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

December 8, 2010

The men of the north: the Sami

Ole Magga, Norwegian politician

ResearchBlogging.orgOn this blog I regularly get questions about the Sami (Lapp*). That’s because I often talk about Finnish genetics, have readers such as Clark who are of part-Sami origin, and, the provenance and character of the Sami speak to broader questions about the emergence of the modern European gene pool. More precisely questions about the Sami are relevant to the broader nature of the Finnic presence in Europe, and their relationship to other Baltic and northern populations. Are these people “indigenous” to Europe, or relatively newcomers (prehistoric Magyar or Turks).? These questions are prompted by the peculiarity of their languages (as well as the physical appearance of some of the Sami). With Basque they are the only living non-Indo-European European languages whose origins are prehistoric (Magyar and Turkish were arrivals within the last 1,000 years).**

Because of affinities to other Uralic languages which are found in Central Siberia it has often been conjectured that the Finns, Sami, and Estonians are relative newcomers to Norden from that region. This has some equivocal support from Y chromosomal lineages. On the other hand, there are those who argue that the Finnic peoples were present in the north of Europe before the arrival of Indo-European speakers (often these are Finnish nationalists). This has some support from maternal lineages. Naturally, some have been tempted to synthesize these two genetic lines of evidence, and the linguistic affinities, to argue that Finns are a hybrid population of Asiatic men and Paleolithic European women! But we need to go further than uniparental markers, the direct male and female ancestral lines. We need to look across the broader swath of the genome. It just happens that a new paper was published in The European Journal of Human Genetics on autosomal Sami affinities to other populations, A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies:

The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

They had 352 Sami samples, and looked at ~38,000 SNPs. For the questions they’re focusing on 38 K SNPs seems fine. That’s enough to smoke out inter-population variation. In their paper they compared the Sami to the HGDP populations using standard techniques. Assuming 7 ancestral populations in the data set, this what ADMIXTURE popped out:


There is a definite “eastern” affinity among the Sami. Interestingly, it is broken down into a major and minor component. The major one is what is found among the Han, while the minor one resembles Native Americans. The natural interpretation for this is that what one is seeing is the shadow of the circumpolar northern Eurasian populations which spanned eastern Europe to Siberia. In comparison with other European populations the Sami affinity with Russians is clear, though interestingly they lack the “blue” component which peaks in northwest South Asian populations, which the Russians have, and Sardinians and French Basque lack.

samieigenTo the left you see a PCA which breaks out the top two components of genetic variation for the data set. The two axes seem to be roughly west-east, north-south. Whatever ancient affinities the Sami may have with Southern Europeans via mtDNA haplogroup U5, it is not evident in the total genome content. The position of the Sami between Russians and Orcadians (from north of Scotland) is probably attributable to the fact that the Sami share much genetically with other Scandinavians, who are closer to British populations than the Russians are.

I’m not sure these analyses really shed any light on the on the questions I mentioned earlier. The authors themselves note that the “eastern” component of the ancestry in the Sami is probably very old, so they may be an ancient stabilized hybrid population, mostly indigenous with a non-trivial exogenous element. That does not tell us whether Finnic languages are indigenous to Europe, or whether they are indigenous to Central Siberia (indigenous here is in reference to the Indo-European languages). Additionally, there is the matter that for such fine-grained questions the HGDP sample is suboptimal as reference populations. Dienekes Pontikos points this out:

It is unfortunate that they included Native American HGDP populations, but did not include the most relevant published data on Siberians that I first used to study population structure across north Eurasia here and here and here.

Hence, they discover a “Native American”-like component in Saami, which in all likelihood can be further resolved into Siberian-specific components utilizing the Rasmussen et al. dataset.

The “closest approximation” to the East Eurasian component in Saami in the HGDP panel are the Yakuts, but finer-scale analysis (see my previous posts) reveals that the Yakuts are made up almost entirely of an Altaic-specific component tying them to Turkic, Mongol, and Tungusic populations, while the eastern component in European Finns, Vologda Russians and Chuvashs has relationships with Central Siberians such as Kets, Selkups, and Nganasans, all of which are missing in this paper.

Below is a re-edited ADMIXTURE plot from Dienekes:


Note: There are many ways to spell Sami. They used two a’s, but I find that confusing, so I just used one in my text.

Citation: Maki-Torkko, Elina, Aikio, Pekka, Sorri, Martti, Huentelman, Matthew J, & Camp, Guy Van (2010). A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies European Journal of Human Genetics : 10.1038/ejhg.2010.179

* Apparently “Lapp” is considered derogatory among Norwegians, though Finnish Sami refer to themselves as lappalainen. I will use Sami to avoid irritating Norwegian terminology police.

** I am implicitly excluding much of European Russia west of the Urals, but so be it.

April 22, 2010

Phylogeography of deep European genetic history

Filed under: Genetics,Sami,science — Razib Khan @ 5:08 am

cromagThere’s a lot of circumstantial evident that mtDNA haplogroup U5 was brought to Europe by the first anatomically modern populations. Though this haplogroup is extant around frequencies of ~10% in modern European populations, with the highest proportions in northern Fenno-Scandinavia and the east Baltic region, extractions of DNA from hunter-gatherer remains in northern Europe yield very high proportions of this lineage. This is not totally surprising, in the early aughts Bryan Sykes wrote a book, The Seven Daughters of Eve, and correctly pointed out that the coalescence for the U5 lineages is very deep in Europe, suggesting that it has had a lot of time to diversify. Sykes’ main thesis though was that most of the genetic heritage of Europe predates the expansion of Neolithic farmers within the last 10,000 years. The rough implication was that ~80% of the ancestry of modern Europeans could be derived from people who were resident within the modern boundaries of the continent of Europe during the last Ice Age.

But Ancient DNA extractions and more thorough analyses of modern population variation are muddling the picture somewhat. Some of the lineages which were presumed to be Paleolithic, such as R1b, may not be so. But the fact remains that we do know that modern humans began to settle Europe within the last 40,000 years, and extirpated the Neandertals within 10,000 years of their initial arrival. Unless those initial populations were totally replaced, there has be a very ancient lineage which dates to the Paleolithic, and in particular the Ice Age. U5 is the mtDNA lineage which is the best candidate, and its frequencies within modern European populations may be a clue to who the real “aboriginals” are. For example, the Sami have very high frequencies of U5, which may be ironic in light of theses that the Finnic populations of the Baltic are hybrids between populations from eastern Eurasia and native Scandinavian groups (the other group which high frequencies of U5 are Basques).

In any case, that is why U5 is of some interest, though the “golden age” of mtDNA & Y studies is probably in the past. A new paper in PLoS one surveys central and eastern European groups, , The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective:

It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ~25–30 thousand years (ky), and ~16–20 and ~20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ~15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans.

The simple reality is that much of northern Europe was not habitable during the Last Glacial Maximum, so naturally hunter-gatherers would rapidly expand to settle the new territory as it became accessible. This may be why the Basques have a more diverse array of U5 lineages than the Sami, northern populations are sampled from the diversity of the southern. But after the expansion it may be that the original genetic substrate of Paleolithic Europe was heavily overlain by agriculturalists, and it is only in the far north and east than the Paleolithic populations persisted because of ecological parameters. This is why I suspect that a deeper analysis of northeast European genetics will give us some clues as to the demographic process of the shift from hunter-gatherer lifestyles to agriculture.

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