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Thursday, November 25, 2010

Experiment: digging out previously unreported Sub-Saharan African admixture in Sardinia


The Sardinian samples from the HGDP are always, as far as I know, classified as entirely of West Eurasian origin via clustering algorithms like ADMIXTURE and STRUCTURE. In other words, these Sardinians completely fit into clusters that peak north of the Sahara and west of Central Asia. So it would appear that gene flow to Sardinia from neighboring Africa has been minimal, or even non-existent.

But that's not what I found when I took a closer look at their genomes, as well as those of over 250 other Europeans with apparently no extra-European ancestry, as shown by my own ADMIXTURE analyses. I picked one of my favorite "local admixture" programs for the job, called RHHcounter (see here for more details), setting the rare genotype detection level at 0.01%.

Quite a few of the individuals showed tiny clusters of 3-4 genotypes that were only common outside of Europe, usually in Africa, East Asia or the Americas. These were often too small to investigate further. However, I spotted two segments that were large and clear enough to warrant more detailed analyses. Surprisingly, these belonged to two of the HGDP Sardinians - HGDP00672 and HGDP00673. Below are their Chromosome Mosaics, courtesy of RHHmapper, along with MDS plots based on all the SNPs from the aforementioned segments (marked by arrows). The MDS plots include samples from Europe, North Africa and Sub-Saharan Africa.







As per above, the MDS plots were produced using all the genotypes contained within the relevant segments (over 300 and 2000 SNPs respectively), and not just those that were detected by RHHcouter in the analysis. Obviously, what this shows is that only a fraction of the extra-European genotypes were flagged, while the rest nearby remained undetected at this threshold.

I can't see any explanation for these results other than relatively recent gene flow from Sub-Saharan Africa to Sardinia. What this means, of course, is that there must be a reason why model-based algorithms can't pick up such admixtures in certain samples. As suggested by the authors of RHHcounter, perhaps the segments are too small and/or contain too few SNPs to have an impact on overall ancestry estimation? However, I also suspect that because Sardinia is something of a Southern European genetic isolate, the Sardinians are too easily classified as Europeans by ADMIXTURE, STRUCTURE etc., which might mask at least some of their minority admixtures.


Tuesday, November 9, 2010

Ancient Y-DNA and mtDNA from early Neolithic Germany


These results from an LBK burial site in Germany (5,500-4,900 BC) look surprisingly Near Eastern. So the question is, where were the ancestors of modern Central Europeans at this time?

Interestingly, we do not find the most common Y chromosome hgs in modern Europe (e.g., R1b, R1a, I, and E1b1), which parallels the low frequency of the very common modern European mtDNA hg H (now at 20%–50% across Western Eurasia) in the Neolithic samples. Also, while both Neolithic Y chromosome hgs G2a3 and F* are rather rare in modern-day Europe, they have slightly higher frequencies in populations of the Near East, and the highest frequency of hg G2a is seen in the Caucasus today [15]. The few published ancient Y chromosome results from Central Europe come from late Neolithic sites and were exclusively hg R1a [31]. While speculative, we suggest this supports the idea that R1a may have spread with late Neolithic cultures from the east [31].



Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, et al. (2010)
Ancient DNA from European Early Neolithic farmers reveals their Near Eastern affinities. PLoS Biol 8(11): e1000536. doi:10.1371/journal.pbio.1000536

Thursday, February 25, 2010

Bronze Age Tarim Basin Caucasoids belonged to Y-haplogroup R1a1a


Ancient DNA evidence of major population movements from West Eurasia all the way to China just after the Neolithic is really piling up now. Here's an open access article from BMC Biology that focuses on a 4,000-year-old burial site in the Taklamakan desert.

Besides the East Eurasian lineage, two West Eurasian mtDNA haplogroups H and K were found among the Xiaohe people. H lineage is the most common mtDNAhaplogroup in West Eurasia [20], but haplogroup H with a 16260T was shared by only nine modern people in Genbank, including one Italian, one German, one Hungarian,one Portuguese, one Icelander and four English people. Haplogroup K, a western Eurasian–specific haplogroup, is mainly distributed in Europe, central Asia, and Iran [20, 21]. However, haplogroup K with 16134T, found in the Xiaohe people, has not been found in modern people to our knowledge.

...

Regarding the Y chromosomal DNA analyses, the seven males identified all belonged to haplogroup R1a1a. It is most frequently found in Eastern Europe, South Asia and Siberia. In contrast, it is relatively uncommon in Middle Easterners and rare in East Asian [22-24]. It is thought to be a trace of the migration events of early Indo-European [38-39]. The presence of haplogroup R1a1a in the ancient Xiaohe people implies that the parental ancestry of the Xiaohe people originated from somewhere in Siberia or Europe, which is consistent with the origin of maternal ancestry.

Chunxiang Li et al., Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age, BMC Biology 2010, 8:15, doi:10.1186/1741-7007-8-15

Friday, January 1, 2010

30,000 year old mtDNA U2 from Kostenki, Russia


This is quite a result because it suggests at least some genetic continuity in Europe since the Upper Paleolithic:

We next analyzed how the Kostenki 14 mtDNA sequence relates to Neandertal and current human mtDNAs. It is clearly distinct from Neandertal mtDNAs and carries five diagnostic substitutions that define mtDNA haplogroup U2 (Figure S4) (rCRS positions 11,467, 12,308, 12,372, 1,811, and 16,051, based on Phylotree.org-mtDNA, build 5).

...

Today, haplogroup U2 exists in North Africa, western Asia, and Europe [10]. The presence of haplogroup U in an early modern human in Europe is in agreement with analyses of present-day mtDNA, which suggested that haplogroup U has a deep coalescence and may thus be older than other haplogroups in Europe [10, 26].

At this stage it appears that Europe's Mesolithic inhabitants showed high frequencies of mtDNA U4 and U5 (see
here). So it seems the U family of mtDNA haplogroups was well represented in pre-Neolithic Europe, and indeed might have dominated the continent.


Johannes Krause et al., A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia, Current Biology, 31 December 2009, doi:10.1016/j.cub.2009.11.068