Are Sardinians like Iberians?

By Razib Khan | February 28, 2012 10:32 pm

Dienekes asks:

In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

This trend aroused a little curiosity in me too. I’m sure Dienekes & company will be probing these issues a lot in the near future, but I couldn’t wait. I took the IBS data set, which includes a lot of individuals from various areas of Spain, the Sardinians, French and French Basque from the HGDP, and the Tuscans from the HapMap, and threw them together into a pot. I added HGDP Russians & Orcadians (the latter a British group) to make sure there was a North European “outgroup.” In terms of technical details the combined data set had ~220,000 SNPs, not too shabby. Additionally, I decided to run a PCA, where this number of SNPs is more than sufficient.

On a technical note, the Sardinians were swamped in raw numbers by Iberians and Tuscans (over 100 and around 80 respectively). This means that the peculiarities of the Sardinian genetic heritage didn’t show up, rather, what you see are the Sardinians as they arrange themselves in relation to the genetic variation of these more numerous groups. I used SmartPCA to generate the 10 largest independent dimensions of variation. To make a long story short there really wasn’t much variation added from the second dimension on in this relatively homogeneous sample. So below is PC 1 and 2 (E1 and E2).


I’d be curious if someone could replicate this. I’m rather surprised that the Tuscans form such a tight cluster, but then again the IBS sample is very geographically distributed across Spain. The analogy to the HapMap Tuscans might be if Spain was represented by just Galicians. So what you’re really seeing is a lot of Spanish variation, and of course the north-south range in Europe (which is really a southwest to northeast cline). I don’t see a very strong affinity between Basques and Sardinians, but repeated trials indicated that the Sardinians do not cluster with Tuscans when it comes to their position within the Iberian genetic spectrum.

 

CATEGORIZED UNDER: Anthroplogy, Human Genetics
MORE ABOUT: Sardinians
  • http://dienekes.blogspot.com Dienekes

    In the K12b

    http://dodecad.blogspot.com/2012/01/k12b-and-k7b-calculators.html

    The “Atlantic_Med” component is bimodal in Sardinians and Iberians

    Sardinians differ from Basques by having higher Caucasus/no North European compared to no Caucasus/higher North European

    It is rather upsetting that the long-awaited arrival of the Iceman genome consists -at the moment- of a genome browser and no download options. As such, it is not really usable at the moment.

  • http://forwhattheywereweare.blogspot.com/ Maju

    “there really wasn’t much variation added from the second dimension on in this relatively homogeneous sample”

    That’s like saying that Tuscans are like (some) Spaniards, almost a subset of Iberians. I really miss the usual E-W Mediterranean axis in this PCA, why does it shows up this way?

    Then also who are those Spaniards that diverge more than Basques in the PC1 and PC2 positive extremes? They are like “super-Basques” but with Spanish label.

    The combined answer is, I understand, that the only thing measured here is two “Basque” (Basque-plus) components: PC1 is a component that is highest in the Basque-plus cluster and lowest in Russians/North Europeans, instead PC2 is a component highest also in the Basque-plus cluster and lowest among some Spaniards and Italians (notably Sardinians).

    Sardinians, like North Basques, seem to have relatively high PC1 component but not as extremes as the “South Basque cum some Spaniards” cluster. The PC2 component seems instead enhanced (after the Basque-plus extreme cluster) for North Basques and North Europeans.

    Tuscans and the Spaniards clustering nearby are only defined in negative terms of non-Basqueness.

  • free thinker

    The fact that the Iceman clusters with the Sardinians is no surprise. I have always felt that the Southern Europeans in Deniekes study were just a proxy group for the Neolithic expansion. The fact that he is more distant from the present inhabitants of Northern Italy is also what you would expect. The lack of any Indo-European admixture is enough to explain that. What I was curious about is whether the Iceman had any paleolithic admixture. I would like to see some admixture runs which included people like the Saami and Berbers. The purest group of Paleolithic Europeans which survived to modern times were the Guanches of the Canary Islands. The Spanish didn’t invade until 1402–so it should be possible to get a full genome from skeletal remains prior to that time. If we want a better proxy group than the Lithuanians for the Indo-Europeans, why don’t we do a genome for one of the bog people. Or if the Indo-Europeans were already an admixed people by the time they got to Europe, we could probably go back to the Kurgan mound builders with a fair chance of success. We are just getting started with this stuff, but we need older and purer examples of the founding populations of Europe.

  • pconroy

    @FreeThinker,

    I’m all for a Guanche Full Genome, as they are the nearest morphologically to the Cro-Magnon people of the Late Paleolithic in Europe. They are also probably related to the Iberomaurusian culture of the Maghreb (North African littoral).

    http://en.wikipedia.org/wiki/Iberomaurusian

    Plus the Guanche mummified their dead and there are plenty of well preserved mummies in the Canaries and possibly elsewhere in museum collections.

  • Halvorson

    The Guanche are not the closest morphologically to Cro-Magnons. See Loring Brace and co. here:

    http://www.pnas.org/content/103/1/242.full

    “Basques and Canary Islanders are clearly associated with modern Europeans. When canonical variates are plotted, neither sample ties in with Cro-Magnon as was once suggested.”

    Canary Y haplogroups are mostly J and E, which is what you would expect given that the islands were only settled from NW Africa less than 2,000 years ago.

    http://dienekes.blogspot.com/2009/08/ancient-y-chromosomes-from-canary.html

    Jantz and Owsley found affinities between UP Europeans and medieval Norse, but I doubt modern Norwegians are a perfect proxy for their ancestors. Carleton Coon seemed to think that the Iron Age Norwegians were exceptional UP survivors and that their descendants have since regressed to the Scandinavian mean.

    http://dienekes.blogspot.com/2005/08/affinities-of-early-upper-paleolithic.html

  • pconroy

    So in Dienekes’s K12b, the Basques have none of the Caucasus component, while both my parents (Irish) had about 2.4% Caucasus.
    However in Davidski/Polako’s WE12 run, my mother had 5.4%, while my father had no Caucasus, which seems to be rare in this WE run.

    Meanwhile in Maju’s list of Basque mtDNA, my father matches one from Bearn – H5’36.

    Doug McDonald also estimates my father at 76% Irish/24% Basque.

  • pconroy

    @Halvorsen,
    …which is what you would expect given that the islands were only settled from NW Africa less than 2,000 years ago.

    Where are you getting that from?

  • pconroy

    @Halvorsen,
    Some info on early Guanche traditions:
    See here – http://en.wikipedia.org/wiki/Canary_Islands

    Alternatively, it is said that the original inhabitants of the island, Guanches, used to worship dogs, mummified them and treated dogs generally as holy animals.[22] The ancient Greeks also knew about a people, living far to the west, who are the “dog-headed ones”, who worshipped dogs on an island.[22] Some hypothesize that the Canary Islands dog-worship and the ancient Egyptian cult of the dog-headed god, Anubis are closely connected[23] but there is no explanation given as to which one was first.

    Also, as I speculated about 3 years ago, I think we’ll find evidence that Y-DNA E is from Eurasia. There is no Y-DNA DE* found in Africa AFAIK, but recently some has been found in Syria.
    Also, I may be misreading your intent, but the jury is out on whether Y-DNA J is old in Europe. Of course Y-DNA R1b1a2 is very young in Europe, so not finding that in the Guanche would be expected.

  • free thinker

    …which is what you would expect given that the islands were only settled from NW Africa less than 2,000 years ago.

    I thought it was generally accepted that the Berbers were UP Europeans who migrated to Africa during the Younger Dryas–probably settling in the Canaries along the way. Why would you assume the migration was in the other direction. The Berbers are clearly not indigenous to Africa.

  • Halvorson

    My original source for the Canary Islands settlement date was the the venerable Wikipedia, but I have since upgraded it to this:

    http://www.nature.com/ejhg/journal/v12/n2/full/5201075a.html

    @8

    As of right now, it isn’t generally accepted that anybody is primarily descended from UP Europeans, even the Europeans themselves. Berbers seem to be mostly descended from Afroasiatic migrants from the Middle East, although they have both an unusually high frequency of mtDNA haplogroup H and a weird maternal connection to the Saami which suggests distant (emphasis on distant) affiliations with old Europeans.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1199377/

  • tt9j

    Since we are OT at this point, anyway, may I suggest full sequence attempts on Cheddar Man or the other Cheddar tooth? Those specimens are clearly pre-Neolithic (based on age). If Bryan Sykes can get DNA from them with 1996 techniques, just think what Svante Paabo et al. could do with them 16 years (several sequencing generations) later?

    Also OT: It would be interesting and informative to survey our great RK’s blog readership for recommendations for which ancient MH specimens should be sampled for sequencing, as RK did for existing human populations (http://blogs.discovermagazine.com/gnxp/2011/09/which-undersampled-groups-would-you-like-to-see/). RK’s fabulous reader base should turn up some remarkable candidates.

  • free thinker

    @tt9j

    Just in case the Iceman has some Paleolithic admixture (The Alps strike me as a place where hunters and gatherers could have held out against the farmers quite a while) I think we should get some genomes that are more certainly pure Neolithic–from the bodies buried at Stonehenge for example. I really like my suggestion of the Kurgan Mound Builders as well.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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