Neandertal DNA

Now watching the NOVA ScienceNOW about "What makes us human".

9:06: "The idea of another species of humans sharing our cities isn't that far-fetched. 30,000 years ago, there were at least four different kinds of humans sharing the earth, including the Neandertals"

The introduction to Neandertals isn't bad, although I really don't like it when people say "the ones who stayed in Africa became us" -- that minimizes the contribution of other people, and glosses over the possibility that some ancient Africans didn't become "us", or were among the ancestors of some Africans but not all.

9:08: "Daniel Lieberman from Harvard looks for answers in the way human heads evolved" -- Lieberman: "What makes you different from Neandertals is basically above the neck."

9:09: Now Pogue is showing himself in a makeup studio being made into a Neandertal character. Back to Lieberman explaining how the Neandertal head is different from ours. It's really interesting to hear him describe this, because the description is completely typological -- there's no conception here of variation within Neandertals or within humans.

9:11: OK, the makeup transformation is complete. I don't want to cast aspersions on the artists, but the result doesn't compete with the makeup jobs on Face/Off.

Pogue goes walking down a city street. I don't see anybody noticing..but of course there's a cameraman following him around.

9:13: Differences in the shape of the brain. Lieberman "wouldn't bet his mortgage" on human brains being better than Neandertals.

Now Pogue is presenting several just-so stories about why we were superior to Neandertals. He dismisses these as "speculation" and starts talking about the Neandertal genome. We see a Max Planck scientist grinding up some bone with a Dremel tool.

9:15: Yay, Ed Green!

Green: "They had sex, they had descendants, we find this trace in our DNA today. Amazing."

9:18: This is the fourth show I know of where they have a presenter get their DNA sampled to find the Neandertal fraction. It's really cool that they are getting this news out there.

Green shows Pogue a part of chromosome 12 where he has a Neandertal nucleotide. They're showing a laptop screen with a slot machine-like display of nucleotides. I suppose it was really a blank screen and they did it in post-production. Either that, or I have to get the slot machine DNA typing program!

9:20: "We may not see Neandertals among us, but they are still here, within us."

Still walking down the street. An older lady seems to have decided Pogue is some kind of freak.

Oh, no! An animated Neandertal in drag! She/he is putting on makeup (this is about the shells and pigments associated with Neandertals). I have only this to say: Through the Wormhole has way better short animations than ScienceNOW.

Whew, that was over quick. Now he's on to the origin of language.

9:22: It's Dave Frayer! He's got a suitcase with skulls inside. Man, it would be cool if it were like the one in Pulp Fiction!

OK, well, it's cooler to have one with skulls inside, I guess.

Going through Homo erectus brain size. A symmetrical stone tool becomes a way to look into the cognitive abilities of early Homo.

9:26: On to Dietrich Stout, who is discussing the pathways in the brain used for stone tools. He works with Bruce Bradley, expert stone knapper, who is giving Pogue a lesson in toolmaking.

With toolmaking we're looking at complex, sequential thought. Bradley: "Because what are we looking at with language, it's complex sequential thought"

9:29: Now Cynthia Thompson, who is looking at people with brain injuries that lead to aphasia. "Agrammatic aphasia patients share a common characteristic: damage to the left hemisphere of the brain, which contains an area called Broca's area...does Broca's area have anything to do with stone toolmaking?"

9:31: Going into a scanner, where people are watching stone toolmaking via a projector, on the argument that watching an activity and doing the activity involve the same brain area. "Watching the video of simple choppers resulted in mild activity in Broca's area, but watching the video of making a handaxe caused four times as much activity"

9:34: A short interlude on babies learning language.

9:35: Looking at babies learning to laugh. Gina Mireault is studying babies smiling and laughing. "What we found with these very young babies, is that when we tell parents to make their babies laugh, they do some very outrageous things. Laughter is irresistible"

9:37: Now at the Cincinnati Zoo to see if animals laugh. Pogue tickles a penguin -- "he's laughing" -- "no, that's the noise they make when they want to breed"

Pogue is really talented at this part, he totally commits himself to being silly in the name of science.

Marina Davila-Ross is studying primate laughter. They are at the Stuttgart Zoo with gorillas. She collected sounds from all the great apes being tickled. Super cool audiogram images of the laughter sounds going from most distant -- orangutans -- to humans across the phylogenetic tree. Gorillas always use the same kind of panting laughter, as a part of horseplay.

9:42: Now with psychologist Michael Owren, looking at acoustic models of laughter sounds in people.

9:43: Pogue asks a great question: "How did that make me have more babies?" The program gives an answer (for laughter and social relationships) but it's great that they edited it to emphasize this question.

9:44: Zeray Alemseged in Ethiopia: "I went to start the first Ethiopian-led project in paleoanthropology ever, but it wasn't easy". The show gives a great short biography of Alemseged. This is an awesome segment.

9:48: Now at Dikika. They do a great job illustrating the discovery of the skeleton.

9:50: Don Johanson discussing how we "did not instantly become human".

9:51: "Day after day, for six years, Zeray chipped away at the piece of stone." They're comparing the Selam teeth to apes and humans, inferring its age and pattern of development. The show has him at a computer with Fred Spoor examining CT data.

9:53: Describing the hoopla that arose upon the publication of the Dikika skeleton. This has been a great 12-minute segment on Alemseged.

9:55: And that's the program. Very well done, a range of segments that go together very naturally. They really did save the best for last, but really everyone in the program did a great job.

Science today has released the new paper on the Denisova high-coverage genome by Mattias Meyer and colleagues from Svante Pääbo's group [1]. There is a lot of material in the supplements of the new paper, and it will take some time to work through implications.

The basics are quite simple: The paper confirms the initial interpretation of the genome by David Reich and colleagues [2] in most respects. The mixture with a whole-genome sample from Papua New Guinea is estimated at 6% Denisovan ancestry. Confirming the later paper by Reich and colleagues [3], the new analysis finds no significant evidence of Denisovan ancestry in a mainland south Chinese (Han Dai) individual, and can exclude it down to a very small fraction:

However, in contrast to a recent study proposing more allele sharing between Denisova and populations from southern China, such as the Dai, than with populations from northern China, such as the Han (17), we find less Denisovan allele sharing with the Dai than with the Han (although non-significantly so, Z = –0.9) (Fig. 4B) (table S25). Further analysis shows that if Denisovans contributed any DNA to the Dai, it represents less than 0.1% of their genomes today (table S26).

That is a mystery to be explained. How did Asians end up lacking any evidence of Denisovan ancestry, when the peoples of Sahul (Australia and New Guinea) have six percent? It's nutty! The early modern humans who were the ancestors of present Sahulian peoples surely came from Asia, and they surely mixed with Denisovans there somewhere, right? But today there's no sign that present Asian peoples descended from those early Asian peoples.

We must, I think, conclude that there was at least one, and possibly several episodes of massive population movement across South and Southeast Asia.

I have recently completed a review of the analogous problem for Neandertals in Europe -- late and early Neandertals themselves appear to have been a dynamic population. I'm now working on a review of the situation in Southeast Asia. We may fundamentally have to look at the archaeological record in a new, and much more dynamic, way than has been the case.

Neandertal gene flow

To me at the moment, this is the most interesting paragraph of the new paper:

Interestingly, we find that Denisovans share more alleles with the three populations from eastern Asia and South America (Dai, Han, and Karitiana) than with the two European populations (French and Sardinian) (Z = 5.3). However, this does not appear to be due to Denisovan gene flow into the ancestors of present-day Asians, since the excess archaic material is more closely related to Neandertals than to Denisovans (table S27). We estimate that the proportion of Neandertal ancestry in Europe is 24% lower than in eastern Asia and South America (95% C.I. 12–36%). One possible explanation is that there were at least two independent Neandertal gene flow events into modern humans (18). An alternative explanation is a single Neandertal gene flow event followed by dilution of the Neandertal proportion in the ancestors of Europeans due to later migration out of Africa. However, this would require about 24% of the present-day European gene pool to be derived from African migrations subsequent to the Neandertal admixture.

This is a very interesting result, partially because it is the opposite of what we are finding. As I explained earlier this year, we are finding Europeans to share more Neandertal alleles than Asians do. The difference in our results has been much smaller than 24%; really only an increase of less than 0.5% on the whole genome, or maybe 10% relative to the overall amount in Europe (which is on the order of 3%).

My initial reaction to this difference is that it reflects the sharing of Neandertal genes in Africa. Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison. But if Africans have some gene flow from Neandertals, eliminating alleles found in Africans will create a bias in the comparison. If (as we think) some African populations have Neandertal gene flow, that probably came from West Asia or southern Europe. So as long as the present European and Asian (and Native American) samples have undergone a history of genetic drift, or if (as mentioned in the quote) they mixed with slightly different Neandertal populations, this bias will tend to make Asians look more Neandertal and Europeans less so.

Anyway, this demands further investigation. The Denisova genome makes a more compelling outgroup for these kinds of comparisons, because it is much closer to us than chimpanzees are. But it isn't really an outgroup because it shares alleles by descent with Neandertals. So it takes some clever genetics to compare the distributions of derived alleles in these genomes in terms of introgression versus incomplete lineage sorting.

Denisovan demography

It has become possible to make some good estimates of demographic history using only a single diploid genome, using a technique developed by Li and Durbin [4]. Meyer and colleagues applied this technique to the Denisova genome, finding that its genetic history contrasts with that of living human populations:

To estimate how Denisovan and modern human population sizes have changed over time we applied a Markovian coalescent model (22) to all genomes analyzed. This shows that present-day human genomes share similar population size changes, in particular a more than two-fold increase in size before 125,000–250,000 years ago (depending on the mutation rates assumed (23), Fig. 5B). Denisovans, in contrast, show a drastic decline in size at the time when the modern human population began to expand.

There is not yet enough data from Neandertal genomes to apply the same method, but to the extent that we understand their diversity, they show a similar picture. These archaic humans in Eurasia had much, much smaller effective population sizes than the ancient population of Africa. That's not surprising, given what we understand about ancient hunter-gatherer population dynamics.

What may be a bit more surprising is the geography. We know that Neandertals of Europe and Central Asia lived in an environment that was relatively marginal for their technology and subsistence pattern. The Denisovan population could well have lived in parts of South or Southeast Asia -- subtropical and tropical areas comparable to Africa in their ecological diversity and resource richness.

We might have imagined that the Denisovan population would be more diverse than Neandertals -- that it might have been comparable in diversity to part of Africa, if not the entirety of Africa. The genome is inconsistent with that picture.

How can we explain the apparent contrast?

1. Maybe Denisovans didn't live in South or Southeast Asia at all. If not, that demands that we explain how Australians got their genes.

2. Maybe the population was geographically extensive and diverse, but the genome from Denisova Cave doesn't represent it well. If so, we might discover that Sahulians actually have even more ancestry from this group. Alternatively, we might find that the early history of the population was widely shared, but the recent history diverged between Siberian and other branches of the Denisovan-inhabited region.

3. Maybe African diversity emerged from a much more complex series of interactions than we now appreciate. The demographic model of Li and Durban doesn't encompass admixture, just the probability of gene coalescence across time. We have recently begun to appreciate the reality of ancient African population structure. If those initial African populations were more divergent from each other than Neandertals and Denisovans, their later mixture would give rise to a picture of early population expansion, even if each of them had relatively low (Denisovan-like) diversity.

This picture is already complicated. It will get more so. We have a long way to go before the archaeology of MSA and Middle Paleolithic peoples will be reconciled with these genetic models.

The "modern human" catalog

I think it's tremendously interesting that the authors have compiled a list of gene variants shared by living humans that are absent from this high-coverage archaic human genome. It's a first step to identifying networks of genes that have been subject to recent evolutionary change in human ancestors.

That being said, the list of genes itself doesn't lend itself to concrete conclusions:

One way to identify changes that may have functional consequences is to focus on sites that are highly conserved among primates and that have changed on the modern human lineage after separation from Denisovan ancestors. We note that among the 23 most conserved positions affected by amino acid changes (primate conservation score ≥ 0.95), eight affect genes that are associated with brain function or nervous system development (NOVA1, SLITRK1, KATNA1, LUZP1, ARHGAP32, ADSL, HTR2B, CBTNAP2). Four of these are involved in axonal and dendritic growth (SLITRK1, KATNA1) and synaptic transmission (ARHGAP32, HTR2B) and two have been implicated in autism (ADSL, CNTNAP2). CNTNAP2 is also associated with susceptibility to language disorders (27) and is particularly noteworthy as it is one of the few genes known to be regulated by FOXP2, a transcription factor involved in language and speech development as well as synaptic plasticity (28). It is thus tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans.

Interesting. I can imagine a Ph.D. dissertation looking into the function of each of those genes. It is surely true that in the last 300,000 years, human brains have been evolving. But why these genes as opposed to others? And how many regulatory changes (as opposed to amino acid changes) may have been further involved?

Maybe even more interesting: How many times will the human alleles be found in some other Denisovan (or Neandertal) genomes, and how often will the "archaic" allele be found in anyone living now?

A limited series of comparisons is too small to exclude that the range of variation will overlap, as fossil analysts have known for a long time. So we will need to work on extending our knowledge of the range of variation within living people, by increasing the sample of genomes representing populations around the world, particularly in Africa.

The technology

Of course, the most exciting thing about the new paper is the proof of concept for future high-coverage archaic genomes. The lab was able to generate the high-coverage sequence using its existing samples, by sequencing single-strand DNA instead of requiring double-strand DNA. This is a massive advantage when working with ancient DNA, because damage to the sequence often prevents double-stranded DNA from being amplified.

The paper makes explicit that the Denisova phalanx simply has better endogenous DNA preservation than any other specimen known. That being said, the new sequencing method has greatly increased the sequence yield from the sample:

We applied this method to aliquots of the two DNA extracts (as well as side fractions) that were previously generated from the 40 mg of bone that comprised the entire inner part of the phalanx (2, 8). Comparisons of these newly generated libraries to the two libraries generated in the previous study (2) show at least a 6-fold and 22-fold increase in the recovery of library molecules (8), which is particularly pronounced for longer molecules (fig. S4).

It would be too soon to say that a similar increase in yield will happen for other specimens, but obviously, this may bring higher coverage into reach for several specimens that are currently only sequenced at very low coverage, including the Vindija, Mezmaiskaya, and El Sidron Neandertals. We will have to wait and see how the new technique affects ancient DNA recovery going forward.

I keep telling people that I think it's exciting that research into human evolution is now pushing technology forward. It has often been that paleoanthropology uses technological advances in other fields. But with ancient DNA, we really see an organic growth of technology along with research questions about our evolution. In our work on the ancient genomes, we're making some progress pushing forward knowledge about human biology by understanding human evolution. Evolution really is the fundamental principle of biology, but using evolution to learn about biology sometimes requires traveling through time. Ancient DNA gives us a time machine bringing new insights into reach.

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