Just after posting my last entry I realized that it might seem a bit confusing to those who don't really have much experience in reading PCA/MDS plots. So instead of rehashing it, I decided to make another entry about how to read such plots, which might come in handy to my project members. It's really not that difficult, if you keep in mind that they're never really geographic maps, but at the same time, always contain at least some results that show high correlation with geography.
In that last blog entry about the Balto-Slavs I concluded that, in terms of intra-European genetic diversity, Balts were more easterly than Slavs. I based this on both PCA/MDS plots and genetic distances. The reason I did this was because, as mentioned above, PCA/MDS results don't always gel with geography, especially when relative genetic isolates are included in the analysis. The plot I used from Nelis et al. 2009 showed clearly how adding a relative genetic isolate, like Eastern Finns from Kuusamo, can wreck the correlation between genes and geography.
Adding the samples from the Kuusamo isolate basically means that "east" is no longer in the same direction for all the samples on that plot. If we are to assume that it is in the same direction, we get absurd results like Swedes being more easterly than Russians. Obviously, there are now two, perhaps more, directions which correlate well with the geographic "east" within Europe. As you can see, I marked the two obvious ones on that plot as East 1 and East 2.
So now, it seems, we're facing a problem. Which "east" applies to the Balts and Slavs? If it's East 1, then Russians are more easterly than Lithuanians. If it's East 2, then it's the other way around. But not to worry, because it's easy to work that out. The simplest thing to do is to focus on the samples we're interested in, and zoom in on that area of the plot. So let's just leave the Swedes, North Germans, Czechs, Poles, Russians, Lithuanians and Latvians in the analysis, and ignore the Finnic and Southern European samples.
OK, so now the plot makes much more sense; Swedes and North Germans are located west of Poles and Russians, as we'd expect. At the same time, if we're to follow this line of thinking, Lithuanians and Latvians are located east of Poles and Russians. Just to make sure this is correct, let's see what happens on a plot that doesn't include the Kuusamo isolate.
The difference is clear; there's now only one "east", which runs towards the bottom of the plot (ie. west to east = vertical axis).
In order to cement these findings, we can now look at some pairwise intra-European genetic distances. Let's double check, for instance, that the Lithuanians and Latvians are indeed more easterly than the Poles and Russians, as opposed to just being, say, more northerly. For this I use the same table as in my last log entry.
Russians from Tver versus...
- Utah Americans of Northern and Western European origin (1.56)
- French (1.94)
- Swedes (1.59)
- Finns from Helsinki (2.10)
- Southern Italians (2.68)
- Spanish (2.32)
Lithuanians versus...
- Utah Americans of Northern and Western European origin (1.74)
- French (2.20)
- Swedes (1.74)
- Finns from Helsinki (2.33)
- Southern Italians (2.96)
- Spanish (2.62)
Lithuanians and Latvians are much less similar to western Europeans than Russians are. Therefore, they are more easterly than Russians in terms of intra-European genetic diversity. At the same time, they're not more similar to Northern European populations such as Swedes and Finns. Therefore, any claims, for instance, that they're simply more northerly than Russians don't hold up. In fact, based on all the pairwise scores, the best way to describe the situation is to say that Russians are more mainstream as far as intra-European genetic diversity is concerned, while there's something fairly unique about the Balts, which is especially evident when looking at Latvians.
As I've already noted in my last blog entry, I can't see this as being a recent development. Rather, the close genetic relationship between current Northern Slavs and Balts seems like the recent development, and likely due to mixing in the last 1000 years or so. Before that, I suspect, these two groups were much more distinct from each other than they are today.
By the way, there are two points I'd like to stress before signing off. Firstly, it's important to understand that what is "east" on an intra-European PCA/MDS plot, need not be "east" on an inter-continental plot. For instance, consider a Central European ethnic group with some minor East Eurasian admixture, and an Eastern European group with less East Eurasian admixture. The former will cluster "west" of the latter on an intra-European plot. However, when East Asian samples are added to the analysis, it then becomes an inter-continental plot, and the Central European group with the more significant Asian influence will pull "east" further than the Eastern Europeans. You can actually see something like that on the following two plots I published recently; intra-North Eurasian where Lithuanians cluster west of Hungarians, and intra-European, where the situation is reversed.
Anyone with an interest in these sorts of analyses should try and sort this out in their minds before attempting any sort of interpretation of PCA/DS plots.
Secondly, and this goes without saying, but I'll say it anyway; beware of making generalizations about entire language groups based on small sample sets. For instance, it's not reasonable to draw inferences about the relationship between Balts and Slavs based on the 10 Lithuanians from the Behar et al. study. These are just 10 people, possibly from near the Belorussian and Polish borders, and might be very different from their countrymen from another part of Lithuania, and even more distinct from Latvians. However, it is reasonable to do what I did, and that was to look at sample sets of tens and hundreds of individuals, from Poland, Lithuania, Latvia and Russia, featured in recent peer-reviewed studies. As I say, this all pure logic, but sometimes it needs to be reiterated.
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Originally Posted by Franz
(the second bar is me)
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