Razib Khan One-stop-shopping for all of my content

February 28, 2012

Ötzi the Iceman and the Sardinians

Well, the paper is finally out, New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. In case you don’t know, Ötzi the Iceman died 5,300 years ago in the alpine region bordering Austria and Italy. His seems to have been killed. And due to various coincidences his body was also very well preserved. This means that enough tissue remained that researchers have been able to amplify his DNA. And now they’ve sequenced it enough to the point where they can make some inferences about his phenotypic characteristics, and, his phylogenetic relationships to modern populations.

The guts of this paper will not be particularly surprising to close readers of this weblog. The guesses of some readers based on what the researchers hinted were correct: Ötzi seems to resemble mostly closely the people of Sardinia. This is rather interesting. One reason is prosaic. The HGDP sample used in the paper has many Northern Italians (from Bergamo). Why is it that Ötzi does not resemble the people from the region that he was indigenous to? (we know that he was indigenous because of the ratio of isotopes in his body) A more abstruse issue is that it is interesting that Sardinians have remained moored to their genetic past, enough so that a 5,300 year old individual clearly can exhibit affinities with them. The distinctiveness of Sardinians jumps out at you when you analyze genetic data sets. They were clearly set apart in L. L. Cavalli-Sforza’s The History and Geography of Human Genes, 20 years ago. One reason that Sardinians may be distinctive is that Sardinia is an isolated island. Islands experience reduced gene flow because they’re surrounded by water. And sure enough, Sardinians are especially similar to each other in relation to other European populations.


But Ötzi’s affinities reduce the strength of this particular dynamic as an explanation for Sardinian distinctiveness. The plot to the left is a PCA. It takes the genetic variation in the data set, and extracts out the largest independent components. PC 1 is the largest component, and PC 2 the second largest. The primary cline of genetic variation in Europe is North-South, with a secondary one going from West-East. This is evident in the plot, with PC 1 being North-South, and PC 2 being West-East. The “Europe S” cluster includes northern, southern, and Sicilian Italians. Now notice the position of Ötzi: he is closest to a large cluster of Sardinians. Interestingly there are also a few others. Who are they? I do not know because I do not have access to the supplements right now. The fact that the Sardinians are shifted closer to the continental populations than Ötzi is also striking. But totally intelligible: Sardinia has had some gene flow with other Mediterranean populations. This obviously post-dates Ötzi; Roman adventurers and Genoaese magnates could not be in his genealogy because Rome and Genoa did not exist 5,300 years ago. These data strongly point to the possibility of rather major genetic changes in continental Europe, and in particular Italy, since the Copper Age.  Juvenal complained that the “River Orantes has long flowed into the Tiber,” a reference to the prominence of easterners, Greek and non-Greek, in the city of Rome. The impact of this is not to be dismissed, but I do not think that it gets to the heart of this matter.

The second panel makes clear what I’m hinting at: Ötzi is actually closer to the “Middle Eastern” cluster than many Italians! In fact, more than most. Why? I suspect that rather than the Orantes, the Rhine and the Elbe have had more of an impact on the genetic character of Italians over the past ~5,000 years. Before Lombardy was Lombardy, named for a German tribe, it was Cisapline Gaul, after the Celts who had settled it. And before that? For that you have to ask where Indo-Europeans came from. I suspect the answer is that they came from the north, and therefore brought northern genes.

A Sardinian

And what of the Sardinians? I believe that the “islanders” of the Mediterranean are a relatively “pristine” snapshot of a particular moment in the history of the region. This is evident in Dienekes’ Dodecad Ancestry Project. Unlike their mainland cousins both the Sardinians and Cypriots tend to lack a “Northern European” component. Are the islanders in part descendants of the Paleolithic populations? In part. Sardinians carry a relatively high fraction of the U5 haplogroup, which has been associated with ancient hunter-gatherer remains. But it is also possible that the preponderant aspect of Sardinian ancestry derives from the first farmers to settle the Western Mediterranean.  I say this because the Iceman carried the G2a Y haplogroup, which has of late been strongly associated with very early Neolithic populations in Western Europe. And interestingly some scholars have discerned a pre-Indo-European substrate in Sardinian which suggests a connection to the Basque. I wouldn’t read too much into that, but these questions need to be explored, as Ötzi’s genetic nature makes Sardiniaology more critical to understanding the European past.

Image credit: Wikipedia

October 24, 2011

Ötzi, the dead sea scrolls of genomics?

Filed under: Genomics,Human Genomics,Ötzi,Ötzi the Iceman — Razib Khan @ 2:48 pm

Dienekes points me to the fact that Ewen Callaway has the dirt on what’s going on with Ötzi:

To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from a shard of hip bone. Their sequence covers more than 90 percent of the Iceman’s genome. Their team also analysed DNA preserved in Ötzi’s stomach in hopes of revealing the microbes that colonized his gut.

Zink says his team is keeping most of the results of these studies under wraps, pending publication. They had hoped to have the paper out in time for last week’s Mummy Congress and a television special called Iceman Murder Mystery.

His team plans to use the sequence to determine Ötzi’s status for genetic variations linked to diseases in modern humans, particularly arthrosclerosis. A full nuclear genome will also paint a more detailed picture of the Iceman’s ancestry and his relationship to present-day humans. Zink’s team will ask whether Ötzi is an ancestor of people living in Central Europe today, or whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East. To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe.

~90 percent of a genome is way more than you’d need for some basic analysis and inference of relationships to contemporary populations. So what’s the big deal? No idea, but this tardiness makes me turn the needle up in terms of assuming that they found some interesting stuff. If it’s what you’d expect, why recheck and beef up your analysis with as much support as you can find? Of course, I hope that they found some interesting stuff, so I shouldn’t trust my own judgments in this area. My own suspicion is that they have found extensive genetic turnover over the past 6,000 years in Western Europe, and they are using modern and ancient samples to flesh-out their model. The two dominant paternal haplogroups in Europe today, R1a and R1b, are suspiciously scarce in the ancient DNA samples.

October 17, 2011

Ötzi tidbits

Filed under: Anthroplogy,Genomics,Human Genetics,Human Genomics,Ötzi the Iceman — Razib Khan @ 12:25 pm

The genome of Ötzi the Iceman is floating around somewhere, but for now we only have to go on what leaks out via the media. From National Geographic, Iceman Autopsy:

The genetic results add both information and intrigue. From his genes, we now know that the Iceman had brown hair and brown eyes and that he was probably lactose intolerant and thus could not digest milk—somewhat ironic, given theories that he was a shepherd. Not surprisingly, he is more related to people living in southern Europe today than to those in North Africa or the Middle East, with close connections to geographically isolated modern populations in Sardinia, Sicily, and the Iberian Peninsula. The DNA analysis also revealed several genetic variants that placed the Iceman at high risk for hardening of the arteries. (“If he hadn’t been shot,” Zink remarked, “he probably would have died of a heart attack or stroke in ten years.”) Perhaps most surprising, researchers found the genetic footprint of bacteria known as Borrelia burgdorferi in his DNA—making the Iceman the earliest known human infected by the bug that causes Lyme disease.

I’d guess that we’re talking about the HGDP samples from Sardina and the Basques, though those Basques were from the French side of the border. As you might know there are current models which posit that groups like the Basques and Sardinians are the descendants of Paleolithic Europeans who took up farming by and large through cultural adoption, and others which suggest that they’re mostly descendants of newcomers from the eastern Mediterranean. It doesn’t seem like Ötzi’s genome is going to resolve that, though we can at least peg a lower bound for when the last major demographic changes occurred in Sardinia. But, the fact that Ötzi is being compared to “isolated” populations in southwest Europe does tell us that there has been significant demographic turnover across this region over the past ~5,000 years, as Ötzi himself was from northern Italy. There is a northern Italian sample from Bergamo that Ötzi could have been compared to, and the fact that he wasn’t suggests that the modern people of the region are not easily explained as unaltered descendants of the relatives of Ötzi.

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