I was interviewed last month for the CBC radio broadcast, "Quirks and Quarks". They have done a segment on the Denisova genome, with contributions from David Reich, Peter Parham, Chris Stringer and me, and it's part of this week's episode of the show.
The 23andMe blog reports on a recent genome-wide association study of type 2 diabetes in South Asian people: "SNPWatch: Genetic Variants Associated with Type 2 Diabetes in South Asians and Europeans". The study was published in August in Nature Genetics, by Kooner and colleagues . As described in the post:
The authors behind this study carried out one of the largest type 2 diabetes studies to date, scanning the genomes of nearly 19,000 people with the disease and 40,000 without it, all of South Asian descent. Their analysis identified six SNPs linked to this condition. When they combined their results with previously published findings in other ethnicities, they found suggestive evidence that five of the six SNPs were also associated with type 2 diabetes in European populations. Similarly, there was some evidence that the majority of the genetic risk factors in Europeans were also linked to disease in South Asians. Only three genetic factors were not shared at all between the two groups.
Type 2 diabetes is presently a very interesting topic from an evolutionary viewpoint, and we're beginning to think about it very seriously now. Whenever I see a study like this, I quickly look at the Neandertal and Denisovan genomes to see if any interesting patterns emerge. Sharing GWAS SNP alleles is not necessarily very interesting, because the GWAS risk alleles are mostly not causative themselves; each may be linked to some causative allele that remains to be discovered. The linkage is a function of the evolutionary history of that chromosome region, and many of the key historical events that affect linkage happened within the last 10,000 years. So we really shouldn't expect GWAS alleles to be predictive of phenotypes in Neandertals or Denisovans.
Still, these alleles are associated with disease in living people, and their genotypes in ancient humans may illuminate cases where the evolutionary history links the population across the gene networks that influence disease. A closer examination of the genealogy around these loci will be more informative, but as a first look I often just genotype the archaic genomes for SNPs in a study. The six SNPs reported here include two cases where the archaic genomes have the derived risk alleles, one of them present in Neandertals but not the Denisova genome. Again, that doesn't tell us anything about the phenotype of the ancient people, but worth a closer look to see if one or both of these is an introgressive allele.
We have here the GWAS Catalog genotypes for all the archaic genomes. Not much actionable information but there are some interesting phenotypes in there. I'll share some more of those later this week.
- Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Nature genetics. 2011;43(10):984-9.
David Reich and colleagues today report on the persistence of Denisova-like ancestry in island Southeast Asia and Australia (citation not yet available). Meanwhile, Morten Rasmussen and colleagues (citation not yet available) report on the whole-genome sequencing of hair from an Aboriginal Australian who lived some 100 years ago.
The most obvious story: These data utterly destroy the hypothesis of a single out-of-Africa colonization of Southeast Asia by modern humans. Many human geneticists have argued our present pattern of diversity originated in a wave of successive founder effects coming from a single recent African origin. They were wrong.
Instead, we can turn to a complex model with successive dispersals and episodes of population mixture. This is not a static model of isolation-by-distance; it is a dynamic model in which populations grow and spread across large spans of the Old World, again and again and again. By my count, at least three massive episodes of population dispersal and mixture are necessary in Reich and colleagues' model. A picture of their admixture hypothesis:
This model depicts (a) an early divergence of an African (represented by Yoruba) and Asian/Australasian populations. These mix with first Neandertals and then (for the Australian/New Guinea/Mamanwa populations) with Denisova-like people. Later (b), after the initial habitation of the Philippines by the ancestors of Mamanwa, a population like Andamanese Onge pushes into the islands, mixing with the ancestors of New Guinea and Australian populations. Later still (c), a population ancestral to today's Chinese people mixes with Philippines and other Southeast Asian people.
As complicated as it looks, even this model must be a vast oversimplification. I don't like or attribute much belief to mixture models like this, as they assume too much about relative population sizes and the timing of mixture. Many recent hunting and gathering populations of Southeast Asia are not included in the current samples, and the Chinese sample is itself the result of very recent demographic events, covering what once may have been a wider diversity of peoples. Depicting Australian and New Guinean populations as monolithic is an artifact of the small sample; these places themselves housed a tremendous diversity of peoples. Nevertheless, the true model won't be simpler than this one; it will involve many more events that the data cannot yet resolve.
Hints of that complexity emerge from the Aboriginal Australian whole genome. Rasmussen and colleagues show that this individual shares some ancestry with East Asian peoples, but on the whole populations in Europe and East Asia are much more genetically similar to each other than to this genome. The picture from the whole genome is essentially the same as that drawn by the SNP comparisons by Reich and colleagues, but with the potential (in the long run) to actually trace the histories of individual genes. And I think the gene-by-gene account of history will be important, because we already have some evidence that a few Denisovan genes do persist in mainland Asia, even though most are gone.
To explain why, we can look at the proportion of Denisovan ancestry in different populations as depicted in a map by Reich and colleagues. The pie charts are confusing here, because they report the fraction of ancestry from Denisovans in each population relative to the 5% estimate for New Guinea. So Australians also have 5% in this figure, Timorese have around 2.5%, and Bougainville has more than 4%.
Notice the apparent lack of Denisovan ancestry in anyone who lives anywhere that was once connected by land with mainland Asia. I say "apparent" deliberately: Abi-Rached and colleagues reported last month on the widespread distribution of Denisovan HLA types among today's Asian populations, and those may well be products of Denisovan genes that were later selected. I've already identified a handful of other loci that seem to reflect Denisovan ancestry in mainland Asian people. According to the comparisons by Reich and colleagues, such loci must be exceptions.
At the same time, the mixture model presents an important idea: Once there were people in Southeast Asia who had much more Denisovan ancestry than any populations still remaining today. Both Australian/New Guinea populations and Philippine populations like the Mamanwa have subsequently mixed with new immigrants who lacked any sign of Denisovan ancestry. Prior to this later mixture, the ancestors of those populations must have been more Denisovan -- Reich and colleagues estimate 7%. This is the first evidence that ancestry from archaic people of Eurasia was diluted to a lower value by later population movements. If the population mixture originally happened somewhere in mainland Asia, any traces of Denisovan ancestry in those areas has been diluted almost to nonexistence. But the persistence of some genes would be predicted if natural selection were maintaining them in the face of demographic pressure from elsewhere.
About the Australian genome, there will be much more interesting analyses to come, I expect. As whole-genome data come to represent more of the variation within human populations, we get a larger store of information about how we came to be variable. Variation traces not only to population movements and demography, but also to natural selection. Australia's population history has been very different from many populations of the Old World, and this genome should give us new perspective on the effects of that demographic history.Synopsis:The hypothesis of a single out-of-Africa dispersal is rejected by new data about Denisovan mixture and whole-genome sequencing of an Aboriginal Australian.
I'll be in the U.K. the rest of this week. The University of Birmingham has invited me to give a lecture for their "Great Read" event as they begin the new academic year. If you're in the area, the talk is at 3:30 on Thursday, September 22, in the Concert Hall of the Barber Institute. I'll be appearing after Ken Miller, widely known for his work in evolutionary biology and his advocacy of evolution education in the U.S.
As for myself, I'll be talking about Neandertal and Denisovan DNA and what they tell us about human evolution. All my talks have new, unpublished stuff in them, and this is no exception.
I notice that the topic of evolution education has really hit the news this week in the U.K, as a group of 30 prominent scientists, including Paul Nurse and Richard Dawkins, have signed a letter protesting lax evolution education standards ("David Attenborough joins campaign against creationism in schools", "Scientists demand tougher guidelines on teaching creationism in schools"). Looks like I'll be going there just in time.
My host has planned some exceptional activities later this week for us, and I'll plan to report back when I can.
Dear Dr. Hawks,
In case you don't already know, the current issue of Science has 2 articles on the Denisovans:
Who Were the Denisovans?
A Denisovan Legacy in the Immune System?
Also, their podcast discusses what is covered in the issue:
Have a wonderful night!
You'll see I make a brief appearance in the article, and I'll be writing more about the site and my trip there in the next few weeks. Hope everything's going well with you!
With draft sequences of genomes from several Neandertals and from Denisova, we can begin to investigate known human variations that affect phenotypes. In practice, this is a very simple approach -- take alleles that we know exist in recent human populations, and see if they are in the DNA sequences of these ancient people. My lab has been following this line of research, trying to get information about aspects of biology that are not evident from the skeleton. The immune system is one of the most fascinating, both because of its extensive variation in living people, and because we might be able to test hypotheses about the diseases and parasites that ancient humans faced.
Today Science has released an early manuscript edition of a paper by Laurent Abi-Rached and colleagues (bibliographic information not yet available), which identifies the HLA class-I alleles present in the three highest-coverage Neandertal genomes from Vindija (Vi 33.16, 33.25, and 33.26) and the Denisova pinky genome. The paper is very brief and fairly straightforward, providing provisional HLA class 1 allele types for these individuals, discussing possible haplotype associations among these alleles that may have been in the ancient genomes, and providing the frequency of those alleles in present-day human populations.
These archaic individuals carried HLA types that are presently rare in Africa and more common outside of Africa, supporting the hypothesis that these alleles in living people originated in those archaic populations. The linkage between alleles at different HLA class-I genes also supports that hypothesis. The present immune system biology of humans was strongly shaped by the interaction of different regional populations of archaic humans.
The title of the paper calls this "multiregional admixture", and the word "introgression" appears 8 times. Good for us!
(This is the point where I grumble about the lack of citations in this paper....OK, done grumbling.)
Selected genes may have a very different pattern from neutral genes
This paper is the first demonstration that gene variants of functional importance were not only inherited from Neandertals and Denisovans but were valuable and selected in later populations.
We already knew that humans today have gene variants from these archaic humans. Neandertal genes presently account for around 3 percent of the genomes of people outside Subsaharan Africa. My lab has been studying the pattern of frequency of these genes ("Europe and China have different Neandertal genes"). Most of the genes shared between the Neandertal genome and living people outside Africa are presently very rare -- most occur only in a single individual in our sample of Europeans and Chinese people, for example.
These HLA class-I alleles are different. Some of them are quite common today. If they came from the Neandertals and Denisovans -- that is, if they were not present in the African people who make up most of our ancestry genome-wide -- then these alleles must have increased quite a lot during the recent evolution of people outside Africa.
The best explanation for the large increase in frequency of these genes in modern human populations is selection. If readers want to get an introduction to the scientific literature on the topic of functional genes, I can suggest a detailed review paper I wrote with Greg Cochran on the dynamics of introgression and selection as applied to Neandertals , and a review paper we wrote in Trends in Genetics about identifying genes in living humans that that may have come from archaic populations . In both papers, we discuss the dynamics of functional genes that may be affected by selection in modern human populations and how they differ from the predictions for neutral loci affected only by genetic drift. The new paper by Abi-Rached and colleagues follows on that line of inquiry.
I think the hypothesis of adaptive introgression is very likely, and that we shouldn't be at all surprised that the immune system might house many good examples of it.
A look at the most extreme examples, involving the Denisova genome, shows the extent that these functional genes might reflect introgression well beyond that indicated by most of the genome. The HLA class-I alleles present in the Denisova genome are most common today in South Asia (HLA-C*12:02, HLA-C*15 which is also common in Australia) and Southeast Asia (HLA-A*11). These regions of the Old World have no substantial evidence of Denisova inheritance across their genomes. Yet they may very well have substantial frequencies (up to 48 percent for HLA-A*11) of HLA class-I alleles from the archaic Denisovan population.
Reasons to be cautious
This is the point where I have to make a note of caution. Even though I personally think it is likely that these HLA alleles really did introgress into the modern population from Neandertals and Denisovans, their geographic pattern really isn't enough to demonstrate this without question.
Reports earlier this summer described some of the work this group was doing on HLA class-I loci, including a public lecture by PI Peter Parham. I noted at the time that the geographic distribution of the alleles mentioned in that lecture seemed a mismatch for the hypothesis of a Denisovan origin for the alleles ("The immune systems of archaic humans"). For example:
HLA-A*11 is very common in Papua New Guinea, but it is also very common in north India and in China. These two areas otherwise show no significant evidence of Denisova ancestry. We might conclude that the HLA-A gene just has an unusually high level of introgression into Asian populations, not typical of the genome as a whole. That's certainly possible. But without finding any substantial number of derived mutations in the HLA-A*11 variant in the Denisova genome and in living Asians, it is hard to rule out that the sharing of HLA-A*11 in all these populations is just coincidence.
Of course, if the allele were absent in Africa, that would weigh in favor of the idea it is shared by Late Pleistocene interbreeding outside Africa. But HLA-A*11 is in Africa, just very rare. And it's in Europe. This is the kind of locus that is difficult to interpret: if it has any tiny disadvantage against malaria, for instance, its rarity in Africa is easily explained as a function of recent evolution, while its presence almost everywhere outside Africa would be no surprise even if there were never any interbreeding.
The story of HLA-C*12:02 is similar. It's common in PNG, but also broadly across South Asia and into Iran, areas where no substantial evidence of Denisovan ancestry has been demonstrated.
Introgression under selection is a good hypothesis for why these alleles should be so much more broadly distributed than the evidence from the rest of the genome. But introgression isn't the only explanation, because the alleles might have been retained by balancing selection, with recombinant haplotypes suppressed by purifying selection. We might use haplotype age to test the hypothesis. If the alleles were retained by ILS, they would look much older than if they came in from an archaic population by introgression. But as I'll describe below, in this case we actually have the opposite problem: these haplotypes look too young to have come in by introgression, likely a consequence of selection long after the Neandertals and Denisovans had contributed their genes to us.
The curious case of HLA-B*73
If I agree that the results of this paper are pretty likely, why am I still cautious? Well, the most confusing thing in this paper is an allele described in great detail that they didn't find in the archaic genomes. And I know from experience that not finding things is a pretty common occurrence when we go looking for odd things that might have come from Neandertals.
There's a detective story here, that probably explains the initial interest of this group in the Neandertal genome, but that just didn't pan out in their search through the archaic genomes. The allele is HLA-B*73.
Parham and colleagues  first characterized this allele, which is remarkably different from other HLA-B alleles. Homologs of HLA-B*73 are present in living apes, suggesting that the different human alleles originated before we diverged from gorillas. The retention of such an ancient allele in humans isn't a surprise in the HLA system, because many very divergent alleles have been kept in the population across evolutionary time by balancing selection. What's a bit surprising about HLA-B*73 is its limited diversity in living people. It appears to have persisted in humans throughout our evolution, but people today who carry the allele have very similar sequences, and it is nearly always linked to one single allele at the nearby gene, HLA-C (HLA-C*15). Also, the allele is very rare inside Africa and reaches its highest frequency in West Asia., where it occurs in only 4.5 percent of people. Because of this strange pattern, Parham and colleagues suggested that the allele may have been inherited from Neandertals.
When I was in graduate school working on modern human origins, I took a special interest in genes that had this pattern of variation. HLA-B*73 was not the only one, there are others.
The variation of the HLA-B*73 allele and its association with HLA-C*15 correspond very well to the predictions we presented in our paper on identifying introgression from archaic humans . It's a highly divergent allele in humans compared to others, and it appears not to have recombined much with nearby genes, suggesting it was sequestered in another population through much of the diversification of present-day HLA alleles. But the HLA system is actually a rotten place to look for this kind of evidence, because there are many, many instances where ancient alleles have been retained in human populations by balancing selection. As we pointed out in 2008, a deep root to the gene tree and a rarity of recombination can be good evidence of introgression, but balancing selection and inhibitions to recombination are alternatives to introgression for explaining this pattern of variation.
There's no necessary contradiction between the two processes, and ancient DNA in this case could establish that the allele was both under selection and came from archaic humans. The problem: they didn't find the allele in the archaic genomes.
So why did they spend so much time in this paper discussing this allele? My guess is that they were surprised not to find it. But they did find HLA-C*15 in the Denisova genome, which is often linked to HLA-B*73 in living people who carry it. That makes for an indirect argument:
C*12:02 and C*15 were formed before the Out-of-Africa migration (Fig. 2H and fig. S15) and exhibit much higher haplotype diversity in Asia than in Africa (fig. S16), contrasting with the usually higher African genetic diversity (20). These properties fit with C*12:02 and C*15 having been introduced to modern humans through admixture with Denisovans in west Asia, with later spreading to Africa (21, 22) (Fig. 1F and fig. S11 for C*15). Given our minimal sampling of the Denisovan population it is remarkable that C*15:05 and C*12:02 are the two modern HLA-C alleles in strongest LD with B*73 (Fig. 1E). Although B*73 was not carried by the Denisovan individual studied, the presence of these two associated HLA-C alleles provide strong circumstantial evidence that B*73 was passed from Denisovans to modern humans.
I would go one simpler: Given that HLA-B*73 is most common today in West Asia, I suspect it came from West Asian Neandertals. There's no reason why the HLA genes of European Neandertals should have been identical to West Asian Neandertals. Today's Europeans are different from today's West Asians in the frequencies of these alleles, so why not in the past as well? For that matter, we really only have two alleles from European Neandertals for HLA-B (since the paper finds that
Why do the Vindija Neandertals all have the same HLA types?
It's a pretty good question. The paper cannot distinguish the genotypes from these three individuals. That's not the same as saying they're exactly the same type, since the sequences are very low coverage, but probably they were. Here's what the paper says:
Genome-wide analysis showing three Vindija Neandertals exhibited limited genetic diversity (3) is reflected in our HLA analysis: each individual has the same HLA class I alleles (fig. S17). Because these HLA identities could not be the consequence of modern human DNA contamination of Neandertal samples, which is <1% (3), they indicate these individuals likely belonged to a small and isolated population (fig. S18).
Still, I think this indicates a pretty high degree of inbreeding among these individuals. I wonder what the organ registry for Neandertals would have looked like.
(Not so) final words
I have more to write on the topic of linkage disequilibrium among these genes. The rate of recombination between HLA-B and HLA-C is high enough that a haplotype between these genes should have mostly decayed in the time since our mixture with archaic humans. HLA-C and HLA-A are an order of magnitude further apart, so linkage between alleles of these genes should have been totally erased in the time since any archaic admixture.
That means that the extended haplotypes reported in this study must reflect selection in the period since the population mixture and introgression. The story isn't a simple case of inheritance from archaic humans, it is rather more complex. But more on that later.
I think this paper confirms that it will be really productive to look at archaic genomes for variants present in living humans. Identifying modern human alleles in a Neandertal isn't really very exciting science, though. I've been doing this on my blog for a year now. It's a tricky job to type these HLA alleles, compared to genotyping many other genes, as we discovered. Still, I never really expected that reporting on genotypes in the public domain would be sufficient to get printed in Science.
Still, this set of three genes is particularly interesting. And the paper does add evidence from one additional locus, KIR3DS1, which also has the pattern where an allele rare in Africa but common in Asia is present in the Denisova genome.
If it turns out that we have widespread adaptive introgression in Asia today from Denisovans, that will change the game of studying the origins of these populations. Based on the genome-wide comparison, it looks like the genetic interaction that led to the habitation of Asia did not involve Denisovans, who contributed only to populations at the most eastern extreme of habitation in island Southeast Asia. But the only Denisovans we know about lived near the geographic center of the Asian landmass, not at the extreme southeastern extreme.
The HLA pattern may suggest a more widespread pattern of mixture across Asia, which was later overwritten by population movements of people who didn't have Denisovan ancestry. That means that the habitation of Asia was a process of successive migrations and replacements, which imperfectly covered up the evidence of archaic intermixture. The genes that remain as signs of this intermixture are those that had selective advantages in later populations.
Synopsis:Abi-Rached and colleagues report that the human system owes much to the Neandertals and Denisovans.
- . Dynamics of Adaptive Introgression from Archaic to Modern Humans. PaleoAnthropology. 2006;2006:101–115.
- . A genetic legacy from archaic Homo. Trends in Genetics. 2008;24(1):19 - 23.
- . The HLA-B73 antigen has a most unusual structure that defines a second lineage of HLA-B alleles. Tissue Antigens. 1994;43(5):302 - 313.
Mark Stoneking and Johannes Krause present a review article in the current Nature Reviews Genetics  that gives an overview of the science of ancient genomes.
I think the article is very good about presenting aspects of ancient genome sequencing and assembly, and the attendant problems and biases. I find myself explaining this stuff a lot and it's useful to have the concise descriptions that Stoneking and Krause provide here. For example, here's a paragraph that describes mapping bias:
However, there are important limitations to current approaches to ancient genome assembly owing to the short length of ancient DNA fragments and the repetitive nature of large parts of mammalian genomes (which creates ambiguities in sequence read mapping). For example, short fragments can cause mapping bias, as highly divergent short fragments cannot be accurately mapped to a reference genome. Fragments may also map to different locations in different reference genomes depending on the completeness and accuracy of the reference genomes. For example, to calculate divergence times between an ancient hominin genome sequence, modern humans and chimpanzees, it is important to first verify that the ancient DNA sequences map to orthologous positions in both the human and chimpanzee genomes. These issues mean that even at 20-fold coverage (which was the coverage obtained for the Saqqaq genome) not more than 85% of the genome could be reconstructed; full genome sequences from fossil samples can probably never be achieved with current methods.
The article discusses chemical changes in ancient genomes, methods to detect contamination, and specialized methods such as targeted DNA hybridization capture.
I'm less happy with the second half of the article, which discusses population genetics. A few computational techniques are very briefly described (for example, unsupervised versus model-based approaches) and Stoneking and Krause give quick synopses of some population genetic inferences reported during the last year.
I guess where I perceive a difference between the first (sequencing) and second (population genetics) parts of the article, is that the sequencing part emphasizes the many problems with analysis and describes approaches to overcome them. It seems as if there's a vibrant discussion of sequencing and biochemistry, giving rise to a fuller account. Meanwhile, the second part, discussing human population history, seems to accept results relatively uncritically. There is very little citation of anthropological or archaeological work, and little indication that the methods of population genetic inference may have weaknesses or assumptions that color their results.
It's great to see review articles on this topic, given the broad interest I expect we'll see more of them soon. A flood of ancient genetic data means a lot of new results that need to be summarized. But a summary is really not enough -- we need critical examination of the assumptions underlying population genetic inferences and a discussion of how they accord with what we know from archaeology and paleontology.
Synopsis:A new review article by Mark Stoneking and Johannes Krause presents some useful information.
- . Learning about human population history from ancient and modern genomes. Nature Reviews Genetics. 2011;12(9):603 - 614.
Last week, Nature ran a story by Ewen Callaway  that hits the highlights of research on ancient genomes this year: "Ancient DNA reveals secrets of human history". The news hook is a bevy of studies trying to estimate the time that Neandertals contributed their genes to recent human populations.
By comparing individual DNA letters in multiple modern human genomes with those in the Neanderthal genome, the date of that interbreeding has now been pinned down to 65,000–90,000 years ago. Montgomery Slatkin and Anna-Sapfo Malaspinas, theoretical geneticists from the University of California, Berkeley, presented the finding at the Society for Molecular Biology and Evolution meeting in Kyoto, Japan, held on 26–30 July.
It will be great to dig into the details of these comparisons, which Callaway reports have also been carried out by some other groups. The basic idea is that over time, recombination would have broken up chunks of chromosome inherited from Neandertals. If we know the intensity of recombination across the genome, we should be able to use the lengths of Neandertal-derived blocks to estimate the time that their population contributed to ours. But much depends on the details of the population model. The simplest model supposes that all the gene flow from Neandertals happened at a single moment in time. If we doubt that assumption (as I do) then the estimate will not represent reality. But until we see papers reporting these results, it's hard to know how much they may be affected by different assumptions.
The article turns toward functional insights from the ancient genomes, and my lab puts in an appearance:
Unlike most scientists mining the ancient genomes, Hawks has reported some of his more prosaic findings — Denisovans didn't have red hair, for example — on his blog (see go.nature.com/irclra). "These genomes are publicly available. There's nothing stopping high-school students from doing this, and the kind of stuff that I'm putting out on my blog is the stuff that a smart high-school student could do."
I was really pleased that the article featured some of the research from my graduate student, Aaron Sams, who has been investigating the evolution of celiac disease. What does celiac disease have to do with Neandertals? Short answer: We're feeling our way though the study of gene networks that connect genetic evolution with phenotypes. We can use our knowledge of human evolution during the last 100,000 years to figure out how genes work. And we can use knowledge from living humans about how genes work to investigate their evolution in archaic people. Ancient genomes give us that potential, because genes that work together have evolved in ways that reflect selection on the system as a whole.
Synopsis:A news article in Nature features our lab's research in a report on ancient genomes.
- . Ancient DNA reveals secrets of human history. Nature. 2011;476(7359):136 - 137.
On July 3, around 20 scientists left Novosibirsk by van to drive out to the permanent field camp at Denisova Cave in the low Altai mountains. The place is 520 km from Novosibirsk, which turned into a total travel time of around 9 hours. I'm posting compilations of my tweets along with some description and photos.
Novosibirsk airport: tweeting via Kindle free wireless. Yea, Amazon! Looks like Kansas out there.johnhawks
July 2, 2011 at 12:46
This is a running joke for me: Everywhere looks like Kansas. Here's a shot of the south Siberian plain, looking out from atop the first foothills.
What do you think?
Kansas actually has a historical link to Siberia: during and even before the Dust Bowl, people were introducing many Siberian-derived trees and plants into Kansas to try to stabilize the soil and form windbreaks. So the texture of the area around Novosibirsk is actually a lot like my hometown in Western Kansas -- even down to the fading brick buildings.
Of course, Kansas does lack Soviet-era engineering projects, and the fields are a whole lot smaller.
Rest stop. Every road sign in Cyrillic is a puzzle for me to find cognates.johnhawks
July 3, 2011 at 5:25
...Like the very strange looking word with the exotic letters that just turned out to be plain "cement"...johnhawks
July 3, 2011 at 6:11
OK, "cement" isn't all that strange, I guess, but it does start with an exotic-looking letter. Many words are much more fun to work out. As I pointed out later, the fact that "Hawks" becomes "XOKC" caused me endless delight.
If you see a white Mercedes van rolling toward Biysk blaring Europop..well there must be fifty of those..but one has me in the back.johnhawks
July 3, 2011 at 7:12
The restaurant in Biysk was fun: Cafe "Siberian Hunt"!
Debating whether to count it as a chicken fried steak or not. At lunch with good borscht I'm starting to really like this country.johnhawks
July 3, 2011 at 8:46
Those who know me well will appreciate this. Or, for that matter, those who don't know me so well but happen to live in cities with seriously good chicken fried steak options (hello, Austinites!). Now, if I can just get my friends in San Antonio to invite me down there (hint).
I really shouldn't count this Russian one at all, since it was ground meat. Probably more like a salisbury steak without the gravy. But hey, it was my birthday after all!
Kindle wireless still going strong, now on gravel ascending into the Altai. Starting to look like Neandertal country.johnhawks
July 3, 2011 at 11:50
Once we got into the Altai foothills I began to realize that the wireless just wasn't going away!
What an incredible thing. In fact, I had wireless access for the entire trip using my Kindle 3G and phone coverage when I needed it. The Kindle is not a very good device for e-mail (and the Wisconsin webmail client didn't work at all). But it is perfectly suited for Twitter.
Also, as you can see, the Altai doesn't look much like Kansas. More like Montana.
The low Altai are really not very high, but they are rugged. The traditional log or wood Russian homes (pictured here) begin to give way to an Altai style, with decorated sills and a round yurt-like "summer house" in each yard.
Just loved the green rolling hills. Much horse country in these parts.
We've arrived at Denisova base camp. Beautiful cabins and river nearby. Window view: sheer 300 foot cliffs.johnhawks
July 3, 2011 at 12:53
This is the most luxe archaeological camp I've ever seen. Part is used for conferences by other institutes in Novosibirsk.johnhawks
July 3, 2011 at 15:11
I can't really say enough about the facilities at Denisova. The Institute of Archaeology and Ethnography has put a lot into the area, and the cabins are quite modern with hot water and electricity.
No wifi, unfortunately. But the mess hall served very good food, never duplicating a main dish of Russian fare.
Nice steady rain, lovely conversation, only one shot of vodka. Tomorrow we get some first-hand stratigraphy.johnhawks
July 3, 2011 at 18:57Synopsis:Here, I describe the beginning of my 2011 trip to Denisova Cave, in the Altai Mountains of southern Siberia.
By the miracle of Amazon, I have been using my Kindle 3G to tweet from the Altai. It is far from an ideal blogging tool, so I will keep this to a short update. The device is perfectly matched to mobile Twitter, with free Whispernet coverage. I have to say I am really liking this device.
This morning I was tweeting live from inside the south gallery of Denisova Cave. At present I am bouncing in the back of a military surplus truck on the way to Okladnikov Cave. You can follow me on Twitter at @johnhawks.
And let me say, constructing tha link on a chiclet keyboard with no symbols is more than I can take. So don't expect more blogging! I will keep tweeting for the duration.