Estonian biocentre high coverage Y chromosome sequences and Turkic data

Courtesy of the good people of the Estonian biocentre:

• 307 high coverage human Y chrmosome sequences. Paper to be published soon. 
• The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia. Paper in press.

The Y chromosome data seems particularly exciting (there is a spreadsheet of populations in the download directory). One of the weaknesses of the 1000 Genomes data was that it didn't have any populations between Tuscany and East/South Asia, and the new dataset seems to rectify that.

The Turkic dataset is probably the one used for the preprint The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia. Since I overlooked this when it came out last summer, I'll post about it when the paper is published in a journal.

Indo-Europeans preceded Finno-Ugrians in Finland and Estonia

According to an abstract of a Ph.D thesis (below). This would appear to work well with the dating of the signature Y-chromosome haplogroup of Finno-Ugrians. 

Bidrag till Fennoskandiens språkliga förhistoria i tid och rum (Heikkilä, Mikko)

My academic dissertation "Bidrag till Fennoskandiens språkliga förhistoria i tid och rum" ("Spatiotemporal Contributions to the Linguistic Prehistory of Fennoscandia") is an interdisciplinary study of the linguistic prehistory of Northern Europe chiefly in the Iron Age (ca. 700 BC―AD 1200), but also to some extent in the Bronze Age (ca. 1700―700 BC) and the Early Finnish Middle Ages (ca. AD 1200―1323). The disciplines represented in this study are Germanistics, Nordistics, Finnougristics, history and archaeology. The language-forms studied are Proto-Germanic, Proto-Scandinavian, Proto-Finnic and Proto-Sami. This dissertation uses historical-comparative linguistics and especially loanword study to examine the relative and absolute chronology of the sound changes that have taken place in the proto-forms of the Germanic, Finnic and Samic languages. Phonetic history is the basis of historical linguistics studying the diachronic development of languages. To my knowledge, this study is the first in the history of the disciplines mentioned above to examine the systematic dating of the phonetic development of these proto-languages in relation to each other. In addition to the dating and relating of the phonetic development of the proto-languages, I study Fennoscandian toponyms. The oldest datable and etymologizable place-names throw new light on the ethnic history and history of settlement of Fennoscandia. For instance, I deal with the etymology of the following place-names: Ahvenanmaa/Åland, Eura(joki), Inari(järvi), Kemi(joki), Kvenland, Kymi(joki), Sarsa, Satakunta, Vanaja, Vantaa and Ähtäri. 

My dissertation shows that Proto-Germanic, Proto-Scandinavian, Proto-Finnic and Proto-Sami all date to different periods of the Iron Age. I argue that the present study along with my earlier published research also proves that a (West-)Uralic language – the pre-form of the Finnic and Samic languages – was spoken in the region of the present-day Finland in the Bronze Age, but not earlier than that. In the centuries before the Common Era, Proto-Sami was spoken in the whole region of what is now called Finland, excluding Lapland. At the beginning of the Common Era, Proto-Sami was spoken in the whole region of Finland, including Southern Finland, from where the Sami idiom first began to recede. An archaic (Northwest-)Indo-European language and a subsequently extinct Paleo-European language were likely spoken in what is now called Finland and Estonia, when the linguistic ancestors of the Finns and the Sami arrived in the eastern and northern Baltic Sea region from the Volga-Kama region probably at the beginning of the Bronze Age. For example, the names Suomi ʻFinlandʼ and Viro ʻEstoniaʼ are likely to have been borrowed from the Indo-European idiom in question. (Proto-)Germanic waves of influence have come from Scandinavia to Finland since the Bronze Age. A considerable part of the Finnic and Samic vocabulary is indeed Germanic loanwords of different ages which form strata in these languages. Besides mere etymological research, these numerous Germanic loanwords make it possible to relate to each other the temporal development of the language-forms that have been in contact with each other. That is what I have done in my extensive dissertation, which attempts to be both a detailed and a holistic treatise.

Genetic structure in Europeans (Nelis et al. 2009)

Yet another study on Europeans, this time with ~3K individuals and ~270K SNPs. The studied populations now include a wide assortment of Slavs, Balts, as well as Estonians and several other populations from all over Europe.

The most interesting new fact from this study:

Estonia is a small country with no geographic barriers and its Estonian population is merely one million. In order to study the genetic structure of Estonia in more detail, all Estonian individuals were grouped here by their county of birth. Then, PCA was performed and the mean values of the two first PC of the counties were plotted onto the Estonian regional map (Figure 2). Surprisingly, the resulting genetic map correlates almost perfectly with the geographic map, although Estonia is only 43,400 km2 in size, and the mean area of a county only 2,900 km2. Thus, fine-scale genetic difference can be revealed by PC analysis, and the results can be useful for identification of the distant relatives.

Figure 2 is reproduced here; the Estonian map is on the bottom right.

What seems very interesting is how Swedes and Estonians both deviate towards Finns but from different "starting points", a North German-Central European one and Baltic-West Russian one respectively. This is quite reasonable, as Swedes are Germanics who absorbed some Finnish elements, while Estonians are Finno-Ugrians surrounded by Balto-Slavs.

As the authors note, the multi-dimensional scaling plot is quite similar to the results of the PCA analysis:


Also of interest is the result of PCA within individual countries for which more than one geographical sample were available.


as the authors note:

Interestingly, PC analysis was also capable of highlighting intra-population differences, such as between the two Finnish and the two Italian samples, respectively. A low level of intra-population differentiation in Germany has been reported previously [18], and was confirmed here. In addition, we detected intra-population differences within the Czech and Estonian samples (Figure S3).

The two Finnish samples were from Helsinki and Kuusamo. The German ones from Schleswig-Holstein and Augsburg. The Italian ones from Borbera valley in the Piedmont and Apulia.

PLoS ONE doi:10.1371/journal.pone.0005472

Genetic Structure of Europeans: A View from the North–East

Mari Nelis et al.

Abstract

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (F_st) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Link