Atapuerca

Eudald Carbonell and many colleagues report on a partial mandible from Sima del Elefante, one of the caves at Atapuerca, Spain:

The earliest hominin occupation of Europe is one of the most debated topics in palaeoanthropology. However, the purportedly oldest of the Early Pleistocene sites in Eurasia lack precise age control and contain stone tools rather than human fossil remains. Here we report the discovery of a human mandible associated with an assemblage of Mode 1 lithic tools and faunal remains bearing traces of hominin processing, in stratigraphic level TE9 at the site of the Sima del Elefante, Atapuerca, Spain. Level TE9 has been dated to the Early Pleistocene (approximately 1.2-1.1 Myr), based on a combination of palaeomagnetism, cosmogenic nuclides and biostratigraphy. The Sima del Elefante site thus emerges as the oldest, most accurately dated record of human occupation in Europe, to our knowledge. The study of the human mandible suggests that the first settlement of Western Europe could be related to an early demographic expansion out of Africa. The new evidence, with previous findings in other Atapuerca sites (level TD6 from Gran Dolina), also suggests that a speciation event occurred in this extreme area of the Eurasian continent during the Early Pleistocene, initiating the hominin lineage represented by the TE9 and TD6 hominins.

There's not a lot to add. The mandibular fragment is toward the small end of sizes represented in early Homo of earlier or equivalent age. The authors also present some details about the archaeological assemblage associated with the mandible, which is sparse with only 32 artifacts.

This is an extension of the story published last July, at which point I wrote:

Not much more to say, really.

Well, sometimes things really are self-explanatory!

References:

Carbonell E and 29 others. 2008. The first hominin of Europe. Nature 452:465-469. doi:10.1038/nature06815

Edmund Blair Bolles is reporting from the Evolang conference in Barcelona. Unfortunately I had to cancel my presentation there, but it has been great to read these summaries of some of the papers. I wanted to point readers to his account of Francesco D'Errico's talk:

Neanderthals had language comparable to that of Homo sapiens, Bordeaux-based archaeologist Francisco D’Errico told participants in the Evolang conference in Barcelona this morning (Saturday, March 15, 2008). This claim totally discards the older Big Bang theory that said language arose only very recently (40 to 75 thousand years ago), and also challenges the Out-of-Africa theory that proposes Homo sapiens emerged in Africa about 200 thousand years ago and spread over the rest of the world, carrying language and culture with the, beginning about 60 thousand years ago. A new history will have to be written.

If you have been reading here, you have seen many of the new perspectives D'Errico is talking about, but together they make a very compelling package. Consider:

1. We now know that australopithecines had ape-like vocal tracts, complete with pharyngeal air sacs.

2. We now know that Middle Pleistocene humans (Atapuerca) had humanlike hyoids, unlike australopithecines, so modern human vocal tract anatomy was plausibly a derived feature of Homo, including Neandertals.

3. We have good evidence of pigment use from MSA Africa and Mousterian Europe. The Neandertals in particular appear to have been coloring skin with manganese crayons.

4. Decorative/ornamental artifacts were manufactured both by MSA Africans and Neandertals.

5. Neandertals shared the modern human-derived FoxP2 variant.

I have some notes on D'Errico's work (with Maria Soressi) on Neandertal pigment use that I'll post later. Given the confluence of the recent evidence from genetics, archaeology, and anatomy, I do not see how anyone can maintain the hypothesis that Neandertals (and presumably, other Late Pleistocene humans) did not have language.

Now, that is not to say that they (or any Late Pleistocene humans) were identical in their linguistic adaptations to living or recent people. I still think that communication is the most likely focus of evolutionary change in the Late Pleistocene -- but a change based within a pre-existing community of language users, not a newly-sprung linguistic skill. In fact, I think the next constructive step should be to characterize the variation in linguistic adaptations in recent people, who are surely not identical to each other. That verges on the subject of my presentation, which -- if you attend the AAPA meetings this spring, you will still get a chance to hear. That is, if you stick around until Saturday!

It's that time of year again -- the time when those boring ``Year in Review'' magazines are on newsstands, and when pundits make fools of themselves predicting what will happen in the next year.

Well, I'm not too proud to join the fools, as I've shown the last two years. In 2006, I got five predictions right out of ten. Not bad for my first outing, but you'll see that last year's predictions fared even better:

• 10. Sahelanthropus postcrania will be published. I'm frankly shocked that this didn't happen. I don't doubt the rumors, but I'm starting to wonder whether this story is more interesting than it looks....
• 9. Two words: Holocene evolution. OK, this was a little unfair, considering that my work was an important part of making this prediction come true. Still, Discover made ``recent human evolution'' one of its top 100 science stories of the year, even before our December paper came out -- mainly on the strength of the paper by Scott Williamson and colleagues from earlier this year. And "Human genetic variation" was Science's "Breakthrough of the Year" -- most of that variation representing recent evolution.
• 8. Despite (or because of) the success of the Neandertal genome project, there will be no genetics of any kind published on early modern skeletal material. Puzzling, isn't it? But then, considering the trouble with Neandertal contamination reported in August, maybe we're better off leaving the early Upper Paleolithic alone for a while.
• 7. The mitochondrial history of human dispersals will become more and more detailed, but no paper will test against other loci. D'oh! Reading this one a year later, it's pretty obvious that I should have included Y chromosome in this one, since those two get compared all the time! Proofread, Hawks!
• 6. Another (yes, another) paper about the chimpanzee-human divergence will peg it between 5 and 7 million years ago. Will they never tire of these? Hobolth et al. (2007, PLoS Genet 3:e7) pegged the divergence at 4.1 million years. That's too recent to fit my prediction. Instead, I have to turn to Ebersberger et al. (2007, Mol Biol Evol 24:2276), who placed the divergence at 5.7 million years ago. Both estimates are too recent for Sahelanthropus, which the geneticists have started to figure out....
• 5. Three papers with new Ethiopian fossils. The last few years, one annual Ethiopian find seemed to be predictable enough. So I figured, why not three? We got a not-nearly-noted-enough paper this summer by Gen Suwa and colleagues descringing the Konso Homo erectus remains. Then, Suwa brought us Chororapithecus -- hey, I didn't say "hominid!" That's two. But despite the long-ago announcement of the Woranso-Mille skeleton, its appearance in a meetings abstract and a mid-summer press release about further Mille fossils, all we got from the peer review system is a lousy faunal list. Well, the faunal list does include the hominids. Should it count as a "paper with new Ethiopian fossils?" I'll say yes -- hey, unlike Aramis, at least the Mille fossils are new!
• 4. Another early Upper Paleolithic specimen will emerge from a museum collection. The only bizarre thing about this one was the location: South Africa. Hoffmeyr may not be that convincing as a European early Upper Paleolithic skull, but it was sure sold that way. Weird.
• 3. A big year for Miocene apes, which will look increasingly important in the story of human brain evolution. No brains, but it sure was a big year for Miocene apes, with two significant East African discoveries claiming to push back the timeline of African ape divergence.
• 2. Maturation rate in early Homo becomes a dead issue, because of the variation in dental and skeletal maturation in living people. Wishful thinking. Still, did Tanya Smith (2007) breathe new life into perikymata? Let's just say that unresolved questions remain.
• 1. The year will end without a single new hominid species having been named. This one was like dodging a bullet, since new species riffle out of paleoanthropologists' minds all the time. From 2001 to 2006, there were six (six!). In 2007, none.
• BONUS: A dramatic development in the problem of pre-2.0-million-year-old Homo. Rats.

OK, that's seven out of ten. It's beyond belief that I did better in the top five than the bottom five -- I picked those because they were far out there. I mean, really -- a new Upper Paleolithic specimen from a museum collection? After Muierii, that's like calling lightning to strike twice. But there it is, and in January, no less.

I'm clearly going to have to pick stranger predictions this year. And I'll have to be careful about that "dramatic development" line -- I mean, it's appropriately Delphic, but what is it supposed to mean, really? I wonder whether "operatic development" might be better.

And do I dare call down my non-lightning strike for a third year? It's ruining my percentage! It's starting to reek of desperation -- I mean, it starts to look like the stopped watch effect even if it happens.

Oh, well. I mean, those are just the risks of predictions, right? Suppose in the preseason I had picked Kansas to win the Orange Bowl!

• 10. A dramatic development in the Sahelanthropus story.
• 9. Both major-party candidates for the 2008 U.S. Presidential election will accept evolution.
• 8. This year's featured piece of anatomy: the femur.
• 7. No new hobbits, at least, not from Flores.
• 6. An incisive example of introgression in East Asia.
• 5. A viral insertion in the human genome will tell us about a disease of the australopithecines.
• 4. Another language gene joins FoxP2. No word on whether Neandertals have the human version.
• 3. Homo habilis: an endangered species?
• 2. This year, something new from three A's: A. afarensis. A. africanus. Atapuerca.
• 1. Oh, and one more A. Ardipithecus.
• BONUS: A big, big year for Neandertals. I mean, besides the election.

There you have it. I'm not sure which of these is the riskiest, but I'm sure they're more out on a limb than last year!

This week, Johannes Krause and colleagues from the Max Planck Evolutionary Anthropology institute announced that they had tickled FoxP2 out of two Neandertal specimens from El Sidrón, Spain. The bones were excavated in sterile (clean-cave?) conditions, immediately frozen and then shipped to Leipzig, where extracts were taken in clean-room conditions.

Here's an FAQ about what they found.

Why is this paper really important?

Isn't it obvious? It's important because it demonstrates that more than one Neandertal is suitable for nuclear genome recovery. We will know about genetic variation in Neandertals, sooner rather than later. These two bones come from different individuals, because the Leipzig group found two different mtDNA sequences in them. Together with the Vindija Vi 33.16 specimen in the original Neandertal genome papers, this makes three nuclear genome Neandertals. There will be more.

It also shows the possibility of probing ancient skeletons for specific genes. Here, they went in looking for Y-DNA, X-DNA and particular sites on FoxP2, and they found them. That is definitely the way to go if you want to test a biologically significant hypothesis fast -- otherwise, you just have to wait until the sequence comes up in your genome project.

However, I question the value of probing for individual genetic variants in this way. Every probe takes a bit of sample, which might be more efficiently used in whole-genome sequencing. We have 25,000 genes, and every one is potentially interesting. Every small sample used to assay only one of those genes may destroy many sequences from the others. It would be one thing if samples were trivial and easily replaced, but they obviously aren't.

Still, we will certainly see additional probes for genes that are of particular interest. I wouldn't be surprised to see MC1R results soon, to probe whether there were pigmentation variants in Neandertals. The same has already been done for woolly mammoths.

So, Neandertals had the human-specific FoxP2 form. Did they talk?

I think the genetic observation leans toward that direction, but doesn't really change our understanding. Consider:

Neandertals have a hyoid bone with humanlike anatomy, as did the Atapuerca people at more than 300,000 years ago, even though A. afarensis did not. So something related to vocalization evolved in humans by the Middle Pleistocene. Although Neandertal vocal tracts may not have been identical to recent humans, there is nothing about them that would preclude speech. The only paleoneurological observation about language puts a developed Broca's area on the KNM-ER 1470 endocast, Homo habilis.

Like other Middle Paleolithic/MSA people, their technology required more information to learn than earlier, Lower Paleolithic industries, leading to regional differentiation and more task-specific facies. Late Neandertals made use of some technology otherwise used only by Upper Paleolithic modern humans. Their hunting methods must have required cooperation and may have been impossible without a more sophisticated communication strategy than used by other primates.

All of these things argue for some kind of Neandertal language irrespective of FoxP2.

Then again, most of the arguments against humanlike language facility in Neandertals also have nothing to do with FoxP2, either. The slow technological progress, limited collection strategies, the rarity of any artistic or symbolic expression, their high mortality rate, and -- of course -- the fact that they no longer exist have all been considered as evidence that Neandertals lacked some essential aspect of "behavioral modernity." If language is a prerequisite for the modern human pattern of behavior, then Neandertals may not have talked, at least not in the way we do.

I think the FoxP2 story has really confused people much more than necessary. But in this case, the confusion is the same that results from every other gene study: when the press says we've found a gene "for" something, what it ought to say is that we've found an allele that affects something.

No macromutation happened. Language did not spring full-formed into the mind of some ancient African. All members of Homo used communication systems including some (possibly minimal) elements of language, and the evolution of the human brain, along with technological changes throughout the Paleolithic, reflect the evolution of communication. Human language evolved -- like all things -- over a long time, and like all complex phenotypes it required a series of mutational changes. Many of these mutations became fixed during recent human evolution, some may still be changing in frequency today. Language evolution is probably a continuing process.

That means that it must have involved many more genes than FoxP2 -- which after all experienced only two amino acid substitutions in all of human evolution. I would imagine the number of genes involved in language evolution is more than 500, and I wouldn't be surprised if it were much more. In that context, it seems quite silly to say FoxP2 is the "critical" evolutionary change for anything.

Then you agree with Language Log. They told me that FoxP2 isn't a "language gene."

The case is strong that the two FoxP2 coding substitutions in humans were selected because of their role in language. The gene sequence is strongly conserved in most mammals, and shows similar changes in some other species with unusual vocal adaptations, such as echolocating bats (Li et al. 2007). Its expression pattern delineates areas related to vocalizations in both humans and birds, and the pattern itself differentiates between song-learning versus nonlearning bird species (Haesler et al. 2004, Teramitsu et al. 2004, Webb and Zhang 2005). And of course, mutations to FoxP2 can result in specific language impairment (SLI) in humans.

Still, that case is only circumstantial. We know that FoxP2 was under selection, that it became fixed in humans, probably during the Late Pleistocene, and that breaking the gene changes brain development and damages language skills. But we don't know what a human would be like with the chimpanzee form of the protein. We don't know whether both of the human-specific amino acid substitutions have a different effect than one. Most important, we don't know what other genetic changes may have been necessary backgrounds for selection on FoxP2.

This means Neandertals were really modern humans, right?

This study should put an end to the "sudden mutation" model of modern human origins.

There was not a single mutation that made the critical difference in the ancestry of today's people. There was no cognitive Rubicon leading to modern human evolution. I would analogize the process as a slow-motion avalanche: at first a few small sands began to tumble, and then selection on a large number of genes became inevitable. FoxP2 is one of those genes, and as yet we don't know whether it was near the beginning or near the end of the process.

But it is clear that the process began before the Neandertals were gone. Some aspects of behavioral complexity did begin to evolve rapidly sometime after 70,000 years ago. This rapid evolution was multiregional in context -- it was not limited to a single human population. In particular, it was not limited to Africans: the last Neandertals clearly manifested technological and behavioral strategies otherwise defined as "behaviorally modern" (d'Errico 2003). There's a reason why the Neandertal-produced Châtelperronian industry of France and Spain was historically considered the first Upper Paleolithic industry.

But we have undergone light-years of change since the last Neandertals lived. This is not a question of "modern human origins" anymore. We can now show that living people are much more different from early modern humans than any differences between Neandertals and other contemporary peoples. I think that "modern humans" is on its way to obsolescence. What matters is the pattern of change across all populations. Possibly that pattern was initiated by changes in one region but the subsequent changes were so vast that the beginning point hardly matters.

We all know that the Neandertal genome is riddled with contamination from modern humans. Isn't the null hypothesis that we have a modern human sequence here because it is a modern human?

Well, as you know, I'm not all that convinced that contamination explains the interpretive discrepancies between last year's genome papers. But still, this study has done some things to address the problem of contamination.

It is notable that Green et al. (2006) found 25% modern human mtDNA in one of the El Sidrón bones: this shows that even "sterile" excavation, immediate freezing and extraction under clean-room conditions cannot exclude contamination. There is at the moment nothing more that can be done. We will always have the problem of a contamination fraction in ancient Neandertal skeletons. So we have to judge each study by the extent to which we can exclude contaminants with statistical analysis.

For this study, Krause et al. (2007) developed a test of nuclear DNA contamination: they identified seven gene variants that differ between the recovered Vindija Vi 33.16 nuclear genome and all known living humans. In other words, these are human-derived mutations that are absent from the only known Neandertal nuclear genome. Then, they probed the El Sidrón bones for these sites. They found only the ancestral form in their extracts of both bones -- presumably because no human contaminants were present in their samples.

That seems like a pretty good indication that the other sites in their sample represent the true gene variants of the ancient Neandertals. I wouldn't go so far as to say that contamination is ruled out, but it seems like these are good results.

Did FoxP2 introgress into Neandertals?

It sure looks that way to me. Let's consider the evidence:

FoxP2 recently fixed in humans. According to Enard et al. (2002:871):

Under a model of a randomly mating population of constant size, the most likely date since the fixation of the beneficial allele is 0, with approximate 95% confidence intervals of 0 and 120,000 years.

Now, Enard et al. (2002) noted that human populations have grown over time, and that they are not randomly mating, so that this date estimate might be too recent. Allowing for population growth since "10,000--100,000 years ago," they asserted that fixation of FoxP2 must have happened "during the last 200,000 years of human history." But this is not quite accurate. Unlike genetic drift, positive selection can and often does fix genes rapidly in a growing population. It simply doesn't matter that the human population has been rapidly growing: FoxP2 may still have just become fixed yesterday.

Last year, Green and colleagues (2006) considered that the Neandertal-modern population divergence time might have been quite recent, depending on the ancestral population size. According to the estimates of Wall and Kim (2007), the Green et al. data are consistent with a Neandertal-modern population divergence time as recent as 30,000 years ago. Of course, that date would predict substantial admixture between contemporary Neandertal and non-European populations -- they would have been exchanging genes up to the very lifetimes of the last Neandertals. According to those data there would be nothing surprising about Neandertals and living people sharing the human-derived FoxP2 allele. But as mentioned above, Wall and Kim (2007) used the recent divergence estimate as evidence that the Neandertal genome data from Green et al. must be contaminated.

So, if we cannot trust the data, then we have to fall back on some other estimate of the divergence date. Noonan and colleagues (2006) estimated a divergence date between Neandertals and modern populations between 170,000 and 570,000 years ago. If we accept that, then the confidence intervals of the Neandertal-human divergence and the FoxP2 selective sweep might barely overlap. Might. But I will note that a minimal overlap between the 95% confidence intervals of two point estimates does not mean that they are not significantly different. Only if the expected value of one estimate falls within the 95% confidence interval of the other do they fail to be significantly different. It is pretty unlikely that the most recent FoxP2 sweep is older than 170,000 years ago and the Neandertal-modern population split is as recent as 170,000 years.

That is, unless the "split" time reflects widespread genetic introgression.

The current paper (Krause et al. 2007) goes to some contortions to try to establish that the FoxP2 sweep could really have been older than 300,000 years ago (where they place the lower confidence limit on the N-M split):

The third scenario is that the selective sweep started before the divergence of the ancestral populations of Neandertals and modern humans around 300,000-400,000 years ago

Let me just say that I was surprised to read this explanation in a paper from this group. One of the main arguments they have been posing as a scientific value of the Neandertal genome sequencing is that conventional methods don't detect selection at 300,000-400,000 years ago. But here, they consider such an ancient mutation to be the most likely hypothesis. This seems like quite a shift just to avoid the unpleasant idea of Neandertal introgression. Ooooh -- can't have those Neandercooties!

In reality, there is no reason to think the fixation of FoxP2 happened as early as 300,000 years ago, and indeed the very high frequencies of the linked derived alleles (over 97% for six of the linked alleles) suggest strongly that the sweep probably happened within the last 100,000 years -- otherwise, subsquent genetic drift should have caused these linked derived alleles to show more dispersion in their current frequencies. The same features that make the inference of selection so strong at FoxP2 -- it is far (>286 kilobases) from the nearest gene and it includes many high-frequency derived alleles in addition to reduced polymorphism -- make it very unlikely that the selective sweep was ancient.

So, considering that the El Sidrón samples both share the human-derived amino acid substitutions on the same haplotype as modern humans, complete with all the high-frequency derived SNPs, it seems almost certain that the gene introgressed into Neandertals from modern humans.

Or, there's one other option. One of the El Sidrón bones includes a relatively rare (in humans) ancestral SNP allele at one of those linked sites where the derived allele is at very high frequency in humans. One explanation: the selected mutation arose in Neandertals and introgressed into other humans. That would explain why this Neandertal didn't have a SNP variant on its FoxP2 haplotype that later became very common in humans: Neandertals had the new FoxP2 first.

What about that Y chromosome thing?

The El Sidrón bones both tested positive for the Y chromosome site assayed in the study. That means they were both male (duh!). But more important, the Y chromosomes of both individuals lacked the human-specific derived mutation that the researchers tested for. Since all human males yet surveyed have this human-derived mutation, this means that a Y chromosome variant has fixed in modern humans that Neandertals did not have. Since the entire nonrecombining portion of the Y chromosome is completely linked, we can infer that the entire modern human Y chromosome has undergone at least one fixation not shared with the ancestors of these Neandertals.

Here's the text (from page 2):

Both Neandertals yielded products for Y chromosomal primer pairs, indicating that they were males. Strikingly, all 15 Y chromosomal products for the five assayed positions show the ancestral allele. This includes two polymorphisms that define the deepest split among current human Y chromosomes (Y2 and Y4, Figure S1) as well as two polymorphisms that cover less common African Y chromosomes (Y3 and Y5, Figure S1). These Y chromosome results must derive, then, either from Y chromosomes that fall outside the variation of modern humans or from the very rare African lineages not covered by the assay (Figure S1). For our purposes, this result shows that neither the maternally inherited mtDNA nor the paternally inherited Y chromosome shows evidence of gene flow from modern humans into Neandertals or of subsequent contamination of their mortal remains.

That's not such a big surprise. Already we knew that the fixation of the human Y chromosome was very recent -- probably within the last 70,000--100,000 years, and possibly even more recently. Every man on earth shares recent Y chromosome mutations that were completely absent in Middle Pleistocene humans. That is one radical recent evolutionary change.

The paper elsewhere suggests that this absence of the human-derived Y chromosome in Neandertals as evidence that they did not contribute other genes to us. I could not disagree more.

The very recent fixation of the Y chromosome in an expanding human population is extremely unlikely to have resulted from genetic drift. Drift does not eliminate rare variants as quickly in an expanding population. Instead, one or more Y chromosome mutations must have been positively selected, resulting in the fixation of the entire NRCY in recent humans.

In that context, the Neandertal result is quite expected: they had an earlier Y chromosome lacking one or more mutations later selected in the other ancestors of living people.

References:

Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Nat Acad Sci USA doi:10.1073/pnas.0704665104

d'Errico F. 2003. The invisible frontier. A multiple species model for the origin of behavioral modernity. Evol Anthropol 12:188-202. doi:10.1002/evan.10113

Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444:330-336. doi:10.1038/nature05336

Haesler S, Wada K, Nshdejan A, Morrisey EE, Lints T, Jarvis ED, Scharff C. 2004. FoxP2 expression in avian vocal learners and non-learners. J Neurosci 24:3164-3175. doi:10.1523/JNEUROSCI.4369-03.2004

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin J-J, Bertranpetit J, Hänni C, Fortea J, de la Rasilla M, Rosas A, Pääbo S. 2007. The derived FoxP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1-5. doi:10.1016/j.cub.2007.10.008

Li G, Wang J, Rossiter SJ, Jones G, Zhang S. 2007. Accelerated FoxP2 Evolution in Echolocating Bats. PLoS ONE 2(9): e900. doi:10.1371/journal.pone.0000900

Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113-1118. doi:10.1126/science.1131412

Wall JD, Kim SK. 2007. Inconsistencies in Neanderthal genomic
DNA sequences. PLoS Genet 3:e175. doi:10.1371/journal.pgen.0030175.eor

I've read through the new paper by Martinón-Torres et al., on Eurasian continuity in the Middle Pleistocene. They've put out an interesting hypothesis, with some support from previous work, but ultimately I think their methods are too weak to test it.

The press coverage of the paper so far (e.g., this AP article) has been a little confusing, because it misses this point: this paper is not about modern human origins, it's about much earlier evolutionary relationships. National Geographic News resorts to the always-safe:

The finding suggests that the hominid family tree could be much more complex than previously thought.

Ah, so that's what it means! More complex than previously thought! Why isn't there ever a story that makes things simpler than previously thought? I mean, isn't it a sign of a failed science if you have to add complexity to your hypothesis every time you make a new observation? It's like Ptolemaic paleoanthropology!

Anyway, enough of that rant. Let's look at what the paper really says, which is much more interesting than the press! Here's the abstract:

A common assumption in the evolutionary scenario of the first Eurasian hominin populations is that they all had an African origin. This assumption also seems to apply for the Early and Middle Pleistocene populations, whose presence in Europe has been largely explained by a discontinuous flow of African emigrant waves. Only recently, some voices have speculated about the possibility of Asia being a center of speciation. However, no hard evidence has been presented to support this hypothesis. We present evidence from the most complete and up-to-date analysis of the hominin permanent dentition from Africa and Eurasia. The results show important morphological differences between the hominins found in both continents during the Pleistocene, suggesting that their evolutionary courses were relatively independent. We propose that the genetic impact of Asia in the colonization of Europe during the Early and Middle Pleistocene was stronger than that of Africa.

OK, so this is about the initial colonization of Europe and the subsequent evolutionary trends in Europe, Asia, and Africa. The observation is that European teeth show a continued similarity to Asians during the Middle Pleistocene, and there is no evidence that European teeth evolved in the direction of Africans during that time period.

Why is that interesting? Two reasons:

1. The hypothesis directly conflicts with the idea that Middle Pleistocene Europeans were linked to Africans. A large number of anthropologists have been pushing the European-African link, under the old hypothesis that these ancient people belonged to a species that was distinct from East Asians. The European-African clade in this hypothesis is often called Homo heidelbergensis; the Asian clade remains Homo erectus.

2. The hypothesis also seems to conflict with genetic data, which suggest that the relationship of European and African hominids is more recent than the early Middle Pleistocene. In particular, the genetic divergence time between human and Neandertal genomes appears to date to more recently than 700,000 years ago (Green et al. 2006, Noonan et al. 2006), which means that the population divergence must be still more recent. Also, Alan Templeton's papers (e.g., 2002, 2006) claim evidence for migrations from Africa into Europe and Asia during the Middle Pleistocene. Those claims are consistent with the Neandertal genome data, as far as we know it, and they suggest gene flow from Africa into Eurasia.

So, the authors ought to deal with these issues. They do so in their discussion, which in this short paper is one long paragraph. I'm quoting it here in full to comment on the details:

If the population of the Eurasian continent during the Early and
Middle Pleistocene was mainly the result of several out-of-Africa incursions, we should have found African influences in the morphology of the Eurasian populations. However, the continuity of the "Eurasian dental pattern" from the Early Pleistocene until the appearance of the Upper Pleistocene Neanderthals suggests that the evolutionary courses of the Eurasian and the African continents were relatively independent for a long period and that the impact of Asia in the colonization of Europe was stronger than that of Africa.

That is the conclusion of the analysis, in brief. The strength of the conclusion depends on the power of the analytical methods to detect gene flow based on morphological similarities. More on that below.

This finding does not necessarily imply that there was not genetic flow between continents, but emphasizes that this interchange could have been both ways (25, 26).

This seems a little misleading. They have no particular evidence of gene flow from Eurasia to Africa (that would be the "both ways"). Nor do they have evidence in their analysis of gene flow from Africa to Eurasia, after the initial colonization. So they don't have any evidence for gene flow at all. So the finding doesn't emphasize anything about gene flow, other than that the teeth don't show obvious evidence for it.

Around 1 Ma, hominins appear to have dispersed into temperate latitudes as far north as 40 - 45° N (27-29), not only from Africa, but also within Eurasia (29 - 31). These populations were probably descendants of an ancient out-of-Africa exodus, rather than a later one at the end of the Early Pleistocene (30).

This is an important assertion. Other workers have emphasized the similarities of some African fossils to East Asian fossils (mainly from Java, plus Gongwangling in China) in the late Early Pleistocene. That has always been the case with OH 9, and it influenced the description of the Daka and Buia crania as well. The question is how early Asian populations became morphologically distinctive. Here, the authors argue that it was very early, without substantial signs for later interaction, which in the context of the cranial comparisons is now an extreme claim.

In addition, a recent study on the European Lower Pleistocene hominin populations has revealed a possible Eurasian origin for these groups (32).

This refers to the description of the ATD6-96 mandible, which contains an earlier assertion about Asian-European connections. I return to this below.

Furthermore, it has been pointed out that during the Middle Pleistocene there was hardly any faunal exchange bet ween East Africa and the Levant (33) and that the desert between the Sahara and Arabia was an important barrier at that time (26), therefore contributing to the isolation of both continents.

This is an important argument in support of their hypothesis. If movement between Africa and Eurasia was difficult during this time span, that reinforces their claim, and makes it less plausible that there were large-scale dispersals out of Africa during the Middle Pleistocene. That leaves us with a mention of a major exception to their proposed pattern: the evolution of humans in the Late Pleistocene:

With the exception of the SAP [i.e., H. sapiens] out-of Africa dispersion based mainly on genetic data (2), the history of human populations in Eurasia may not have been the result of a few high-impact replacement waves of dispersals from Africa, but a much more complex puzzle of dispersals and contacts among populations within and outside continents. In the light of these results, we propose that Asia has played an important role in the colonization of Europe, and that future studies on this issue are obliged to pay serious attention to the "unknown" continent (Martinón-Torres et al. 2007:3).

The citation of the ATD6-96 mandible leads us to a passage from that earlier paper (Carbonell et al. 2005), which also describes the hypothesis that the founding population of Europe was Asian. Remember that this research group calls the Gran Dolina sample, Homo antecessor, and they initially had written that this species probably colonized Europe from Africa in the late Lower Pleistocene. Here's the relevant paragraph from the cited paper (Carbonell et al. 2005):

The differences in dimensions and robustness between the TD6 mandibles and the East and North African mandibles cast doubt on the African origin of H. antecessor. In contrast, our comparative analysis suggests looking toward the Asian continent. In this respect, it is relevant to mention some data that remained unpublished in 1997, when the new species was named (10), and that are relevant to this discussion. The partial cranium Nanjing I, recovered in 1993-1994 from the Hulu Cave (Tangshan Hill, eastern central China), shows clear modern midfacial traits similar to those observed in the specimen ATD6-69 (19). Wang and Tobias (20) also found similarities between Nanjing I and the Zhoukoudian hominins. Geochronological dates, combined with ecological and paleoclimatic evidence, indicate that the Nanjing skull is ~600 thousand years old (21). Furthermore, the Locality 1 levels at Zhoukoudian, which yielded most hominin specimens, are now considered at least 800 thousand years old (22). Thus, these Chinese hominins may be contemporaneous with or slightly younger than the TD6 hominins. If the Gran Dolina and Chinese populations are phylogenetically related, they should share a common ancestor that also had a modern midfacial pattern and a gracile mandible. In the cranium, this hypothetical common ancestor would have had a low and flat temporal squama, and an unfused styloid process. These traits would have been retained in the Asian hominins but lost in the TD6 hominins, who exhibit a fused styloid process, a convex temporal squama, and probably a significant increase in cranial capacity (19). The Ceprano calvaria (Italy), which has been tentatively assigned to H. antecessor (23), exhibits a convex temporal squama and a cranial capacity of about 1,057 ml (24). Interestingly, TD6 and Zhoukoudian are the only hominins that have a zygomaxillary tubercle before the Upper Pleistocene (19).

So that provides cranial and mandibular evidence of an Asia-Europe connection, supporting the dental evidence provided in the current paper. Still, that evidence is from the initial founding of Europe in the Early Pleistocene and doesn't necessarily apply to the trends during the Middle Pleistocene.

After working through the data supplements for the paper, I think that the analysis is much weaker in statistical power than it could be. In their analysis, they disregard much of the variation within these ancient samples and focus on the differences between samples according to their scoring methods. This may reveal the broad relationships among samples -- if we disregard the possibility of selected parallelisms -- but it does not say anything about the possibility of gene flow among the samples.

Indeed, the result of their analysis (a dendrogram, or branching tree) is quite incapable of showing genetic exchanges at all. It can only show branching events, which means that the result will show either an exclusive relationship between Europeans and Asians, or an exclusive relationship between Europeans and Africans, but never a mixed relationship.

The only result in the paper that indicates a European-Asian relationship is from their cladistic analysis of a subset of the data. And it isn't especially strong evidence, since the Middle Pleistocene Africans are limited to the relatively early sites of Rabat and Tighenif (Ternifine). Granted, the later sample is also small in number, but this isn't really a test of relationships; it's more of a suggestion.

The phenogram inexplicably omits Middle and Lower Pleistocene Africans entirely, and considers only australopithecines and habilines as the African sample.

So, at the moment I consider this to be a very interesting hypothesis in search of a good test. There is no test of gene flow here, just an assertion. Yet, the cranial comparisons give the assertion some plausibility -- and remember, another idea out there is the hypothesis that early Homo originated in Asia and migrated to Africa later.

I think that these topics together constitute the important problem in early human relationships right now, so I'll be writing some more about them. There are many additional interesting facts to consider...

References:

Martinón-Torres M, Bermúdez de Castro JM, Gómez-Robles A, Arsuaga JL, Carbonell E, Lordkipanidze D, Manzi, G, Margvelashvili A. 2007. Dental evidence on the hominin dispersals during the Pleistocene. Proc Nat Acad Sci USA (early) doi:10.1073/pnas.0706152104

Stringer C. 2002. Modern human origins: progress and prospects. Phil Trans Roy Soc Lond B 357:563-579. doi:10.1098/rstb.2001.1057

Rightmire GP. 1998. Human evolution in the Middle Pleistocene: the role of Homo heidelbergensis. Evol Anthropol 6:218-227. doi:10.1002/(SICI)1520-6505(1998)6:6<218::AID-EVAN4>3.0.CO;2-6

Carbonell E and 19 others. 2005. An Early Pleistocene hominin mandible from Atapuerca-TD6, Spain. Proc Nat Acad Sci USA 102:5674-5678. doi:10.1073/pnas.0501841102

Bruner E, Manzi G. 2005. CT-based description and phyletic evaluation of the archaic human calvarium from Ceprano, Italy. Anat Rec A 285A:643-657. doi:10.1002/ar.a.20205

National Geographic News has a short article about the tooth from Sima del Elefante, Atapuerca.

The team notes that the tooth's age, dated at around 1.2 million years old, is similar to that of stone tools and animal fossils bearing human-tool cut marks uncovered at sites in Spain, France, and Italy.

"Now we finally have the anatomical evidence of the [early humans] that fabricated tools more than one million years ago," the team said in a statement.

The researchers added that they are waiting for final analysis of the tooth before publishing their findings in a scientific journal.

Not much more to say, really.

This morning, my irritation level about this Neandertal women hunting story finally reached its boiling point. I unleashed a Neandertal-style cry of anguish -- which if you've never heard one, sounds remarkably like a Wookie-style cry of anguish.

Am I a simple misogynist? Does the idea of deerstalking Neandertal women threaten my manhood? Maybe, although Gretchen assures me I'm not. Mostly, I'm irritated because a full-text search of the paper yields no mention of any possible test of their idea.

I hate being so critical of this idea. I really like Kuhn's and Stiner's other work. But over half of people think that all our raving about ancient humans is fantasy anyway, so I try to be as critical as I can. And this is a real doozy.

It's bad enough for something like this to hit the New York Times. But this one has even invaded Instapundit. Clearly something must be done!

So, I told my class I was incapable of giving a normal lecture, and would continue on the subject of sexual division of labor until they found a satisfactory means of testing Kuhn and Stiner's hypothesis.

Unfortunately, my students actually like seeing me rant and tear out my hair, so they had a positive disincentive to find the right answer. So, if you want a job done right...

Testing the hypothesis

In case you've missed it, the proposition by Steven Kuhn and Mary Stiner -- excellent archaeologists, both -- is that Neandertal women were incapable of the kind of sex-based division of labor found in most human societies, and instead spent their time helping Neandertal men to find and kill large animal prey.

So let me approach this hypothesis with a skeptical eye. What exactly does it entail?

1. Kuhn and Stiner propose that modern humans had a fitness advantage because they mobilized female labor to find and process high-effort plant resources and small animals.

2. Neandertals were so committed to large-animal hunting that they required assistance from their women, compromising their ability to collect low-quality but dependable plant and small animal resources.

3. In Kuhn and Stiner's view, these differences meant that modern humans and Neandertals were locked onto different adaptive peaks, and Neandertals were constrained from adopting the modern human pattern of division of labor, even though it allowed greater population growth.

Why is the adaptive peak story (number 3) necessary? Here's why: if the behavior of Neandertal women was very flexible, then they could have adopted the broader dietary strategy easily. There would be no rugged fitness landscape, because behavioral plasticity would smooth the fitness differences.

In other words, condition (3) is absolutely necessary to the hypothesis that sexual division of labor was the fitness advantage of modern humans over Neandertals.

Testing the adaptive landscape condition

I think that the adaptive landscape assumption is the greatest flaw in this hypothesis. Kuhn and Stiner's hypothesis depends on the assumption that sexual division of labor is quite rigid, so that Neandertals did not adopt a modern organizational strategy even though such a strategy was adaptive for modern humans in the same habitat.

That is a very strong claim, but necessary to their hypothesis. If Neandertal social organization strategies were actually flexible, then cultural variation among Neandertal groups would have enabled some of them to find the high-fitness strategy. Once a few groups reached the high-fitness sexually divided labor strategy, they would have proliferated. That is precisely the logic behind Sewall Wright's shifting balance theory, and it applies here equally well. Plasticity enables a population to explore the fitness landscape.

So if Neandertal foraging behavior was actually flexible, then there would have been no impediment to Neandertal females exploiting collected plants and small animals. In fact, if you showed that Neandertals actually did collect plants and eat small animals, it seems to me that the entire argument about social organization is moot.

As noted in several of the comments on the Kuhn and Stiner paper, Neandertals did collect small animals, marine resources, and plants at many sites. They did use grinding stones occasionally in Eastern Europe. They did collect grass seeds in the Levant, and nuts in Spain. In other words, Neandertals did have substantial dietary flexibility. This evidence for flexibility is currently best outside northwestern and north-central Europe, at least from faunal and plant remains.

The flexibility is also evident in dental microwear, which includes individuals from northwest and north-central Europe (Pérez-Pérez et al. 2003, Lalueza 1996). Based on the dates of specimens with different wear patterns, Pérez-Pérez and colleagues suggested not only that Neandertals had great dietary flexibility, but also that they may have relied on plants more during colder climatic periods. Since the early Upper Paleolithic was one of the colder periods, this seems relevant to the apparent contrast in subsistence strategies. In any event, the idea that Neandertals were invariantly carnivorous is simply inconsistent with the pattern of data.

Let's consider for a moment what would cause Neandertals to continue to pursue a low-fitness hunting strategy when they obviously were capable of acquiring high-fitness plant foods, they experimented with high-fitness plant foods, and many of them ate enough of the high-fitness plant foods to mark up their teeth. It seems quite implausible that Neandertals were locked into a strategy of perpetual experimentation and sampling of a high-fitness resource!

I think we're forced to conclude that either (a) further exploitation of plant foods did not provide a high-fitness strategy, or (b) Neandertals were stupid. Right? All this rigmarole about organizational strategies becomes another way to describe Neandertal stupidity.

Human ecology

The best explanation for why Neandertals didn't use more plant foods is that they didn't pay. Here's what Kuhn and Stiner wrote about plant acquisition:

Vegetable foods may well have been part of Middle Paleolithic diets in Eurasia, but these were more like salads, snacks, and desserts than energy-rich staples. (Grinding stones are known from the contemporaneous Middle Stone Age in Africa, a point we will return to later.)

...Large underground storage organs are common among plant taxa in arid sub-Saharan Africa, but the high-yield edible plant foods of temperate and Mediterranean Eurasia tend to be seeds and nuts that, while potentially nutritious, require more effort to collect and process and thus afford low net yields (Kuhn and Stiner 2006:957).

So Neandertals were using the most energy-rich resource available in Europe, and this is a problem? Many of us like salads, snacks and desserts. If they were making effective use of the available plant foods, then there is no basis whatsoever to suggest that Upper Paleolithic people were pursuing a more effective strategy. As I hint below, Upper Paleolithic people and modern hunter-gatherers both may share demographic pressures that forced a reduction in diet quality and trophic level. We should attend to the ecological changes that made the Upper Paleolithic adaptation work.

The same argument applies to the changes in social ecology, including the use of needles in the Upper Paleolithic. As Soffer ably demonstrates elsewhere (with Adovasio and colleagues), Upper Paleolithic people used needles because they had fabric. Neandertals didn't. That was a technological innovation that changed human ecology.

Somebody might be tempted to say that if Neandertal women had adopted a fundamentally Upper Paleolithic social organization, they would have invented fabric. But that argument doesn't apply to any recent technological innovation (if only 1970's office workers had more time on their hands, they would have invented the spreadsheet!), so I don't see how it can sensibly apply to Neandertals.

The deerstalking women

Note that these observations say nothing about what Neandertal women actually did. In other words, we have shown that condition (3) is very unlikely, but we haven't addressed condition (2). Maybe, as part of their dietary flexibility, Neandertal women really did help with hunting some of the time.

At its boundary -- Neandertal women hunted occasionally -- this idea is nothing more than an untestable suggestion. We cannot negate such a broad suggestion. Besides, in broad form it is likely true. Who could deny that a hungry Neandertal woman might help her male groupmates drive animals into an ambush?

But I think we can at least test the idea that Neandertal women were habitual hunters. I am willing to make one assumption: Neandertal hunting strategies involved a higher mortality risk than Upper Paleolithic hunting strategies.

That assumption is justifiable in terms of technology -- Neandertals killed with close ambush methods because they did not have projectile weapons; Upper Paleolithic people did have projectile weapons, and they apparently also used more logistical hunting strategies. Also, the assumption is justifiable by mortality and injury data -- Neandertals died younger, and they died with lots of healed injuries.

Still, the mortality risk of Neandertal hunting was not uniformly distributed. Some roles were riskier than others. It may well have been that women could participate in hunting, as drivers for example, while bearing a lower mortality cost than men. This is, of course, a sexual division of labor, but such a division would not involve separate male and female collection strategies.

But if Neandertal women could bear a lower mortality cost while participating in hunting, then so could Upper Paleolithic women. And if Neandertal men could spend less time hunting and have a higher return rate with female help, then so could Upper Paleolithic men. And if Neandertal women didn't need to stay in camp to tend their children, then neither did Upper Paleolithic women.

In other words, if hunting was less risky for Neandertal women than for Neandertal men, it was even less risky for Upper Paleolithic women! Upper Paleolithic women should have been more likely to hunt than Neandertal women.

You see, the caloric return of different food sources (meat versus plants, big animals versus small animals) for Neandertals and Upper Paleolithic people would have been precisely the same, assuming the same success rate and risks. So to explain a difference between the two groups in adaptive terms, we need to posit a difference in their success rates or their risks.

We have four options:

a. Upper Paleolithic women achieved a higher return than Neandertal women from plants and small animals.

b. Upper Paleolithic hunting returns were much higher than Neandertal hunting returns, so women had plenty of free time to collect plants and small animals.

c. Upper Paleolithic hunting returns were much lower than Neandertal hunting returns, so women were forced to collect plants and small animals, despite their lower caloric value.

d. Upper Paleolithic camps were intrinsically more dangerous than Neandertal camps, requiring more women (and possibly men) to stay close to defend children and new mothers.

Each of these four options reduces to a very simple proposition. For example, under option (a), Upper Paleolithic women could have achieved higher return rates from plant foods if they had better technology. Option (b) implies that hunting technology increased Upper Paleolithic returns. Option (c) implies that demographic growth placed greater stress on local resources in the Upper Paleolithic (it is very similar to the "broad spectrum" idea as applied to the development of agriculture). And option (d) would imply that demographic growth resulted in more warfare between neighboring groups, also consistent with the increase in social markings and regional tool differentiation in the Upper Paleolithic.

Notice that all of these options come down to technological or demographic changes. None of them give an important causal role to sexual division of labor. Instead, the aspects of division of labor that can be observed in the archaeological record emerge as a result of basic technological or demographic conditions.

I view the demographic factors as more important than technological ones, but I have no strong rationale for this preference. To me, the most important point is that the risk factors constraining the adoption of full-time hunting for recent human women must have been even stronger for Neandertal women. This means if we want to find hunting women, we should look at recent human foragers. And they aren't there.

Technological or demographic conditions may have altered this picture, increasing the likelihood that Neandertal women did hunt. But there is no evidence that they did.

Final lessons

So the idea can be tested! It wasn't even that hard!

To the extent that we can compare with living and prehistoric humans, there is no support for the idea that Neandertals went extinct because their women spent too much time hunting. There are positive reasons that refute this idea -- most importantly, the demonstrated dietary flexibility of Neandertals and other archaic humans, which would have enabled Neandertal women to exploit a systematic plant and small animal collection strategy if it actually had increased their fitness. The fact that they did not do so is probably a reflection of their ecology, not their social organization.

It remains difficult or impossible to refute mere possibilities on the basis of the archaeological and fossil record. But we should remember that such mere possibilities are not testable hypotheses.

Certainly, some Neandertal women may have hunted along with Neandertal men. Maybe they were Neandertal Amazons who severed a breast to better thrust spears into roaming bison. After all, we know that they were capable of amputating limbs, so why not?

The "why not" in this case is, obviously, that Neandertal Amazons are a product of fantasy. Sure, the fossil record cannot rule out the possibility that they existed. But comparisons with our everyday experience and our knowledge of variation in other species both tend to indicate that such a curious adaptation would be unlikely.

The same is true of Kuhn and Stiner's model. A deerstalking Neandertal woman is by no means impossible. Maybe they spent a lot of time hunting, who knows? The problem is that there is no evidence that they did so.

References:

Bamforth DB. 2002. Evidence and metaphor in evolutionary archaeology. Am Antiq 67:435-452.

Kuhn SL, Stiner MC. 2006. What's a mother to do? The division of labor among Neandertals and modern humans in Eurasia. Curr Anthropol 47:953-980.

Lalueza C, Pérez-Pérez A, Turbon D. 1996. Dietary inferences through buccal microwear analysis of Middle and Upper Pleistocene human fossils. Am J Phys Anthropol 100:367-387.

Pérez-Pérez A, Bermúdez de Castro JM, Arsuaga JL. 1999. Nonocclusal dental microwear analysis of 300,000-year-old Homo heidelbergensis teeth from Sima de los Huesos (Sierra de Atapuerca, Spain). Am J Phys Anthropol 108:433-457. Abstract

Pérez-Pérez A, Espurz V, Bermúdez de Castro JM, de Lumley MA, Turbón D. 2003. Non-occlusal dental microwear variability in a sample of Middle and Late Pleistocene human populations from Europe and the Near East. J Hum Evol 44:497-513. DOI link

I've been reading the new paper by Steven Kuhn and Mary Stiner about Neandertal versus modern human organizational strategies. I'm taking a lot of notes about it, and have several reactions.

But first, let me just say this: ten years ago, we were arguing about whether Neandertals could hunt at all, or whether instead they were ineffective scavengers depending on carnivore handouts.

I suppose those days must be behind us, because now we read Neandertals were such committed big game hunters that they needed their females and kids to hunt along with them, which fatally compromised their ability to find and exploit small animals and plant foods.

Apparently it took some tropical mojo to make modern women realize they could eat plant foods like every other primate.

But then, one wonders how the Sima de los Huesos women managed to do what Neandertals couldn't...

UPDATE (12/5/2006): If you've come over by a link to this post, I have followed up with a second post that goes through the paper's argument in detail and provides some criticism. In case it wasn't obvious above, I think this idea about Neandertal women is wrong.

References:

Kuhn SL, Stiner MC. 2006. What's a mother to do? The division of labor among Neandertals and modern humans in Eurasia. Curr Anthropol 47:953-980.

Pérez-Pérez A, Bermúdez de Castro JM, Arsuaga JL. 1999. Nonocclusal dental microwear analysis of 300,000-year-old Homo heidelbergensis teeth from Sima de los Huesos (Sierra de Atapuerca, Spain). Am J Phys Anthropol 108:433-457. Abstract

OK, I just think the Mozart skull DNA extraction is creepy. Not because identifying dead skulls is creepy in itself -- hey, I like forensic anthropology a lot more than the random person on the street.

No, I think it's creepy because of the mammoths. I got ahold of the mammoth DNA paper by Poinar and colleagues a couple of weeks ago; it's on Science Express.

Can I just say, Science Express is super-lame? I mean, a subscription wall inside a subscription wall!

The paper, on the other hand, is decidedly not lame. Here is the abstract:

We sequenced 28 million base pairs of DNA in a metagenomics approach using a woolly mammoth (Mammuthus primigenius) sample from Siberia. Thanks to exceptional sample preservation and use of a novel emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

Of course, they were helped a lot by the unique preservation in the sample, which was found in optimal cold conditions at the shore of Lake Taimyr. That probably cut down substantially on extraneous microbial and fungal DNA.

But the metagenomic approach makes these kinds of contaminants mostly irrelevant. In metagenomics, researchers sequence every last piece of DNA in a sample, and then figure out what all the pieces are by comparing them to genome databases. What you get is illustrated by this pie chart:

Proportion of DNA sequence from different sources in the mammoth sample of Poinar et al. (2006).

There are two beautiful things about this graph. One is that, although there happens to be a lot of mammoth DNA in the sample (over 50 percent), there doesn't have to be. The fact is, it doesn't really matter how much of the original stuff is there or how much junk there is; if there is any minimal level of DNA preservation from the original beast, you are going to be able to find it.

The other beautiful thing is that the ability to recognize sequence is determined not by your own work on a fossil, but by the completeness of genome databases. This means that unknown sequences just sitting on your computer after an extraction gradually, inexorably, will be identified when science gets around to sequencing the organism they came from. The 18.42 percent "unidentified" in the graph will slowly reduce over time. Now, almost none of that will be mammoth-relevant information, but it's still pretty cool.

There are two problems. One is, if the DNA preservation is poor, you are going to have to grind through an awful large amount of bone to get any kind of good genome coverage. In this case, a small sample of mammoth bone was sufficient to sequence 13 million base pairs of mammoth DNA. But there might or might not be anything interesting in those 13 million base pairs. It is certainly possible to sequence more from more samples, and that is the point: if preservation was not as good as in this particular sample, you would have to mill major mammoth mandible to get a full genome sequence.

For mammoths, I don't see that as much as a problem. Remember the Explorers' Club, after all. I imagine a large woodchipper in some DNA lab standing ready to chomp the frosty mammoth meat.

For hominids, that will be a bit more troubling. Will we be willing to put an entire skull in the blender for a complete Neandertal genome? Or if Neandertals are well-enough preserved and we are willing to settle for less-than-full genome coverage, what about more ancient or more marginally preserved fossils, like an Atapuerca femur? Does a genome have more scientific value than a fossil object itself, if we can preserve its anatomical detail with microCT or other techniques?

Then there's the other problem: degradation. How good is the sequence? Even in the exceptionally well-preserved mammoth sample, there was substantial evidence for degradation of sequence, with around twice the number of expected C -> T transitions compared to elephant and a third or so more G -> A transitions. That's an awful lot of potential noise for anyone looking at gene function and evolution. I'm guessing what will have to be done is to simply ignore certain classes of mutations that are likely to derive from postdepositional diagenesis (that is, DNA rot). Even so, some remaining diagenetic changes will remain hard to figure out.

The best approach may be to simply grind up more bone; making sure that each genome section is covered by multiple copies. The multiple copies allow for error correction, since it is relatively unlikely that any single diagenetic change will occur in multiple copies of a gene. The really, really good news is that given enough sample, we are very likely to get accurate genome sequences from ancient humans.

But the whole thing raises a fairly hairy problem concerning fossil humans. It's like that commercial with the owl and the Tootsie Pop -- how many samples does it take to get the genome? CHOMP!

So what about Mozart?

Something we can do to a Neandertal, we can certainly do to bones from any historical figure. The Mozart genome, the King Tut genome, the Lincoln genome, the John Wilkes Booth genome -- we can have them all!

Today, you can have your Y chromosome sent away to find out if you are a descendant of Genghis Khan. Tomorrow, you'll be able to compare every one of your genes to Mozart. In all likelihood, some genetic variants will be associated with musical talent. The obvious next Austrian TV special will be the Mozart genotypes for any music-related genes. The less obvious step will be screening your young Julliard candidate for genetic similarity to Mozart.

There's no way Mozart can cash in on the process. But what about living celebrities, or athletes? Subscribe to iGenes and you can find out whether your kid's genes might give him the chops for the NBA (with proper work and training, of course) or whether he should start hitting the links instead.

That's what I find creepy. And there are an awful lot of composers buried in well-known locations that could be dug up for genetic comparisons.

References:

Poinar HN et al. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (online early) doi:10.1126/science.1123360.