The X-Woman's Fingerbone

In a cave in Siberia, scientists have found a 40,000-year old pinky bone that could belong to an entirely new species of hominid. Or it may be yet another example of how hard it is to figure where one species stops and another begins–even when one of those species is our own. Big news, perhaps, or ambiguous news.

In Nature today, Svante Paabo and his colleagues published a paper describing their work in a place known as the Denisova Cave in the Altai Mountains of Siberia. There are lots of hominid bones and tools indicating people lived in the cave, off and on, for 125,000 years. There’s good evidence of Homo sapiens in the region for at least 40,000 years, and Paabo and his colleagues have also isolated 30,000-year old DNA from Siberian sites that is similar to the DNA from Neanderthals in Europe.

The scientists succeeded in fishing out human-like DNA from a pinky bone found in Denisova, and so far they’ve sequenced its mitochondrial DNA–that is, the DNA that is housed in mitochondria, sausage-shaped, fuel-producing structures in our cells. The majority of our DNA, which sits in the nucleus of cells, comes from both our mother and father. But mitochondrial DNA all comes from Mom. When the scientists compared the pinky DNA to DNA of humans and Neanderthals, they got something of a shock. If you line up the mitochondrial DNA from any given living human to any other living human, you might expect to find a few dozen points at which they are different. Compare human mtDNA to Neanderthal DNA, and you’ll find about 200 differences. But when the scientists compared the Denisova DNA to a group of human mitochondrial genomes, they found nearly 400 differences. In other words, their DNA was about twice as different from ours than Neanderthal DNA.

The scientists then used the DNA to draw a family tree. Here’s the figure from the paper, which you can also see here for full-size viewing.

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The Denisova mitochondrial DNA has been passed down, mother to child, on a lineage of hominids that’s separate from the one that produced mitochondria in Neanderthals and in living humans. Paabo and his colleagues estimated the age of common ancestor from which all the mitochondria evolved, based on the mutations in each branch. They concluded that common ancestor lived 1 million years ago. Below is a simple tree that shows the timing more clearly, from an accompanying commentary in Nature.

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No matter how you slice it, this is very exciting. All the mitochondrial DNA from living humans is believed to date back just 150,ooo years. That doesn’t mean that we all descend from a single “Eve.” There were other woman around at the time, and they passed down their own mitochondria. But those lineages eventually hit dead ends. In some cases, women only had sons. In others, they never had children. Eventually, all the mitochondrial DNA in the human population could be traced to only one of the women alive at the time.

All the Neanderthal mitochondrial DNA also shares a relatively recent common ancestor of its own–probably thanks to the same process. And now, for the first time, scientists have found hominid mitochondrial DNA that comes from a far more ancient split.

So–how to explain this? A couple possibilities present themselves.

1. The DNA belongs to a species of hominid that’s neither human nor Neanderthal.

This is the most interesting, most science-fictionish possibility.

Our hominid ancestors evolved into upright apes in Africa some six million years ago. By about 1.9 million years ago, some of those hominids had made their way out of Africa and strolled all the way to Indonesia. They go by the name of Homo erectus, and they stuck around Asia for quite a long time–some would argue they were still around 40,000 years ago. Neanderthals appear to have evolved from another wave out of Africa, which spread to Europe and Siberia several hundred thousand years ago. Meanwhile, our own ancestors appear to have stayed put in Africa. The oldest fossils of anatomically modern humans come from Africa 200,000 years ago, for example, and studies on human DNA find that African lineages are the oldest.

The Denisova DNA split too recently from our own to have been carried by H. erectus, the first globe-trotting hominids. But paleoanthropologists have found a fair number of other hominid fossils in Europe and Asia that might belong to more recent waves out of Africa. (Here, for example, is a report on hominids in Europe 1.2 million years ago.) So perhaps there was at least one other wave aside from H. erectus, the expansion of Neanderthals, and the spread of modern humans. If that’s true, this new discovery also means that this wave produced a long lineage of hominids that survived long enough to live alongside humans. We coexisted with yet another species of hominid–along with Neanderthals, H. erectus, and those lovable hobbits, Homo floresiensisfor thousands of years. Our current solitude is a recent fluke.

If #1 turns out to be true, then this DNA deserves a species name of its own. But for now, Paabo and his colleagues have refrained from giving it one. Instead, they’ve nicknamed the source of the DNA “X-woman.” Why the reticence? Probably because of possibility #2…

2. The DNA comes from the finger of a Neanderthal or a human–thanks to a love that dare not speak its name. Imagine, if you will, that an early Neanderthal male takes a morning constitutional in search of woolly rhinos when, gadzooks, he meets up with a fetching X-woman hominid. For whatever reason, the two of them decide to have an interspecies tryst, and X-woman gets pregnant. She gives birth to a girl carrying Neanderthal and X-woman DNA in her nucleus–and nothing but X-woman DNA in her mitochondria. Somehow this girl becomes a part of Neanderthal society; she has Neanderthal children of her own, and they continue to carry the X-woman mitochondrial DNA.

Remember that in every generation, nuclear DNA gets mixed up. Half of the DNA a child carries in the nucleus comes from its father, half from its mother. And with the generation of new eggs and sperm, chromosomes from each parent get chopped up and shuffled back into new combinations. So over generations, the X-woman DNA might gradually dwindle away from the Neanderthal gene pool–but some Neanderthals might still carry X-woman mitochondria, handed down from mother to daughter to grand-daughter.

(It’s also possible that the interbreeding male in this scenario was a human–although just in terms of timing, that’s less likely, since Neanderthals were out of Africa sooner than we were.)

One reason to take this possibility seriously is the fact that other primate species regularly mix up their DNA in just this way. Mongoose lemurs expanded into the range of brown lemurs, for example, and mitochondrial DNA ended up jumping the species barrier. In many cases, the species were separated by a million years or so, just like the Denisov DNA and human/Neanderthal DNA. (This is why it’s hard to use DNA-barcoding to tell closely related primates apart.) Another reason to take this possibility serious is lies in our own genomes. Some scientists have made a forceful case for the presence of ancient non-human DNA in the gene pool of living humans.

Still, even if this scenario turned out to be right, it would mean that a previously unknown X-woman hominid line expanded out of Africa and lived in Asia until relatively recently. Whether that lineage could be rightly considered a separate species of its own is tricky. (For more on that trickiness, see my article, “What is a Species?” from Scientific American.)

I can imagine other possible interpretations, but I’m not sure how plausible they really are. I’ve sent out some queries to some experts, and will add anything interesting I get back [Update: See the end of the post]. Fortunately, it may be possible to rule some possibilities out in just a few months. Paabo and company are busily churning out the sequence of the nuclear DNA from the Denisova pinky. It’s conceivable that the nuclear DNA will be a lot more like human DNA, or a lot more like Neanderthal DNA–making it likely that the fossil belongs to a hybrid. But if the nuclear DNA is just as exotic as the mitochondria, then perhaps the finger bone really does belong to a distinct species that lived 40,000 years ago–a species, it’s worth pointing out, that left its bones behind in the same layer of sediment where Russian scientists have dug up tools and ornaments made of stone and antler.

The possibility of a highly intelligent Siberian Other will have to dance in our heads until more studies come out.

Update: After I posted this, the paleoanthropologist John Hawks offers an alternative explanation on his blog. I followed up with a few questions via email, and based on his post and his reply, here’s my quick distillation:

Maybe the X-woman was not a separate species at all.

Wind back the clock to a million years ago. In Africa, there’s a population of hominids that will eventually give rise to Neanderthals and humans. The Neanderthal lineage expands out across Europe and Asia. They take with them a wide diversity of mitochondria. Most of the studies on Neanderthal DNA have focused on European Neanderthals–and have thus only captured a limited sample of that diversity. Now, in Siberia, Paabo and his colleagues have moved so far from the areas they had studied before that they’re finally getting to other branches of Neanderthal mitochondria.

In this scenario, Neanderthals play a role similar to that of Africans in the diversity of living humans. In Africa, you can find people with genes belonging to very old lineages. The Khoisan bushmen of southern Africa, for example, have genes that branched off from all other human lineages long ago. In other words, the genes of other Africans share a closer ancestor with genes from people out of Africa. Likewise, some Neanderthal mitochondrial DNA is more like human DNA than it is to the Neanderthal DNA found in the Denisova pinky.

[3/27/10: Time to go Borges: an update within an update! The Atavism (which has already displayed great skills in visualization by illustrating my recent reader survey) whipped together a diagram that gets this concept across nicely:

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I’ll post more replies as they come in.

Update, 3/25/10 10:15 am: I also got in touch with Laurent Excoffier, a biologist at the University of Bern in Switzerland, who has published models of human evolution indicating that there has been little, if any interbreeding between our own lineage and Neanderthals or other hominids.

Excoffier has argued that some genes that have been claimed to have entered our lineage through interbreeding were actually already present in ancient African human populations. I wondered if the mitochondrial DNA in the Denisova pinky might just be from an old human, not a separate species. Excoffier was skeptical:

This seems relatively unlikely, since it is difficult to understand why this mtDNA lineage would not have been preserved in Africa. Of course some otherwise rare mutations (or DNA sequences) can surf to higher frequencies during range expansions, and this could potentially explain why it could be seen outside Africa and not within Africa. But if that was the case, then it would be difficult to understand why this once frequent sequence would then have disappeared. So, I would thus consider this hypothesis as very unlikely.

I then asked if he thought the best explanation for this DNA was that it came from a separate species, or that it spread from a separate species into Neanderthals or humans through interbreeding.

If this sequence is really true (not an artefact from next-gen sequencing) and if there was no contamination, then a more plausible explanation would be that this sequence comes from a divergent Homo species, as claimed by the authors of the paper.

It is indeed plausible that some non-modern homo or non-Neanderthals roamed in Asia before modern humans spread there, and this sequence could well belong to one of them.

The interesting point for me is that if this sequence is representative of, say, erectus mtDNA diversity in Asia 40-60,000 years ago, then it means that  some divergent erectus were there when modern humans expanded into that region, and that did NOT hybridize with them, or at least not enough to be introgressed by them during their expansion (which is the expectation when hybridization can occur between a local and an invading species).

So there’s a vote for possibility #1.

Reference: Krause et al., “The complete mitochondrial DNA genome of an unknown hominin from southern Siberia” Nature, doi:10.1038/nature08976