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Thursday, November 5, 2009

R1a1a7: a signal of Slavic expansions from Poland

Nature has just published a paper on the discovery of a European-specific subclade of R1a, defined by the M458 mutation and classified as R1a1a7. It's a long-awaited and ground-breaking result, because structure within R1a has been poorly understood to date, despite the fact that it's one of the most dominant Y-chromosome haplogroups in Europe and Asia. The data included in the study point to what is now Poland as the most likely place of origin for R1a1a7. Here's a nice map...

However, as per the figure above, the authors claim that R1a1a7 originated about 10.7K years ago. This, they say, makes it a likely signal of population movements carrying agriculture from Central Europe to what is now Ukraine and European Russia during the Neolithic. Unfortunately, that doesn't make any sense, because R1a1a7 is very rare in Scandinavia, which was largely populated from Central Europe after the Ice Age. Indeed, recent work on the population movements around the Baltic suggests that both R1a and I1a moved up from Germany and Poland into Sweden.

So something's not quite right there, and I think what happened was that the authors grossly overestimated the age of R1a1a7. They did this by using the so called evolutionary effective mutation rate in their Y-STR calculations. This methodology is commonly used by scientists, but it's generally frowned upon by hobby genetic genealogists, who prefer the so called germline mutation rate. The germline rate produces estimates which are about a third of those obtained with the evolutionary effective rate, but they always seem to make more sense. That's been my impression from the results I've seen over the years anyway.

Let's assume then, that R1a1a7 has only been around for 4,000 years or less. If so, that would make it a perfect candidate for a paternal marker of the proto-Slavs, who probably originated in what is now Southern Poland and began expanding during the late Iron Age. Their descendants eventually settled across much of Central, Eastern and Southeastern Europe, but rarely in Scandinavia, which correlates well with the current spread of R1a1a7.

The paper also claims that it's unlikely there were any major post-Neolithic population movements from Eastern Europe to Asia, because R1a1a7 is today basically missing east of the Urals. But what if a different, as yet undiscovered subclade of R1a migrated from Europe to Asia before R1a1a7 had a chance to expand? Ancient DNA results do suggest that Europeans carrying R1a migrated east via the Russo-Kazakh steppe as far as South Siberia during the Bronze Age (see here), but this information was ignored by the authors.

So well done on finding the new R1a subclade, but there's obviously something off about its age/expansion estimates. When will that change I wonder?


Peter A Underhill et al.,
Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a, European Journal of Human Genetics advance online publication 4 November 2009; doi: 10.1038/ejhg.2009.194

T. Lappalainen et al.,
Migration Waves to the Baltic Sea Region, Annals of Human Genetics, Volume 72 Issue 3, Pages 337 - 348, doi: 10.1111/j.1469-1809.2007.00429.x

Update: R1a1a7 is now known as R1a1a1b1a1. See here.

Saturday, May 9, 2009

Northwestern (or rather Eastern) Poles compared to other Europeans across more than 260K SNPs

The 45 Poles sampled in this PLoS ONE paper come from West Pomerania. This means they're mostly the descendants of migrants from what was eastern Poland before World War II, and what is now Lithuania and Belarus. So we might expect many of them to carry Baltic and East Slavic admixture. But even if that's the case, they generally don't differ from the Warsaw and Lodz cohorts I blogged about earlier, and cluster just east of North-Central Europe. Here's the Multidimensional Scaling (MDS) plot from the study, which is almost identical to the Principal Component Analysis (PCA) also shown in the paper.

In terms of fixation index (Fst) genetic distance scores, the West Pomeranians are closest to Czechs, Russians, Hungarians, North Germans, Estonians, Austrians and Lithuanians (all 0.001), and most distant from the Kussamo Finns (0.012) and Southern Italians (0.010). Their relatively inflated Fst with Sweden (0.002) is somewhat surprising, considering geography. It's about the same as between the aforementioned Warsaw and Lodz cohorts and Sweden, so perhaps the Baltic Sea has hindered more recent contacts between Poland and Scandinavia? This appears to be confirmed when Nelis et al. run a barrier analysis using the pairwise Fst data (see here). However, we're yet to see a Polish sample featured in these sorts of studies with pre-WWII origins from near the Baltic shore. Their results might be somewhat different in this context, due to more frequent contacts with countries to the northwest of Poland compared to other Poles.

The inflation factor lambda results are in line with the Fst distances, at least for the Polish sample. Here, the Poles appear most similar to Czechs (1.09), Hungarians (1.14), Estonians (1.17), North Germans (1.18), Russians (1.18) and Austrians (1.19). They're again most distant from the Kussamo Finns (2.49) and Southern Italians (1.99).

It's also interesting to note that the West Pomeranians show the highest Linkage Disequilibrium (LD) pattern after the Kuusamo Finns, who are known to be an extreme genetic isolate. This might suggest a lack of outbreeding in recent times, but the authors aren't exactly sure:

Surprisingly, the Polish cohort showed a similar LD pattern as the Kuusamo population, which is probably reflecting the homogeneity of the Polish population. Here the similarity could be attributed to the founder effect or admixture as the Polish sample comes from West Pomerania, a region that was repopulated after the Second World War, after the expulsion of the German population, with other people from (Eastern Poland) and also some Ukrainians. Small sample size (n = 45) does not provide a sufficient explanation for this finding because the Hungarian and Bulgarian samples were also similar in size (Table 1), but gave LD patterns distinct from the Polish and Kuusamo samples (Figure 1).

Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, et al. (2009) Genetic Structure of Europeans: A View from the North–East. PLoS ONE 4(5): e5472. doi:10.1371/journal.pone.0005472

See also...

More on genetic substructure within Europe, this time focusing on the Northeast

Saturday, February 28, 2009

Painted skulls, genetics and craniofacial phenotypic variation

Believe it or not, there are still people out there who read up on early 20th century anthropology and then wonder what "sub-race" or "type" they are based on the shape of their melons. They're all over the net, on various fora and blogs, discussing the finer points of Carleton Coon's 1939 typological bible, The Races of Europe (aka. TRoE). It's a depressing sight, but hopefully one that won't last much longer, because we're finally seeing detailed studies on the evolution, phenotypic variation and genetics of the human skull.

Some of the best work is being done at the University of Barcelona, which recently published a massive
presentation on its "Hallstatt Project" and a couple of resulting scientific studies. The thing that really jumps out at me from this extremely detailed PDF, apart from the bizarre way in which the Hallstatt folk painted the skulls of their dead, is the conclusion that "the classification between brachy- and dolicephalic skulls is not grounded on the genetic level". This of course means that looking at the basic shape of the head from above, which used to be one of the favorite pastimes of physical anthropologists, won't reveal anything about genetic ancestry. The skull is indeed an integrated phenotypic complex, as these studies confirm, but to learn anything of value, one must focus on the right traits, how they relate to each other, and also be aware to what extent they're influenced by the environment.

Abstract: Quantitative craniometrical traits have been successfully incorporated into population genetic methods to provide insight into human population structure. However, little is known about the degree of genetic and non-genetic influences on the phenotypic expression of functionally based traits. Many studies have assessed the heritability of craniofacial traits, but complex patterns of correlation among traits have been disregarded. This is a pitfall as the human skull is strongly integrated. Here we reconsider the evolutionary potential of craniometric traits by assessing their heritability values as well as their patterns of genetic and phenotypic correlation using a large pedigree-structured skull series from Hallstatt (Austria). The sample includes 355 complete adult skulls that have been analysed using 3D geometric morphometric techniques. Heritability estimates for 58 cranial linear distances were computed using maximum likelihood methods. These distances were assigned to the main functional and developmental regions of the skull. Results showed that the human skull has substantial amounts of genetic variation, and a t-test showed that there are no statistically significant differences among the heritabilities of facial, neurocranial and basal dimensions. However, skull evolvability is limited by complex patterns of genetic correlation. Phenotypic and genetic patterns of correlation are consistent but do not support traditional hypotheses of integration of the human shape, showing that the classification between brachy- and dolicephalic skulls is not grounded on the genetic level. Here we support previous findings in the mouse cranium and provide empirical evidence that covariation between the maximum widths of the main developmental regions of the skull is the dominant factor of integration in the human skull.

Neus Martínez-Abadías et al, Heritability of human cranial dimensions: comparing the evolvability of different cranial regions. Unitat d'Anthropologia, Departament de Biologia Animal, Universitat de Barcelona.

Full PDF link...

Evolutionary patterns of the human skull. A quantitative genetic analysis of craniofacial phenotypic variation.