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Sunday, May 24, 2009

Ancient Siberians carrying R1a1 had light eyes - take 2

Hot on the heels of that recent Bouakaze et al. paper on the pigmentation genetics of prehistoric South Siberians, here's another effort featuring the same samples. This paper attempts to further elucidate the origins of these light-pigmented Kurgan nomads.

Our autosomal, Y-chromosomal and mitochondrial DNA analyses reveal that whereas few specimens seem to be related matrilineally or patrilineally, nearly all subjects belong to haplogroup R1a1-M17 which is thought to mark the eastward migration of the early Indo-Europeans. Our results also confirm that at the Bronze and Iron Ages, south Siberia was a region of overwhelmingly predominant European settlement, suggesting an eastward migration of Kurgan people across the Russo-Kazakh steppe. Finally, our data indicate that at the Bronze and Iron Age timeframe, south Siberians were blue (or green)-eyed, fair-skinned and light-haired people and that they might have played a role in the early development of the Tarim Basin civilization.

Christine Keyser et al., Ancient DNA provides new insights into the history of south Siberian Kurgan people, Human Genetics, Saturday, May 16, 2009, doi: 10.1007/s00439-009-0683-0

Monday, May 18, 2009

Ancient Siberians carrying R1a1 had light eyes

It looks like more than 60% of the Kurgan (including Scytho-Siberian) samples successfully tested here for pigmentation markers were blue or green eyed and fair haired:

In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archaeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry.

The Y-DNA haplogroups reported for the ancient individuals include seven R1a1a and a single C (xC3). On the other hand, the mtDNA results show a lot more variety, with the following haplogroups present: U2e, U4 (2 instances), U5a1, H or U (3 instances), K2b, H5a, HV, T1 (2 instances), T3 (2 instances), T4, I, C (2 instances) F1b, G2a, N9a and Z.

The majority of the males who belonged to Y-DNA haplogroup R1a1 were very similar in terms of the few analyzed nuclear markers to the European reference population (Utah Americans from the HapMap project). On the other hand, the individual with haplogroup C clustered close to East Asians (HapMap Han Chinese and Japanese), along with another sample for which a Y-haplogroup assignment wasn't available.

Caroline Bouakaze et al., Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis, International Journal of Legal Medicine doi:10.1007/s00414-009-0348-5

See also...

Ancient Siberians carrying R1a1 had light eyes - take 2

Saturday, May 9, 2009

Genetic substructures within Northeastern Europe

This PLoS paper is the first academic study to use high density genome-wide SNPs to analyze samples from the Baltic States. It shows some interesting and perhaps surprising outcomes, including the following:

- Estonians are closer to Poles, Latvians and Lithuanians, in that order, than to Finns.

- Finns are distant from all Europeans, including fellow Northeastern Europeans, but closest to Estonians, Poles and Swedes.

- Russians from Tver are more southern and western genetically than Latvians and Lithuanians, despite being located east and northeast of them, respectively.

- Poles from West Pomerania (presumably largely of eastern Polish descent due to post-WWII re-settlements) are closer to Estonians and Austrians than to Lithuanians and Latvians.

- The most northern (or least southern) samples in terms of genetic affinities are Latvians, Lithuanians and Finns.

At least that's my interpretation of the various analyses featured in the paper and supplementary data. Admittedly, most of these aren't results I would've bet on before seeing this study, but now that I have, they do make a lot of sense.

For instance, the large genetic distances between Finns and other Europeans, including even their immediate neighbors and fellow Finnic-speakers Estonians, can be explained by strong founder effect and resulting genetic drift across Finland. However, some Finns do overlap with Estonians and Swedes on the aforementioned PCA and MDS plots, which probably means these individuals are less drifted and/or carry recent admixture from outside of Finland.

The fairly high affinity between Estonians and Poles might be due to shared deep ancestry from near the Baltic Sea as well as similar levels of recent Western European influence. I suspect it's the western admixture which makes Estonians and Poles look more similar to each other in the inflation factor lambda table than to their Baltic neighbors Latvians and Lithuanians, respectively, who probably carry lower levels of this admixture.

It's also possible that Latvians and Lithuanians are being pushed east because of ancient influence from their Eastern Baltic-speaking ancestors, who lived in what is now Russia during the Iron Age. On the other hand, the Russians from Tver are Slavic-speakers whose ancestors arrived in Northwestern Russia from the Slavic homeland somewhere in East Central Europe during the early Middle Ages. These factors might explain the more southern and western genetic character of these Russians compared to the Balts, which is obviously an outcome that doesn't fit geography.

The results for the Swedes are also out of whack with geography. On the PCA/MDS plots they basically look like Central Europeans with varying degrees of Finnish admixture. However, all other Germanic-speaking samples come out very Central European too, so perhaps this says something about the origins of this linguistic group? The Finnish admixture in Sweden is easily explained by heavy migration of Finns to Scandinavia during historic times, although ancient links between Finland and Sweden might also be partly responsible.

Nelis et al. also investigate genetic variation within several European countries. They show that PCA can separate samples from northern and southern Italy with almost 100% accuracy. Germany and Estonia also show some differentiation along the north-south axis, but not to the same extent. On the other hand, samples from northwest and southeast Czech Republic are almost inseparable, and also very similar to Austrians.

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...

Northwestern (or rather Eastern) Poles compared to other Europeans using more than 270K SNPs