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Tuesday, February 28, 2012

Oetzi the Iceman: more Middle Eastern than the average modern Euro


So, Oetzi the Iceman from the Copper Age Tyrolean Alps has turned out more Middle Eastern than the majority of present-day Europeans. You can see that result on the first PCA below (a), where Oetzi (black dot) is closer to the Middle Eastern samples than even most modern Italians (orange dots). Unfortunately, the article doesn't resolve why this is so. But one possibility is that almost all Europeans today, except those from the Mediterranean coastline, have more North European or North European-like ancestry than Oetzi, pushing them up and right on that PCA, away from the Middle East. In any case, this result makes it tough to argue that the ancestors of most modern Europeans (the Y-chromosome R1a and R1b crowd) arrived on the continent after Oetzi's kind (the Neolithic Y-chromosome G crowd). It appears as if they were already there, at the same time as the Iceman, and probably earlier, and then expanded down into South Europe later, leaving only more isolated areas, like Sardinia and Corsica, relatively untouched.


The image above of the figures + tables was edited by me to make it a little more informative than the original. Below is the abstract from the study, and here is the Iceman genome browser. Can anyone tell me where & how I can download this guy's SNPs, so I can make him a Eurogenes project member?

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Keller et al., New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing, Nature Communications, Volume: 3, Article number: 698, DOI: doi:10.1038/ncomms1701


Sunday, February 26, 2012

Genetic substructures within the HapMap CEU sample (and Eurogenes' Northwest Europeans)


In this experiment I attempt to characterize more precisely the origins of some of the individuals from the HapMap CEU cohort. These samples are described by the HapMap project as Utah Americans of Western and Northern European descent. But this doesn't seem to be exactly true for at least two of them, who actually come out very Central European in all my tests. Moreover, it's obvious that some of the samples fit nicely into very specific areas of Western and Northern Europe. For instance, at this level of resolution, a few could pass as Irish, and others for Danes or even Swedes. Below is a quick and dirty ADMIXTURE analysis designed specifically for this experiment.



Key: Red = Sub-Saharan African, Yellow = Southern European, Green = North-Central European, Aqua = North Atlantic, Blue = Baltic, Pink = East Asian. See spreadsheet for details.


Based on the K=6 results it's fair to say that at least six of the CEU samples might pass for unmixed Scandinavians, most likely Danes or southern Swedes (NA12003, NA12057, NA12248, NA12249, NA12776 and NA12875). At least five could be confused for Irish or western British samples (NA10850, NA12005, NA12006, NA12386 and NA12812). The two Central European-like Utahns stick out from the CEU set due to their unusually high Baltic scores (NA11917 and NA12286). From the little I know about the CEU samples, I'd say that these two were of eastern or southeastern German origin. But they might have fairly recent ancestry from further east than that. My own MDS analysis (first image below) and a PCA plot from Lao et al. 2008 (second image, slightly edited by me to remove article text) confirm that such Scandinavian-like, German-like and Irish-like individuals do exist in the CEU set.



I think this experiment is very useful for a number of reasons. Firstly, it shows that the CEU set is not a homogeneous one, and carries clear substructures that can be picked up via fairly basic means. However, this doesn't make the CEU samples less valuable, but more so, due to the lack of public access to continental Northwestern European samples. Secondly, the test reveals some interesting information about the genetic substructures within Northwestern Europe. Here are some of my observations:

- Scandinavians often show very high levels of the North-Central European component, and moderately high levels of the North Atlantic component. Many also carry clear amounts of the Baltic component, but, as a rule, lower levels of the Southern European component.

- Germans mainly differ from the Scandinavians in that they carry the Southern European component at appreciable amounts. They show variable amounts of the Baltic component, with those from eastern Germany carrying the highest levels.

- Irish project members, especially those from western Ireland, show very high levels of the North Atlantic component, but low levels of the Southern European component.

- Western British samples, like those from Cornwall or western Scotland, are generally very similar to the Irish, mainly in that they carry the North Atlantic component at high levels. However, they often show somewhat higher levels of the Southern European component.

I'm eventually going to test these classifications of the CEU samples with ChromoPainter, which is by far the most accurate tool for such things at the moment. Unfortunately, it's also a lot of hard work and computationally intensive, so it might take a few weeks. I do have the allele frequencies from the above ADMIXTURE run, and it is possible to make a stand alone test from them. However, I'm not certain that's a good idea at present, due to the small number of samples involved. It might be worth doing when the right samples swell in number, so I can run a more robust analysis. In particular, I need more people from Ireland, Scotland and Scandinavia.

Reference...

Oscar Lao et al, Correlation between Genetic and Geographic Structure in Europe, Current Biology, Volume 18, Issue 16, 1241-1248, 26 August 2008, doi:10.1016/j.cub.2008.07.049