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July 25, 2017

Ancient Europeans: isolated, always on the edge of extinction

Filed under: Europe,Human Genetics,Scandinavia — Razib Khan @ 12:19 am

A few years ago I suggested to the paleoanthropologist Chris Stringer that the first modern humans who arrived in Europe did not contribute appreciable ancestry to modern populations in the continent (appreciable as in 1% or more of the genome).* It seems I may have been right according to results from a 2016 paper, The genetic history of Ice Age Europe. The very oldest European ancient genome samples “failed to contribute appreciably to the current European gene pool.”

Why did I make this claim? Two reasons:

1) 40,000 years is a long time, and there was already substantial evidence of major population turnovers across northern Eurasia by this point. You go far enough into the future and it’s not likely that a local population leaves any descendants. So just work that logic backward.

2) There was already evidence of low population sizes and high isolation levels between groups in Pleistocene and Mesolithic/Neolithic Europe. This would again argue in favor of a high likelihood of local extinctions give enough time.

This does not only apply to just modern humans, descendants of southern, likely African, populations. Neanderthals themselves show evidence of high homogeneity, and expansions through bottlenecks over the ~600,000 years of their flourishing.

The reason that these dynamics characterized modern humans and earlier hominins in northern Eurasia is what ecologists would term an abiotic factor: the Ice Age. Obviously humans could make a go of it on the margins of the tundra (the Neanderthals seem less adept at penetrating the very coldest of terrain in comparison to their modern human successors; they likely frequented the wooded fringes, see The Humans Who Went Extinct). We have the evidence of several million years of continuous habitation by our lineage. But many of the ancient genomes from these areas, whether they be Denisovan, Neanderthal, or Mesolithic European hunter-gatherer, show indications of being characterized by very low effective population sizes. Things only change with the arrival of farming and agro-pastoralism.

For two obvious reasons we happen to have many ancient European genomes. First, many of the researchers are located in Europe, and the continent has a well developed archaeological profession which can provide well preserved samples with provenance and dates. And second, Europe is cool enough that degradation rates are going to be lower than if the climate was warmer. But if Europe, as part of northern Eurasia, is subject to peculiar exceptional demographic dynamics we need to be cautious about generalizing in terms of the inferences we make about human population genetic history. Remember that ancient Middle Eastern farmers already show evidence of having notably larger effective population sizes than European hunter-gatherers.

Two new preprints confirm the long term population dynamics typical of European hunter-gatherers, Assessing the relationship of ancient and modern populations and Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. The first preprint is rather methods heavy, and seems more of a pathfinder toward new ways to extract more analytic juice from ancient DNA results. Those who have worked with population genomic data are probably not surprised at the emphasis on collecting numbers of individuals as opposed to single genome quality. That is, for the questions population geneticists are interested in “two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage.”

I encourage readers (and “peer reviewers”) to dig into the appendix of Assessing the relationship of ancient and modern populations. I won’t pretend I have (yet). Rather, I want to highlight an interesting empirical finding when the method was applied to extant ancient genomic samples: “we found that no ancient samples represent direct ancestors of modern Europeans.”

This is not surprising. The ‘hunter-gatherer’ resurgence of the Middle Neolithic notwithstanding, Northern Europe was subject to two major population replacements, while Southern Europe was subject to one, but of a substantial nature. Recall that the Bell Beaker paper found that “spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years.” This means that less than 10% of modern Britons’ ancestry are a combination of hunter-gatherers and Neolithic farmers.

And yet if you look at various forms of model-based admixture analyses it seems as if modern Europeans have substantial dollops of hunter-gatherer ancestry (and hunter-gatherer U5 mtDNA and Y chromosomal lineage I1 and I2, associated with Pleistocene Europeans, is found at ~10% frequency in modern Europe in the aggregate; though I suspect this is a floor). What gives? Let’s look at the second preprint, which is more focused on new empirical results from ancient Scandinavian genomes, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. From early on in the preprint:

Based on SF12’s high-coverage and high-quality genome, we estimate the number of single nucleotide polymorphisms (SNPs) hitherto unknown (that are not recorded in dbSNP (v142)) to be c. 10,600. This is almost twice the number of unique variants (c. 6,000) per Finnish individual (Supplementary Information 3) and close to the median per European individual in the 1000 Genomes Project (23) (c. 11,400, Supplementary Information 3). At least 17% of these SNPs that are not found in modern-day individuals, were in fact common among the Mesolithic Scandinavians (seen in the low coverage data conditional on the observation in SF12), suggesting that a substantial fraction of human variation has been lost in the past 9,000 years (Supplementary Information 3). In other words, the SHGs (as well as WHGs and EHGs) have no direct descendants, or a population that show direct continuity with the Mesolithic populations (Supplementary Information 6) (13–17). Thus, many genetic variants found in Mesolithic individuals have not been carried over to modern-day groups.

The gist of the paper in terms of archaeology and demographic history is that Scandinavian hunter-gatherers were a compound population. One component of their ancestry is what we term “Western hunter-gatherers” (WHG), who descended from the late  Pleistocene Villabruna cluster (see paper mentioned earlier). Samples from Belgium, Switzerland, and Spain all belong to this cluster. The second element are “Eastern hunter-gatherers” (EHG). These samples derive from the Karelia region, to the east of modern Finland, bound by the White Sea to the north. EHG populations exhibit affinities to both WHG as well as Siberian populations who contributed ancestry to Amerindians, the “Ancestral North Eurasians” (ANE). There is a question at this point whether EHG are the product of a pulse admixture between an ANE and WHG population, or whether there was a long existent ANE-WHG east-west cline which the EHG were situated upon. That is neither here nor there (the Tartu group has a paper addressing this leaning toward isolation-by-distance from what I recall).

Explicitly testing models to the genetic data the authors conclude that there was a migration of EHG populations with a specific archaeological culture around the north fringe of Scandinavia, down the Norwegian coast. Conversely, a WHG population presumably migrated up from the south and somewhat to the east (from the Norwegian perspective).

And yet the distinctiveness of the very high quality genome as inferred from unique SNPs they have suggests to them that very little of the ancestry of modern Scandinavians (and Finns to be sure) derives from these ancient populations. Very little does not mean all. There is a lot of functional analysis in the paper and supplements which I will not discuss in this post, and one aspect is that it seems some adaptive alleles for high latitudes might persist down to the present in Nordic populations as a gift from these ancient forebears. This is no surprise, not all regions of the genome are created equal (a more extreme case is the Denisovan derived high altitude adaptation haplotype in modern Tibetans).

Nevertheless, there was a great disruption. First, the arrival of farmers whose ultimate origins were Anatolia ~6,000 years ago to the southern third of Scandinavia introduced a new element which came in force (agriculture spread over the south in a few centuries). A bit over a thousand years later the Corded Ware people, who were likely Indo-European speakers, arrived. These Indo-European speakers brought with them a substantial proportion of ancestry related to the hunter-gatherers because they descended in major fraction from the EHG (and later accrued more European hunter-gatherer ancestry from both the early farmers and likely some residual hunter-gatherer populations who switched to agro-pastoralism**).

For several years I’ve had discussions with researchers whose daily bread & butter are the ancient DNA data sets of Europe. I’ve gotten some impressions implicitly, and also from things they’ve said directly. It strikes me that the Bantu expansion may not be a bad analogy in regards to the expansion of farming in Europe (and later agro-pastoralism). Though the expanding farmers initial mixed with hunter-gatherers on the frontier, once they got a head of steam they likely replaced small hunter-gatherer groups in totality, except in areas like Scandinavia and along the maritime fringe where ecological conditions were such hunter-gatherers were at advantage (War Before Civilization seems to describe a massive farmer vs. coastal forager war on the North Sea).

But this is not the end of the story for Norden. At SMBE I saw some ancient genome analysis from Finland on a poster. Combined with ancient genomic analysis from the Baltic, along with deeper analysis of modern Finnish mtDNA, it seems likely that the expansion of Finno-Samic languages occurred on the order of ~2,000 years ago. After the initial expansion of Corded Ware agro-pastoralists.

The Sami in particular seem to have followed the same path along the northern fringe of Scandinavia that the EHG blazed. Though they herd reindeer, they were also Europe’s last indigenous hunter-gatherers. Genetically they exhibit the same minority eastern affinities in their ancestry that the Finns do, though to a greater extent. But their mtDNA harbors some distinctive lineages, which might be evidence of absorption of ancient Scandinavian substate.

I’ll leave it to someone else to explain how and why the Finns and Sami came to occupy the areas where they currently dominate (note that historically Sami were present much further south in Norway and Sweden than they are today). But note that in Latvia and Lithuania the N1c Y chromosomal lineage is very common, despite no language shift, indicating that there was a great deal of reciprocal mixing on the Baltic.

Overall the story is of both population and cultural turnover. This should not surprise when one considers that northern Eurasia is on the frontier of the human range. And perhaps it should temper the inferences we make about other areas of the world.

* You may notice that this threshold is lower than the Neanderthal admixture proportions in the non-African genome. Why is this old admixture still detectable while modern human lineages go extinct? Because it seems to have occurred with non-African humans had a very small effective population, and was mixed thoroughly. Because of the even genomic distribution this ancestry has not been lost in any of the daughter populations.

** Haplogroup I1, which descends from European late Pleistocene populations, exhibits a star phylogeny of similar time depth as R1b and R1a.

September 8, 2012

The Europes

Filed under: Culture,Economics,Europe,geography — Razib Khan @ 9:48 pm

Planet Money recently did a report on the difficulty of maintaining high economic productivity in southern Italy. I won’t rehash the specifics of the story, but, I think it is important to get a visual sense of just how large the contrast between the south and north of Italy is. Too often we speak of nation-states. Nation-states are real, and they are important, but they are often not comparable. Just like comparing the USA to Sweden is only marginally informative, so comparing a small nation like Ireland to a more substantial one like Italy is deceptive. Here is a 2008 regional GDP map with sub-national breakdowns. Though some of the values are certainly lower now (basically, everything outside of Germany and Sweden), the relationships still hold.

There has been a gap between the north and south of Spain and England, as well as the west and east of Germany, but none of these are of the same magnitude of what you see in Italy (for one, southern Italy is much more populous than eastern Germany).  Sicily and the southern provinces are the poorest regions of western Europe. In contrast, the area ...

July 17, 2012

Identity by descent & the Völkerwanderung

Filed under: Demographics,Europe,Europe history,History,Völkerwanderung — Razib Khan @ 8:07 pm

Early this year I received an email from Dr. Peter Ralph, inquiring if I might discuss some interesting statistical genetic results from analyses of the POPRES data set which might have historical relevance. I’ve been excitingly waiting for the preprint to be made public so it could trigger some wider discussion. I believe that the methods outlined in the paper perhaps show us a path into the near future, where we might gain a much sharper perspective upon the recent past. So it’s finally out, and you can read it in full. Ralph and Dr. Graham Coop have posted put it up at arXiv, The geography of recent genetic ancestry across Europe. The paper uses ~500,000 SNPs from the POPRES data set individuals, and looks at patterns of identity by descent as a function of geography. By identity by descent, we’re talking about segments of the genome which are derived from a common ancestor. Because of recombination the length of the segments can give us a sense of the date of the last common ancestor; long segments indicate more recent ancestry because fewer recombination events have ...

April 26, 2012

The last days of Grendel

Filed under: Agriculture,Anthroplogy,Europe — Razib Khan @ 9:27 pm

A new paper in Science has just been published which in its broad outlines has been described in conference presentations. When examining the autosomal genetic variation of three individuals of the hunter-gatherer Pitted Ware Culture (PWC), and one of the agriculturalist Funnel Beaker Culture (TRB), the authors found that the two groups were sharply differentiated. The number of SNPs was on the order of 10,000 or so if I read the methods correctly. This is rather thin for studying contemporary within European population differences (~100,000 or more seems to be safe), in particular using hypothesis based clustering algorithms (it seems more manageable for PCA). But the findings are strong enough that I think we shouldn’t discount them. The most fascinating aspect of the results is that while the PWC seem to exhibit affinities with Northern and Northeastern Europeans, the TRB individual seems more similar to extant Southern Europeans!

Others have already commented extensively on the results. Keeping in mind the small sample sizes, limitation of comparisons, and the relatively thin marker set, I think the primary result we can take away from these findings is that old models ...

January 8, 2012

Europe, 10,000 B.C.

Filed under: Anthroplogy,Europe,Paleolithic Europeans — Razib Khan @ 12:31 am

The image above come from John Hawks’ weblog. I was thinking today about the resettlement of Europe since the Last Glacial Maximum. It is clear that much of northern Europe was not habitable until the Holocene, after the Ice Age. And those regions which were habitable were often marginal. But, there were zones of southern Europe which remained relatively clement. One model of how Europe was settled after the warming is that hunter-gatherers expanded north out of these southern refuges. This can explain the lower heterozygosity of northern populations (see map to left). They may have lost their genetic diversity to some extent through population bottlenecks or simply drift on the wave of demographic advance. And yet something jumped out at me on this map: the southwest portion of Portugal is reputedly the zone with the highest African admixture in continental Europe (for historical reasons). The heterozygosity may simply be a function then of the fact that southern Europe has been in greater contact with other regions of the world because of geographic proximity.

There is also a second pattern which has always elicited curiosity in me: why is it that the largest component of genetic variation in Europe separates north vs. south, as opposed to east vs. west? This does not seem to comport well with a model of expansion from southern refuges. Should not the west-east genetic variation of Ice Age Europeans who faced the tundra and ice be represented among modern populations as they expanded their range northward simultaneously? Something is wrong with the model.

First, it seems clear that a lot has changed since the Last Glacial Maximum. As recently as the late aughts authors were claiming that by ~20,000 years before the present the general shape of genetic variation we see around us had been set. I’d be willing to bet $5,000 dollars that that’s wrong. In the specific case of Europe there may be many explanations for the set of patterns we’re seeing. It may be that the original populations of the refuges were later replaced. Northern Europeans may be legitimate descendants of those groups, but the original patterns of genetic variation in southern Europe were washed away due to being overwhelmed by Neolithic populations from Anatolia. Or, it may be that modern people in the north of Europe descend from a group which moved laterally, and replaced and assimilated the original inhabitants of the continent.

There are many plausible models, and combinations of models. From what I have read people in the Reich lab are now attempting to construct a scenario for the ethnogenesis of Europeans analogous to that of South Asians. In other words, modern Europeans are a compound of the descendants of the Paleolithic hunter-gatherers with an intrusive population. The same lab seems to be positive that Indo-Europeans did have a substantial effect on genetics of South Asians. If so, then I see no reason why the same would not be so in Europe.

In any case, interesting times. We’ll know a lot more in exceedingly great detail soon enough (I’d be willing to bet money on that too!).

October 29, 2011

Unfrying the egg

Dienekes has a long post, the pith of which is expressed in the following:

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.

This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”


The bigger issue which this highlights though is that the reality that many of these clustering methods are temporally sensitive. Given enough time a “hybrid” population is no longer a hybrid, but rather a new distinctive population which itself can be a “parent.” Recombination breaks apart the long range genetic physical associations which are the hallmarks of distinctive admixed ancestry on the genomic scale. That is why clustering methods easily generate a pure “South Asian” component. After at least ~3-4,000 years of continuous admixture the synthesis is now far less coarse, and the elements much more de facto miscible. And yet via other clustering techniques, such as principle components analysis, you get different results. The peculiar position of the “South Asian” individuals between Europeans and East Asians in direct proportion to their caste and regional origins becomes highly indicative of some sort of admixture event in different proportions as a function of geography and social context. The technique in Reconstructing Indian population history allowed for a resolution of this paradox by sifting through the variation and extracting out the ancestral components. The recent papers which came out on Australian Aboriginal genetics do something similar, in terms of making sense of somewhat puzzling results which are found when generating inferences from aggregate genomic variation.

Imagine how much more difficult the task would have been if the ancestral components were much closer! I suspect that’s what’s going on in Europe. I’m not privy to any big secrets, but I have heard of whispers of research groups using Sardinians as a “pure” outgroup to model the changing demographics of Europe since the arrival of agriculture. What David Reich stated at the conference was not particularly surprising to me in light of that possibility. Sardinia regularly pops out as a weird outlier in many analyses. One simple possibility here is that that’s simply a function of the fact that it’s an island, and therefore has diverged from mainland populations due to isolation from conventional village-to-village mate exchange. Another possibility, mooted by Dienekes, is that it may be a repository of European genetic variation from earlier periods, relatively unaffected by later perturbations due to demographic changes. The main reason that I can give some credit to Dienekes’ thesis has less to do with Sardinians than Basques. The French Basques in the HGDP are less atypical than the Sardinians, but in some runs they do lack a component which is most obviously classed as “West Asian,” and which other French have. In Dienekes’ own runs with a diverse array of Iberian populations this same distinction emerges.

All of this reminds us that clustering methods give us great insights into how populations are related to each other, but they don’t tell us about the details of how that relatedness came to be. It makes a great difference if an element is the outcome of relatively recent (<10,000 years) hybridization events, as opposed to having deeper roots. For example, admixture between Polynesians and Melanesians brings together two components, whatever their own prior origins, diverged on the order of 50,000 years before the present. And yet if the two groups mentioned earlier are correct than the Melanesian component itself must be decomposed into two fractions, one of which is much closer to the Polynesians than the other, our understanding of the past changes.

As I implied earlier today I think the era of wild hypothesis generation in the area of the settling of Europe over the last 10,000 years is coming to the end. The combination of more powerful analytic techniques and the emergence of ancient DNA samples with which to calibrate, peg, and check, inferences from those techniques, will probably clarify our understanding of the past to a great extent.

Image credit: yomi955

June 26, 2011

Geert Wilders and banning lying

Filed under: Culture,Europe,Multiculturalism — Razib Khan @ 12:55 pm

A few people have asked me about the Geert Wilders’ affair. If you don’t know Geert Wilders’ is a right-wing Dutch politician prone to making inflammatory remarks about Islam. He’s been brought to court on the grounds of whether his comments violated the speech laws in much of Europe, which sanction inciting or hateful speech.

The main issue as an American that one always has about these sort of things is that because of the First Amendment and the way it has been interpreted our social norms are such that in regards to speech we are exceedingly liberal. Prosecuting Wilders would not be an issue in the United States. Rather, it is much more likely that he’d be marginalized and ignored as a kook.

From my perspective the main problem with prosecutions for hate speech in relation to Islam and immigrants in Europe is that these attempts seem like banning lying; it’s a nominal and symbolic salve on the underlying diseases. Additionally, one must note that the attacks are focused on Muslim immigrants in particular, who from what I can tell have shown (in part) the greatest concerted collective resistance to becoming absorbed into the “European consensus,” as it has evolved.

Some of Wilders’ statements are so extreme and strange that I can’t but help believe that he’s working the Overton window. And from what I’ve read his strategy has worked, the whole center of gravity of public discourse has shifted in the Netherlands and much of Europe. The very fact that Wilders was acquitted is probably a reflection of this, as the enforcement of these laws often is a signal of public mood.

Overall I think there are several issues in Europe which must be addressed in the near future which are relevant to the rise of the right-wing sentiment:

- The likely unworkability of the European “super-state” because of cultural incompabilities

- The nature of employment regulation in Europe which discourages labor market mobility and fluidity

- The welfare state predicated on a common set of values affinity across lines of class and age not always compatible with a multicultural order

- The cultural insularity of many minority ethnic groups in Europe, especially Muslims, vis-a-vis the mainstream

And that’s the tip of the iceberg. The main problem is that because of the nature of politics many of these issues are neatly reduced into catchphrases. Muslim populations in Europe complaining of racism neatly neglect that black Africans who are not Muslim probably experience as much racism, but are not the locus of social unrest or panic, in part because they don’t pose a coherent challenge to Europe as it is. Anti-immigrant voices neglect the fact that even if all immigrants left tomorrow Europe would still be facing massive structural problems because of the reality of their demographics, as fewer and fewer young people are supporting large populations of economically inactive older pensioners.

 

February 8, 2011

God’s Continent: Christianity, Islam, and Europe’s Religious Crisis


Link to review: God’s Contintent, Christianity, Islam and Europe’s Religious Crisis.

God’s Continent: Christianity, Islam, and Europe’s Religious Crisis


Link to review: God’s Contintent, Christianity, Islam and Europe’s Religious Crisis.

December 14, 2010

Re-visualizing European ancestry

I decided to take the Dodecad ADMIXTURE results at K = 10, and redo some of the bar plots, as well as some scatter plots relating the different ancestral components by population. Don’t try to pick out fine-grained details, see what jumps out in a gestalt fashion. I removed most of the non-European populations to focus on Western Europeans, with a few outgroups for reference.

Here’s a table of the correlations (I bolded the ones I thought were interesting):


W Asian NW African S Europe NE Asian SW Asian E Asian N European W African E African S Asian
W Asian * -0.01 -0.18 0.04 0.81 0.59 -0.64 0.39 0.2 0.04
NW African * * 0.19 -0.16 0.23 -0.09 -0.19 0.26 0.67 -0.11
S European * * * -0.38 -0.03 -0.27 -0.42 -0.11 -0.02 -0.36
NE Asian * * * * -0.06 0.5 0.26 -0.04 -0.1 -0.07
SW Asian * * * * * 0.21 -0.62 0.74 0.59 -0.13
E Asian * * * * * * -0.27 0.08 0 0.14
N European * * * * * * * -0.34 -0.28 -0.31
W African * * * * * * * * 0.86 -0.04
E African * * * * * * * * * -0.07

dodenorthdodsouthdodswasiandodwestscatternorthwestscattersouthnorthscattersouthwestscatterwestasiansouthwest

December 8, 2010

The men of the north: the Sami

444px-Ole_Henrik_Magga_closeup
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:

ejhg2010179f2

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:

ADMIXTURE15

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.

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