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Friday, September 20, 2013

Multidimensional views of South Asia, West Asia and Eastern Europe


Individual IDs from the main PCAs (eigenvectors 1 & 2) can be seen on the PDF images here: 1, 2, 3.


See also...

A multidimensional view of Europe + West Asia

PCA of the world

Sunday, September 15, 2013

European-specific mtDNA C from prehistoric Ukraine


Maju points me to a thesis on ancient DNA from Ukraine which has recently become available to the public. I blogged about this paper when it was first announced in 2011, but at that time I could only access the abstract (see here). Not surprisingly, parts of the thesis are now somewhat outdated. For instance, the author suggests that Icelandic and German mtDNA haplogroup C1 lineages might have a recent Amerindian origin. However, we now know that C1 was present in Europe during the Mesolithic (see here). Nevertheless, there's still plenty of interesting reading in this report, like the comments below about the mtDNA C subclades specific to prehistoric and modern Europe.

Interestingly, the HVSI motifs present in the three Kurgan individuals appear to represent unique branches within the haplogroup C network. D1.8, L8, and L15 all branch directly from the ancestral node defined by Ya34, although D1.8 occupies a separate terminal branch from L8 and L15 (Fig. 5). This “L branch” is defined by the mutation at position 16218. L15 is separated from Ya34 by this mutation alone, whereas L8 occupies a terminal node due to its additional HVSI mutations mentioned previously (Table 4; Fig. 5). We have labeled this branch “C4a6,” since it has not been previously observed in other mtDNA studies of modern and ancient humans.

...

The C5 subgroup (HVSI motif 16223-16288-16298-16327) has a distinct presence in Europe. In fact, it contains a haplogroup C lineage unique to Europe, which possesses a derived mtDNA sequence type with mutations at positions 16223, 16234, 16288, 16298, and 16327. It is geographically restricted to northern Poland (Malyarchuk et al., 2002; Grzybowski et al., 2007) and northeastern Germany (Poetsch et al., 2003; Poetsch et al., 2004). This derived subcluster extends the presence of haplogroup C in Europe from the Carpathian Basin north to the Baltic coast. One individual belonging to the same European-specific lineage (except with two additional mutations) was reported in a study of Romanian Aromuns (Bosch et al., 2005) suggesting this subcluster has a persistent presence within Europe. Other examples of haplogroup C5 in Europe include another individual from Poland lacking the 16234 mutation (Malyarchuk et al., 2002) and one individual from Northern Greece with the HVSI motif 16223-16261-16288-16298 (Irwin et al., 2008). An additional member of C is located in Greece (Bosch et al., 2005) but belongs to an entirely different lineage.


Newton, Jeremy R., Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The Presence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt (2011). Masters Theses. Paper 5.

Thursday, September 5, 2013

A multidimensional view of East Asia


Asia isn't the focus of my project, but I thought many readers would find these PCA interesting:


Basically, there are three main poles of genetic variation on these plots: Northeast Siberian (Koryaks and Chukchi), East Asian (Japanese and Korean) and Southeast Asian (Malayan).

Overall, the Northeast Siberians appear to be the most distinct group, and that's because they're more closely related to some Amerindians (like Greenlanders) than even other Siberians. Interestingly, the two Koreans cluster firmly with the Japanese across the first two PCs, but are clearly separated from them in PC 4.

It's also worth noting that the Han Chinese sample from Beijing (from the HapMap project) doesn't look particularly homogenous, with some individuals overlapping with the Japanese and others with the Vietnamese.

See also...

PCA of the world

Tuesday, September 3, 2013