Natural selection continues (in the Viking world)


Nature has published a new Viking genomics paper. This morning I didn’t even bother to check it out, as I had other things going on, and there’s been so much ancient DNA from Scandinavia that my thought was “what else could we learn?” Well, it turns out I should have checked it out. The sample size is large enough that it reinforces and nails home the important point that natural selection in many traits has been continuing across the world.

Population genomics of the Viking world:

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci—including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response—in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

The phylogenetic patterns are not surprising at all. I’ve looked at enough Scandinavian genomes from Norway, Sweden, and Denmark, to be able to intuitively figure out the sources of random genomes without a label as long as I know they’re Nordic. The Danes will be south-shifted, the Swedes will be Finn-shifted (unless they’re from the far south across from Denmark), while the Norwegians will be neither. Basically this massive ancient DNA transect just confirms that things such as geographic proximity matters, and, that differential population size matters.

Gene flow from Denmark to Sweden, and from continental Europe into Denmark, is not surprising. This follows naturally from different population sizes, and after extensive Christianization of Denmark, the marriage networks of northern Germany and further south no doubt included Denmark. Perhaps of more interest is confirmation of reflux gene flow from the British Isles into Scandinavia. Some of these individuals may have been slaves, but also likely would be people of mixed background, as was the norm in Iceland Greenland, or even individuals who assimilated into totality to the Scandinavian culture through induction into warbands.

There are lots of details of phylogenomic note. For example, look in the supplements, and it seems that the “Picts” were pretty generic post-Bell Beaker people. Their “mystery” is somewhat solved? On the whole, most of the genomic variation of Northern Europe was established by the Bronze Age, but not all. On the margins, there are subtle and nuanced stories you can tell, and you need a sample size this large to tell that.

The most interesting aspect though is that this dataset confirms what many of us have suspected and seen in other results more tentatively: natural selection on complex traits is reshaping the human genome, in the past, and now. In 2016 Field et al. came out with a paper using pretty intense genomic methods to detect lots of sweeps in the European genome recently, and continuing. The method was persuasive, but the results were perplexing. I didn’t know if they were some strange artifact or not, and when I asked people in that lab at ASHG many of them weren’t sure either. Ancient DNA shows us that these were not artifacts or flukes, the allele frequencies have been changing over the last 2,000 years.

Last year last year I noticed that ancient DNA from the Baltic indicates that these people, the palest in the world using most measures, have gotten more lightly complected since the Iron Age. Noticeably so. If you look at the supplements of this paper the pigmentation loci don’t make it as clear. I think on the whole Vikings would not be visually distinctive from modern Scandinavians. But their statistical method makes it hard to refute that this ancient DNA transect is indicative of a reduction in frequency associated with very dark hair in Scandinavia. The fact that this happened in both the western and eastern Baltic region with culturally distinctive people tells me that some underlying cultural or more likely environmental pressure was being applied.

And, it is clear we don’t know the whole story with lactase persistence. Denmark and southern Sweden have among the highest percentages in the world, and that’s clearly not a function of the deep past, but sweeps continuing down into the present.

Are Scandinavians exceptional? I doubt it. It’s just that the climate and concentration of researchers mean that there is a whole lot of study and analysis of many individuals across Holocene time periods. Rather, think of them as a “model organism.” Evolution isn’t done with our species, not by a long-shot, and though we can detect a lot of selection in the genome…there is very little clarity why the selection is occurring (i.e., what are humans adapting to?).*

* Most human population geneticists seem to be now coming to a consensus that there’s a lot of “soft sweeps” on “standing genetic variation.” Since a lot of these soft sweeps happen at a lot of genomic positions, strong selection for trait x is going to result in side effects on a lot of other traits. The “genetic correlation.”

Natural selection continues down to the present in Estonia

One of the dynamics which is always operative in evolutionary biology is adaptation through natural selection. We know that it happens in humans, and it is clear that it has happened in the past and is happening in the present. It’s most obvious when it comes to disease. You can see the spread of malaria adaptations in the New World, for example, and that’s clearly due to strong natural selection.

But it’s not just disease. A few years ago I noticed that ancient DNA was detecting evidence of rather recent depigmentation across Northern Europe. This is not to say that the general features of the phenotype in Northern Europeans were not mostly there by the Bronze Age. The Beaker People in Britain don’t seem that much different from modern British people.

Nevertheless, using the genomic resources now available to us, a few years ago researchers developed methods looking deep in the genome and found evidence of selection in English populations over the last few thousand years. One of those characteristics was pigmentation. Using similar methods, the Estonian group has found something similar, Differences in local population history at the finest level: the case of the Estonian population, has found something similar:

Another SNP from this list, rs7114857, lies within the GRM5 gene which has been shown previously to be a potential target of natural selection for the pigmentation phenotype [28]. See Supplementary text 5.4 for details.

If you look at my post above, it’s pretty clear Baltic populations were pretty fair-skinned 3,000 years ago. But, these are the fairest populations in the world. And, it looks like that both ancient DNA and “best-of-breed” selection detection methods like SDS are pointing to further allele frequency shifts on the margin.

The question is why? First, there are two issues

– Pigmentation alleles can be pleiotropic. Pigmentation may not be the target of selection.

– If it is the target, then the debate moves to sexual and natural selection.

Pigmentation is an easy trait to discern. There is surely lots of selection in and around disease. But what other traits? The paper points to bone density is one characteristic, and size seems to go up and down a lot.

It’s sad George Williams wasn’t around to see the 21st century renaissance of “adaptationism.”

No one understands the targets of selection in humans (except disease)

I’m proposing on an upcoming episode of The Insight that we should talk about natural selection in the context of humans. The reason is that there seems to be a lot of it. It may even be ubiquitous. But, in most cases which aren’t trivial, we have no good idea what’s going on.

By not being trivial, I mean when there is selection on loci implicated in immunological variation in response, it’s pretty clear what’s going on. Infection by pathogens is arguably the reason that humans have sex, where some sort of frequency-dependent selection is obvious.

When it comes to something like lactose tolerance (lactase persistence), the genomic evidence seems indisputable that there was natural selection (a very long haplotype in Eurasia sweeping up in frequency recently). And there’s a reasonably plausible story. The adoption of agro-pastoralism by disparate populations across the world has produced similar adaptions, albeit via different genetic pathways. But, it isn’t as if we have experimental or ecological evidence as to the differential fitness of humans “in the wild” on this trait. Does milk sugar really make that huge of an impact? (disease kills, its selective power is clear)

Then, you have cases like pigmentation where there are numerous explanations which part of the story, but not most of it. And finally, you have situations like the EDAR variant among East Asians and Amerindians where selection seems likely, but there is zero plausible explanation of what the target of selection is.