Wednesday, July 27, 2016
Huge difference in this ADMIXTURE bar graph from the recent Pankratov et al. paper between Lipka Tatars from Belarus and nearby Balts and Slavs. The Lipka Tatars are almost identical to Volga Tatars despite residing in their current homeland for about 500 years. I'm guessing the fact that they're Sunni Muslims might have something to do with it.
Pankratov, V. et al. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci. Rep. 6, 30197; doi: 10.1038/srep30197 (2016).
Saturday, June 18, 2016
Harvard's Human Origins dataset is being updated with 238 new samples, including 23 from Poland (15 from Poznan in western Poland and 8 from Lublin in eastern Poland). It should be available for download soon at the Reich Lab website here, although many of the new samples will only be accessible to people who sign a waiver. Below is a Principal Component Analysis (PCA) from Lazaridis et al. 2016 featuring the new samples. Interestingly, most of the Poles, probably those from Poznan, cluster with Sorbs from eastern Germany. The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi: http://dx.doi.org/10.1101/059311
Sunday, May 1, 2016
This ESHG 2016 presentation about Danish population structure is sure to be interesting. I wonder how the authors were able to discern ancient Polish admixture from more recent Polish admixture? Keep in mind that lots of Poles settled in Denmark during the past 150 years or so. For instance, former Danish national team goalkeeper Peter Schmeichel is half Polish. And Caroline Wozniacki is totally Polish.
Abstract: Denmark’s genetic history has never been studied in detail. In this work, we analysed genetic and anthropometrical data from ~800 Danish students as part of an outreach activity promoting genomic literacy in secondary education. DNA analysis revealed remarkable homogeneity of the Danish population after discounting contributions from recent immigration. This homogeneity was reflected in PCA and AMOVA, but also in more sophisticated LD-based methods for estimating admixture. Notwithstanding Denmark’s homogeneity, we observed a clear signal of Polish admixture in the East of the country, coinciding with historical Polish settlements in the region before the Middle Ages. In addition, Denmark has a substantially smaller effective population size compared to Sweden and Norway, possibly reflecting further lack of strong population structure. None of these three Scandinavian countries seems to have suffered a depression due to the Black Death in the Middle Ages. Finally, we used the students’ genetic data to predict their adult height after training a novel prediction algorithm on public summary statistics from large GWAS. We validated our prediction using the students’ self-reported height and found that we could predict height with a remarkable ~64% accuracy.Athanasiadis et al., Nationwide genomic study in Denmark reveals remarkable population homogeneity, ESHG EMPAG 2016 Presentation Abstract, P18.091C Update 24/08/2016: The paper is now available at Genetics and open access. See here: On the remarkable genetic homogeneity of Denmark.
Monday, March 21, 2016
The genetic evidence presented in this paper is underwhelming; a single, low resolution mtDNA haplogroup I haplotype that appears to be of Scandinavian origin because it was also found in remains from Iron Age Denmark (sample B5 in Melchior et al. 2008). However, the authors' conclusions are also based on archaeological evidence, and they also match recent isotopic results (see here).
Abstract: Contemporary historical anthropology and classical archaeology are concerned not only with such fundamental issues as the origins of ancient human populations and migration routes, but also with the formation and development of inter-population relations and the mixing of gene pools as a result of inter-breeding between individuals representing different cultural units. The contribution of immigrants to the analysed autochthonous population and their effect on the gene pool of that population has proven difficult to evaluate with classical morphological methods. The burial of one individual in the studied Napole cemetery located in central Poland had the form of a chamber grave, which is typical of Scandinavian culture from that period. However, this fact cannot be interpreted as absolute proof that the individual (in the biological sense) was allochtonous. This gives rise to the question as to who was actually buried in that cemetery. The ancient DNA results indicate that one of the individuals had an mtDNA haplotype typical of Iron Age northern Europe, which suggests that he could have arrived from that area at a later period. This seems to indirectly confirm the claims of many anthropologists that the development of the early medieval Polish state was significantly and directly influenced by the Scandinavians.Płoszaj T. et al., Analysis of medieval mtDNA from Napole cemetery provides new insights into the early history of Polish state, Ann Hum Biol. 2016 Mar 11:1-4., DOI:10.3109/03014460.2016.1151550
Tuesday, February 2, 2016
I wasn't confident enough to run these three ancient genomes in Principal Component Analyses (PCA) when they were first published last year. Their SNP counts were too low for comfort. But since then I've discovered a few things about PCA projection, so here goes: 101 ancient Eurasian genomes (Allentoft et al. 2015)