Neanderthal fossils from many parts of the Old World. And today they can offer us a rough picture of all the DNA it takes to be a Neanderthal.

To create a rough draft of the Neanderthal genome, the scientists gathered DNA from the fossils of individual Neanderthals that lived in Croatia about 40,000 years ago. The scientists sequenced fragments of DNA totalling more than 4 billion nucleotides. To figure out what spot on which chromosome each fragment belonged, they lined up the Neanderthal DNA against the genomes of humans and chimpanzees. They are far from having a precise read on all 3 billion nucleotides in the Neanderthal genome. But they were able to zero in on many regions of the rough draft and get a much finer picture of interesting genes.

One of the big questions the scientists wanted to tackle was how those interesting genes evolved over the past six million years, since our ancestors split off from the ancestors of chimpanzees. So they compared the Neanderthal genome to the genome of chimpanzees, as well as to humans from different regions of the world, including Africa, Europe, Asia, and New Guinea.

This comparison is tricky because human DNA, like human skulls, is loaded with variations. The DNA of any two people can differ at millions of spots. Those differences may consist of as little a single nucleotide, or a long stretch of duplicated DNA. Each of us picks up a few dozen new mutations when we’re born, but most of the variations in our genome have been circulating in our species for centuries, millennia, and, in some cases, hundreds of thousands of years. Over the course of history these variants have gotten mixed and matched in different human populations. Some of them vary from continent to continent. It’s possible to tell someone from Nigeria from someone from China based on just a couple hundred genetic markers. But a lot of the same variations that Chinese people have also exist in Nigeria. That’s because Chinese people and Nigerians descend from an ancestral population. The gene variants first arose in that ancestral variation and then were all passed down from generation to generation, even as humans migrated and diverged across the planet. And when Paabo and his colleagues looked at the Neanderthal genome, they discovered that Neanderthals carried some of the same variants in their genome too.

The scientists compared the variants in the Neanderthal genome to those in humans to figure out when the two kinds of humans diverged. They estimate that the two populations became distinct between 270,000 and 440,000 years ago. After the split, our own ancestors continued to evolve. It’s possible that genes that evolved after that split helped to make us uniquely human. To identify some of those genes,Pääbo and his colleagues looked for genes that were identical in Neaderthals and chimpanzees, but had undergone a significant change in humans.

They didn’t find many. In one search, they looked for protein-coding genes. Genes give cells instructions for how to assemble amino acids into proteins. Some mutations don’t change the final recipe for a protein, while some do. Pääbo and his colleagues found that just 78 human genes have evolved to make a new kind of protein, differing from the ancestral form by one or more amino acids. (We have, bear in mind, 20,000 protein-coding genes.) Only five genes have more than one altered amino acid.

The scientists also found some potentially important changes in stretches of human DNA that doesn’t encode genes. Some of these non-coding stretches act as switches for neighboring genes. Others encode tiny pieces of single-stranded versions of DNA, called microRNAs. MicroRNAs can act as volume knobs for other genes, boosting or squelching the proteins they make.

Another way to look for uniquely human DNA is to search for stretches of genetic material that still retain the fingerprint of natural selection. In the case of many genes, several variants of the same gene have coexisted for hundreds of thousands of years. Some variants found in living humans also turn up in the Neanderthal genome. But there are some cases in which natural selection has strongly favored humans with one variant of a gene over others. The selection has been so strong sometimes that all the other variants have vanished. Today, living humans all share one successful variant, while the Neanderthal genome contains one that no longer exists in our species. The scientists discovered 212 regions of the human genome that have experienced this so-called “selective sweep.”

You can see the full list of all these promising pieces of DNA in the paper Pääbo and his colleagues published today. If you’re looking for a revelation of what it means to be human, be prepared to be disappointed by a dreary catalog of sterile names like RPTN and GREB1 and OR1K1. You may find yourself with a case of Yet Another Genome Syndrome. In all fairness, the scientists do take a crack at finding meaning in their catalog. They note that a number of evolved genes are active in skin cells. But does that mean that we evolved a new kind of skin color? A new way of sweating? A better ability to heal wounds? At this point, nobody really knows.

If you believe the difference between humans and Neanderthals is primarily in the way we think, then you may be intrigued by the strongly selected genes that have been linked to the brain. These genes got their links to the brain thanks to the mental disorders that they can help produce when they mutate. For exampe, one gene, called AUTS2, gets its name from its link to autism. Another strongly-selected human gene, NRG3, has been linked to schizophrenia. Unfortunately, these disease associations just tell scientists what happens when these genes go awry, not what they do in normal brains.

The most satisfying hypothesis the scientists offer is also the one with the deepest historical resonance. It has to do with the brow ridge that so puzzled Schaafhausen back in 1857. One of the strongly selected genes in humans, known as RUNX2, has been linked to a condition known as cleiodocranial dysplasia. People who suffer from this condition have a bell-shaped rib cage, deformed shoulder bones, and a thick brow ridge. All three traits distinguish Neanderthals from humans.

Pääbo and his colleagues then turned to the debate over what happened when humans emerged from Africa. Scientists have debated for years what happened when our ancestors encountered Neanderthals and other extinct hominin populations. Some have argued that they kept their distance and never interbred. Others have scoffed that any human could show such self-restraint. After all, humans have been known to have sex with all sorts of mammals when given the opportunity, so why should they have been so scrupulous about a very human-like mammal?

The evidence that scientists have gathered up till now has been very confusing. If you just look at mitochondria, for example, all the Neanderthal form tiny twigs on a branch that’s distant from the human branch. If Neanderthals and humans had interbred often enough, then some people today might be carrying mitochondrial DNA that was more like that of Neanderthals than like other humans.

On the other hand, some scientists looking at other genes have found what they claim to be evidence of interbreeding. They would find gene variants in living humans that had evolved from an ancestral gene about a million years ago. One way to explain this pattern was to propose that modern humans interbred with Neanderthals or other hominins. Some of their DNA then entered our gene pool and has survived till today. In one case, a team of scientists proposed that a gene variant called Microcephalin D hopped into our species from Neanderthals and then spread very quickly, driven perhaps by natural selection. Making this hypothesis even more intriguing was the fact that the gene is involved in building the brain.

Pääbo and his colleagues looked for pieces of the Neanderthal genome scattered in the genomes of living humans. The scientists found that on average, the Neanderthal genome is a little more similar to the genomes of people in Europe, China, and New Guinea, than it is to the genomes of people from Africa. After carefully comparing the most similar segments of the genomes, the scientists propose that Neanderthals interbred with the first immigrants out of Africa–perhaps in the Middle East, where the bones of both early humans and Neanderthals have been found.

Today, the people of Europe and Asia have genomes that are 1 to 4 percent Neanderthal.That interbreeding doesn’t seem to have meant much to us, in any biological sense. None of the segments our species picked up from Neanderthals was favored by natural selection. (Microcephalin D turns out to have been nothing special.)

While working on this post, I contacted two experts who have been critical of some earlier studies on hominin interbreeding, Laurence Excoffier of the University of Bern and Nick Barton of the University of Edinburgh. Both scientist gave the Neanderthal genome paper high marks and agree in particular that the interbreeding hypothesis is a good one. But they do think some alternative hypotheses have to be tested. For example, interbreeding is not the only way that some living humans might have ended up with Neanderthal-like pieces of DNA. Cast your mind back 500,000 years, before the populations of humans and Neanderthals had diverged. Imagine that those ancestral Africans were not trading genes freely. Instead imagine that some kind of barrier emerged to keep some gene variants in one part of Africa and other variants in another part.

Now imagine that the ancestors of Neanderthals leave Africa, and then much later the ancestors of Europeans and Asians leave Africa. It’s possible that both sets of immigrants came from the same part of Africa. They might have both taken some gene variants with them did not exist in other parts of Africa. Today, some living Africans still lack those variants. This scenario could lead to Europeans and Asians with Neanderthal-like pieces of DNA without a single hybrid baby ever being born.

If humans and Neanderthals did indeed interbreed, Excoffier thinks there’s huge puzzle to be solved. The new paper suggests that genes flowed from Neanderthals to humans only at some point between 50,000 and 80,000 years ago–before Europeans and Asians diverged. Yet we know that humans and Neanderthals coexisted for another 20,000 years in Europe, and probably about as long in Asia. If humans and Neanderthals interbred during that later period, Excoffier argues, the evidence should be sitting in the genomes of Europeans or Asians. The fact that the evidence is not there means that somehow humans really did find the self-restraint not to mate with Neanderthals.

Because interbreeding involves sex, it dominates the headlines about Pääbo’s research. But I’m left wondering about the Neanderthals themselves. We now have a rough draft of the operating instructions for a kind of human that has been gone from the planet for 28,000 years, which had its own kind of culture, its own way of making its way through the world. Yet I found very little in the paper about what the Neanderthal genome tells us about their owners. It’s wonderful to use the Neanderthal genome as a tool for subtracting away our ancestral DNA and figure out what makes us uniquely human. But it would also be great to know what made Neanderthals uniquely Neanderthal.

[Image from Project Gutenberg]

Comments (61)

Links to this Post

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  1. Ricky

    “[neanderthals] might well have had brains capable of recognizing themselves as both individuals and as members of a group. Humans are the only living animals with that package of cognitive skills.”

    Our doggie knows his name, and knows he’s a member of our group.

    And it’s not limited to pack animals, since the herd’s bull knows he is the herd’s individual bull (“he da man,” “there can be only one”).

    Perhaps you should have used the already-mentioned representative art as our humanity’s defining feature ;-)

    Also, while we humans may have shown the self-restraint to not initiate interbreeding, we may also have formed the defenses against being “victim” of forced interbreeding.

    A couple days ago, a friend of a friend was rescued from a sexual assault by two construction workers. They were humans protecting a human from being raped by a neanderthal (of whatever pedigree).

    To top it off, the victim requested the rescuers not beat up the attacker.

    Is perhaps Mercy the sine qua non of Humanity?

  2. Great post as always! I just have to point out that Svante Pääbo is from Sweden, not Germany (even if he works in Germany).

  3. A couple of corrections: the name is Svante Pääbo and he is Swedish (though he works in Germany at a Max Planck Institute).

    http://en.wikipedia.org/wiki/Svante_P%C3%A4%C3%A4bo

    [CZ: Thanks–I’ve fixed the post.]

  4. “The evidence that scientists have gathered up till now has been very confusing. If you just look at mitochondria, for example, all the Neanderthal form tiny twigs on a branch that’s distant from the human branch. If Neanderthals and humans had interbred often enough, then some people today might be carrying mitochondrial DNA that was more like that of Neanderthals than like other humans.

    On the other hand, some scientists looking at other genes have found what they claim to be evidence of interbreeding.”

    Why is this confusing? One obvious, off-the-cuff speculation is that since, as you mentioned, mitochondrial DNA is only inherited maternally, any Neanderthal DNA in our genome would come from male Neanderthals copulating with female H. S. Sapiens, whereas mixed offspring of female Neanderthals either did not occur, or lived with the Neanderthals and did not contribute to modern humans, or…

    Now, I imagine that since this is so obvious to a layman like me, it’s probably wrong (since it wasn’t mentioned), but that only makes me more curious about why!

  5. Petter H, I came to the same conclusion – that the Neanderthal DNA contributers might have all been male. That the offspring would automatically live with the mother’s tribe makes sense.

  6. Peter and Jackal–The trouble with your scenario is that all those Neanderthal males should have infused our species with their Y chromosomes. But all Y chromosomes in living human males can be traced back to Africa around 60,000 years ago. You’d expect Neanderthal Y’s and human Y’s to have a common ancestor more like 500,000 years ago.

  7. Sili

    There’s not such thing as ‘just’ 230 miles in Europe.

  8. Very nice post, Carl — I especially like your references to the history.

  9. Janet Holmes

    It doesn’t mean the didn’t have sex, just that there were no fertile offspring, so disappointing.

  10. Janet Holmes

    So we didn’t interbreed with neanderthals after all, oh well. I guess that’s that then.

  11. manju

    The trouble with your scenario is that all those Neanderthal males should have infused our species with their Y chromosomes. But all Y chromosomes in living human males can be traced back to Africa around 60,000 years ago. You’d expect Neanderthal Y’s and human Y’s to have a common ancestor more like 500,000 years ago.

    What if male Neanderthal and female Sapiens’ offsprings were only females? Had it been female Neanderthal and male Sapiens, mtDNA should have been part of both male and female hybrids. And we don’t observe this situation. However, in the case of male N and female S introgression, only male child has to carry Y-chromosome (and we don’t observe this too). So we are left with the scenario where male N and female S mated resulting in female hybrids.

    Okay, I’m probably little annoyed with this Neanderthal mtDNA talk.

  12. Occam's Razor

    Thanks for the words of caution from Excoffier.
    By the way, even if the interbreeding explanation holds for the Neandertals and the Out-of-Africans, this should not be overinterpreted that the other aspects of the multiregional model are somehow indirectly validated. Homo erectus is not Homo sapiens.

  13. MF

    I quite agree that from the genome sequence we learn surprisingly little about the biology of this successful species (if it still is to be a species). There have been a few studies on Nenadertal genes before, revealing that they shared the FoxP2 (the so-called speech and language gene) variant of modern humans and that they carried pigmentation gene variants found in red-haired people… But which genetic traits have underlied their success and ultimately their demise remains as of now obscure…

  14. Steviepinhead

    Hello, Janet! You may wish to re-read Carl’s article, one more time.

    There’s something very basic that you seem to be missing:
    Janet Holmes Says:
    May 6th, 2010 at 8:21 pm
    It doesn’t mean the didn’t have sex, just that there were no fertile offspring, so disappointing.

    15. Janet Holmes Says:
    May 6th, 2010 at 9:20 pm
    So we didn’t interbreed with neanderthals after all, oh well. I guess that’s that then.

  15. Arnold Mousetrouser (Australia)

    Ref to comment 16 (manju): Speculation – what if male babies from the interbreeding were killed at birth and only the female babies allowed to live. Something like this happens in other contexts (or vice versa) even today. AM

  16. Curtis

    I wonder whether the phenomenon of the evidence of Neanderthal could be explained in the same way we explain the existence of, but dwindling population of Melungeons … tri-racial isolates … in Appalachia.

    1. One group is “in charge,” preferred, or has some characteristic considered necessary to survival (in society or in biology).
    2. Dominion of one group over the other–or successful hostility, prowess, physical or mental dominance, etc.–is stacked in favor of one group over the other.
    3. Mixing leads to the creation of a “hybrid” group with members who either resemble Group A, Group B, Group C or a combination … such that offspring of offspring [i.e., hybrids marrying hybrids] may eventually produce members who can “pass” for one of the other groups in terms of their physical features. Or …
    4. Hybrids often enough combine the best traits of both (or all three) genetic pools that they become desireable mates for one, two or three of the contributing original groups, thus pulling the combination back into the primary (i.e., dominant) gene pool … while the hybrid populations and the other groups that contributed to the melange languish as uncompetitive and die of diseases brought in by the more vital, more aggressive, more adaptive group that both gained power and then kept it–edging the others out.

    If Humans attacked and killed (and ate?) Neanderthals, they may well have kept some as “slaves.” If the American history of slavery is any clue, that would have led to forced mixing of the so-called “species” … though they must have really been one species or they would not have been able to produce offspring … and close enough in kind for the offspring not to have been sterile! So the Human-Neanderthal story may have been very much like the situation in the Old South when Planters produced offspring–and free mulatto slaves–with their African slaves, thus changing the “complexion” of slavery with each succeeding generation, especially after in-coming shipments of slaves were banned decades before the end of slavery in America.

    But like with the Melungeons, there would have been “free” hybrids–by escape or intermarriage–who would have developed in pockets (like the Melungeons in the ridges of Tennessee near Kingsport who were not Black, White or Indian, but had the characteristics … and the DNA … of all three groups). If beautiful and handsome, physically fit, intelligent examples arose from the vitality of interbreeding (which is likely), they would have (and did in the case of the Melungeons), simply “passed” for White [or, if the were closer to those other branches of the family, for Indian or Black), and would thereby, quietly passed their hybridness back into the general population.

    It seems likely that most interbreeding between Neanderthals and Humans would have been started out forced. But given the thousand different scenarios for how offspring could have survived–over more than 50 thousand years repeating and repeating in unrelated incidents across thousands of miles of territory, affecting every band and tribe of both “sub-species” always to the same effect, one can only conclude that OF COURSE the two groups affected each other. Of course at least two different kinds of offspring began appearing–whether individuals had been abandoned, marooned, escaped, or assimilated–whether it was the father or the mother who was Neanderthal. And there IS a difference to consider– whether biological or psychological–whether the affected (mixed) child is the son of the rapist or the rapist’s daughter; or was raised by the mother who was raped or a mother who assented to lie down with the “other.” Were some combinations likely to have, themselves, been dominant in the group they were left with, who raised them or adopted them? Would the success of some hybrid offspring in a band of Neanderthals or Humans have led to conscious decisions to interbreed as a means improving the bloodline?

    It is clear from the current evidence that the hybrids DID combine back into the “mainstream” human genome to enough of an extent that the human genome was altered. I am pleased to hear about this long-overdue acceptance of what has always seemed the most likely scenario. From the sound of it, Jean Auel was prophetyic in her “Clan of the Cave Bear” stories–in which Neanderthals and Humans, while competive enemies, did produce offspring that were not sterile … meaning exactly what the new DNA studies mean: Same species, different looks and adaptations. Cool.

  17. David B. Benson

    With the extremely low population densities, the meetings of various tribes might well have been rare and by chance. So interbreeding (if such occurred) and sucessfully leaving breeding offspring was probably an exceedingly rare event.

    However, let us all be reminded about the body lice shared just by Amerindians and H. erectus, hmmm?

  18. K DeHond

    If humans and Neanderthals did interbreed, and that seems likely, it also seems likely that their offspring were unable to reproduce. Lions and Tigers can interbreed but I believe their offspring do not have the ability to reproduce. I think the same is true of Mules.

    [CZ: It is true that in many cases, two species that can interbreed produce sterile hybrids. However, this cannot be true for humans and Neanderthals. The very evidence for their interbreeding was passed down to us by fertile hybrids–their DNA.]

  19. Magnus Malmborn

    Lion/Tiger hybrids are interesting in that only female hybrids are fertile, the male ones are sterile. If the same pattern happened with human/Neanderthal hybrids then that would explain the trouble in comment 10.

  20. Luna_the_cat

    KDeHond — Actually, you remind me of something interesting. Ligers and tigons offer an intriguing possibility for the direction of gene flow noted. Male ligers/tigons are sterile while the females are usually fertile. Which is how we end up with Ti-Ligers, Ti-Tigons, Li-Tigons, and Li-Ligers. Think: if that sex-linked fertility were reversed for Homo sap./Neandertal hybrids, so that male hybrids were fertile and female were not, that would explain the complete divergence of mitochondrial DNA. [Note,– drat, even as I typed that, I noticed Magnus Malmborn at #34 beat me to it!]

    That aside, many, many distinct species can breed and produce fully interfertile hybrids — for example Canis latrans and Canis lupus, Ursus arctos and Ursus maritimus, and any number of bird species from hawks to gulls to parrots. The biological species concept centers around normal reproductive isolation, not absolute reproductive isolation.

    And, aside from that, one of my friends has a very classically Neandertal skull and barrel chest; I’ve always thought she made a good argument for some gene flow between species. (She’s alive and well and living in Ireland, by the way.)

  21. Luna_the_cat

    Following on from that last thought about sex-linked fertility, and the divergence of Y chromosomes that Carl Zimmer mentions…..

    There are actually multiple scenarios which can account for the persistance of Neandertal genes in the nuclear genome, but their absence in either Y chromosome or mtDNA. Any situation in which only males of one generation and only females in the next have offspring, or other way around, only females in one generation and males in the next, essentially make both lineages invisible. So, if only male hybrids were fertile, but only their daughters and not their sons were assimilated into human populations, or only female hybrids were fertile but only their sons and not their daughters were accepted and assimilated, then we would get precisely the picture we have. There could also be an active genetic form of selection against Y-chromosome Neandertal genes. Given that many sex-linked diseases only manifest in men, it is possible that hybrids with a Neanderthal Y had a condition which left them unhealthy and considerably less likely to reproduce.

    Of course, another alternative explanation is that in fact we have not in fact sampled all human Y chromosomes, we have a small number of reference sequences, so genes which persist at a low frequency are statistically likely to be missed.

  22. Kilian Hekhuis

    Another correction: “a cave in a valley called Neander” – the valley is not callde “Neander” but “Neandertal” (“Neander valley”), named after a pastor. See here: http://en.wikipedia.org/wiki/Neandertal

  23. But they were also part of a much larger lineage of humans that spanned the Old World. Their peculiar features, like the heavy brow, were just a local variation. Over the past million years, the linked populations of humans in Africa

  24. Miikeb

    On the issue of why Asians and Europeans have Neantherthal DNA, it could be that it happened after the split, but Europeans and Asians have interbred quite a lot, with the Huns, Mongolians, Turks, and various other groups adding their DNA to the European pot. Unlike the African branch, the Euro Asian branch never really split completly.

  25. Aad

    Could you explain what it means that Eurasians have 1-4% Neandertal DNA? Does it mean that 1-4% of my DNA is exclusively Neandertal (i.e. not found in Africans)? Or is it equivalent to having one Neandertal great great great grandparent and the rest Sapiens?

    [CZ: It means that 1-4% of your DNA–consisting of many short segments scattered among Homo sapiens DNA–came directly from a Neanderthal ancestor. It’s possible that you have only one Neanderthal in your ancestry, or acquired DNA from more than one.]

  26. Aad

    Thank you. According to Wikipedia, “When copy number variation is included, human to human genetic variation is estimated to be at least 0.5% (99.5% similarity)” I read that Eurasian and Neandertal DNA are about 99.7% similar. Does this percentage have the same meaning, or a different meaning?

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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