Denisova genome at high coverage (Meyer et al. 2012)

The high coverage Denisova genome had been made available online in February, and now the paper to accompany it has appeared in Science. I do appreciate the fact that the Max Planck folks did not wait until publication to share their data; anything that can accelerate the process of scientific discovery is good in my book. I'll post any comments on this paper as an update when I read it.

UPDATE I: The most exciting thing about this paper, even above and beyond the new information it provides is the new technology of single strand sequencing. From a ScienceNOW story:

Meyer's breakthrough came in developing a method to start the sequencing process with single strands of DNA instead of double strands, as is usually done. By binding special molecules to the ends of a single strand, the ancient DNA was held in place while enzymes copied its sequence. The result was a sixfold to 22-fold increase in the amount of Denisovan DNA sequenced from a meager 10-milligram sample from the girl's finger. The team was able to cover 99.9% of the mappable nucleotide positions in the genome at least once, and more than 92% of the sites at least 20 times, which is considered a benchmark for identifying sites reliably. 

... 

Back in Leipzig, the mood is upbeat, as researchers pull fossil samples off the shelf to test anew with "Matthias's method." First on Paabo's list: Neandertal bone samples, to try to produce a Neandertal genome to rival that of the little Denisovan girl.

There are two reasons to be very happy: 

First, the new method will probably open new vistas in ancient DNA, as it represents an order of magnitude improvement in the amount of coverage that can be accomplished. 

Second, the authors were able to estimate the age of the specimen by cleverly measuring how much it differed from chimpanzees vs. how much we, living humans, so differ. As they explain in the supplement:

Based on the differences in branch length to the common ancestor of human and chimpanzee (1.13% to 1.27%; see Table S13), we estimate that the observed branch shortening corresponds to 73,614 – 82,421 (average 75,443) years assuming a human-chimpanzee divergence time of 6.5 million years.

Note that recent developments in dating human-chimpanzee divergence may push it to an older date than 6.5 million years. But, even if that date is accepted, the Denisova specimen is now the oldest Homo sequenced and our ability to get high-coverage DNA from a ~75ka specimen means that we may be getting DNA from other really old samples. Human evolutionary genetics is going to be very interesting in the coming years!

UPDATE II (East Eurasians more Neandertal than Europeans): 

There were hints of this in the previous papers, but they did not reach statistical significance. Now, it appears that they are confirmed. From the 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%). 

This finding is important, because it shows that the simple model of modern humans expanding Out-of-Africa, interbreeding with Near Eastern Neandertals and carrying on to the rest of the world, carrying with them a fraction of Neandertal ancestry is incomplete.

Some explanations for this finding are discussed on p. 41 of the supplement. The fact that Neandertals were a West Eurasian-distributed species is at great odds with the finding of greater Neandertal admixture in Asian/American populations. But, if the Iceman, and, by implication, Paleolithic Europeans were more similar to Neandertals still, a further complication is added. This may be consistent with ideas from palaeoanthropology about great levels of variation in late Pleistocene humans compared to recent ones. One can imagine that groups varied substantially in their proportions of Neandertal ancestry until fairly recent times, but homogenizing gene flow evened out what was initially a very uneven distribution, but not completely.

UPDATE III (Mutation rate):

The paper appears in a transitional period in our understanding of mutation rates. So, while it presents a much better Denisova genome than the earlier published one, our understanding of how and when the Denisova population diverged from modern humans is now less clear. I have covered some of the mutation rate controversies recently on the basis of three papers: Kong et al., Sun et al., and Langergraber et al.

The discussion in Supplementary Note 10 summarizes the increased uncertainty about the topic:

An important date in human evolution is when the ancestors of modern humans diverged from Denisovans and their sister group the Neandertals. In the paper on the draft sequence of the Neandertal genome, we estimated this date for Neandertals (1). Since Denisovans are a sister group of Neandertals (2), they should have approximately the same population divergence; however, we never assessed this directly. Furthermore, the inference in the Neandertal genome paper was based on assumptions about mutation rates from early 2010. Since that time, better data have become available, lower mutation rates have been suggested, and the true value of the mutation rate has become less certain. It is important to obtain a new date estimate in light of this. 

Paleontological calibration can only take us so far; for example, Neandertaloid traits in the Atapuerca hominins suggest an early split with modern humans and therefore a low mutation rate, but they also suggest a much earlier human-chimp speciation time than commonly thought. I think that a technical solution to the problem will eventually be found, which will show why there is the 2-fold difference in mutation rate estimates.

UPDATE IV (Demographic History): 

The plot on the left shows inferred changes in population size for 12 different populations, using the PSMC approach of Li & Durbin.

One can see that the different populations seem to match quite well until ~750/375ky (depending on mutation rate), when Denisovan population starts decreasing, and the population of the modern human groups starts increasing. Then at ~110/55ky, population sizes in modern humans begin diverging.

There are two ways to look at this: if one assumes tree-like divergence of population, then obviously the fact that Denisova spends the period between 750/375 to 100/50ky at a much lower population size than modern humans speaks of an isolated population with limited genetic diversity.

But, as I've mentioned before in this blog, genetic diversity can be created by admixture. Take two populations that diverged a long time ago, even ones with low intra-population diversity, mix them, and the end result will be one very diverse population. In the absence of admixture, variation is generated by mutation, and culled by drift and selection. But, mutation is a random process that adds variation incrementally into the population, with new alleles appearing at a rate ~ to the number of breeding bodies times the mutation rate/per genome. Admixture, on the other hand, introduces a whole bunch of new alleles in a limited amount of time.

Here is what I think may have happened; I will use the older dates, as they currently make more sense to me:

1. Homo heidelbergensis emerges in western parts of the Old World c. 750ky. Whatever adaptations gave heidelbergensis a bigger brain than erectus spread quickly throughout Europe and Africa. Admixture between European and African hominins at this time and/or expansion of the H. h. population lead to an increase in population size.
2. Further east, heidelbergensis is less visible, and older erectus populations persist. The Denisovan population can then be seen as an eastern H. h. that had more limited opportunity to expand and/or experience gene flow, because of its remote location; the Deniosovans were not unlike isolated Siberian groups of today: substantially less diverse than the bulk of mankind.
3. Pre-100ka sees the rise of the modern humans. According to my "two deserts" theory, these were a population of AMH living in North Africa.
4. Post-100ka population histories begin to diverge, but with all population sizes decreasing (consistent with the rise of behaviorally modern humans carrying a small subset of the genetic variation in the broader group of archaic H. sapiens / anatomically modern humans). This is the major bottleneck of modern human origins that has transformed us into a fairly homogeneous species.
5. But, Africans and non-Africans follow different trajectories, with the former maintaining higher population sizes than the latter. This is probably related to the ecological calamities that befell Eurasians during the 100-50ka period (notably the drying up of the Sahara-Arabia belt post-70ka and /or the Toba eruption), and also to a partial breakdown of African population structure as modern humans expanded deeper into Sub-Saharan Africa and started mixing with pre-existing humans living there, consistent with signals of archaic admixture detected for this period.

Science DOI: 10.1126/science.1224344

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Matthias Meyer et al.

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity, indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

Link