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Friday, March 22, 2013

A revised timescale for human evolution + new revelations about Paleolithic European mtDNA


Doubts have been raised about one of Europe's most talked about ancient DNA results, the mtDNA haplogroup H sequence from the Paglicci Cave remains. A preprint at Current Biology suggests the Paleolithic sample was contaminated with modern DNA:

To further evaluate the authenticity of the ancient DNA we calculated the proportion of nucleotide misincorporations arising from DNA damage, a quantity that is known to increase over time after the death of an individual [12] and has been used as an indication of authenticity in previous work [10]. It was suggested that bone samples 100 years and older have a minimum of 20% C to T misincorporations concentrated at the 50 end of the molecule [13]. Using this criterion, we excluded Paglicci Str. 4b from further analysis as the rate of C to T misincorporation at the 50 end was only 8.8%, thus making an ancient origin for the DNA in this sample uncertain [14].

Another sample thought to be from a Paleolithic European, dubbed "Cro-Magnon 1" and belonging to haplogroup T2b1, was also eliminated from the study after radiocarbon dating revealed it to be of medieval origin. What this means is that all Paleolithic European remains successfully tested to date belong to mtDNA haplogroup U, including six new samples featured in this paper.

It has been argued that hg U5 is the most ancient subhaplogroup of the U lineage, originating among the first early modern humans in Europe [18]. Our results support this hypothesis because we find that the two Dolni Vestonice individuals radiocarbon dated to 31.5 kya carry a type of mtDNA that is as yet uncharacterized, sits close to the root of hg U, and carries two mutations that are specific to hg U5. With our recalibrated molecular clock, we date the age of the U5 branch to approximately 30 kya, thus predating the LGM. Because the majority of late Paleolithic and Mesolithic mtDNAs analyzed to date fall on one of the branches of U5 (see also [15]), our data provide some support for maternal genetic continuity between the pre- and post-ice age European hunter-gatherers from the time of first settlement to the onset of the Neolithic.


Oh yeah, the paper also shows a revised timescale for human evolution based on most of the ancient mtDNA sequences listed above. However, I'd say this timescale will probably be revised a few more times as more aDNA samples become available.


Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes, Current Biology (2013), http://dx.doi.org/10.1016/j.cub.2013.02.044


Sunday, March 10, 2013

Genetic structure of European Russia


A paper at PLoS One reports on the genetic heterogeneity of Russian populations and the discovery of a "new pole of genetic diversity in Northern Europe":

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.


Figure 1. Geographic locations of the populations analyzed. Key: Komi_Izh – Izhemski Komi, Komi_Pr – Priluzski Komi, Rus_Tv – Russians from Tver, Rus_Ku – Russians from Kursk, Rus_Mu – Russians from Murom, Rus_Me – Russians from Mezen, Finns_He – Finns from Helsinki, Finns_Ku – Finns from Kuusamo, Rus_HGDP – Russians from the Human Genome Diversity Panel.


The distinct genetic character of the Komi and other North Russian populations isn't much of a surprise. These groups come from remote and sparsely populated regions near the Urals and the Arctic, and are thus affected by heavy genetic drift as a result of isolation and endogamy. They also carry higher levels of East Eurasian admixture than other Europeans due to contacts with populations of mostly Siberian origin from east of the Urals.

To explore the potential effect of population demographics on the population structures identified, ROH were compared across populations. ROH may indicate prolonged isolation and a reduced population size [29,35].

...

Regardless of the variations in the analysis, the highest nROH and cROH values were found in Izhemski Komi and in the Finnish sample from Kuusamo. Intermediate estimates were observed in Priluzski Komi, Veps, Finns from Helsinki, and Mezen Russians. Other populations had lower nROH and cROH values. An analysis of LD decay across genomes showed that Izhemski Komi and Finns from Kuusamo also exhibited elevated LD (Figure S6). Concomitantly, Priluzski Komi, Veps, Mezen Russians, and Finns from Helsinki exhibited only slightly elevated LD and were more comparable to the level observed in other European samples, including the remaining Russian samples.


These pronounced effects of genetic drift show up on the ADMIXTURE bar graph below, where the most drifted samples, like the Finns from the Kuusamo isolate, create their own clusters at the higher K (number of ancestral populations assumed). On the other hand, the inflated East Eurasian ancestry among the Komi and North Russians, as well as Veps and Baltic Finns, is most easily seen at K=2. It's represented by the green component which peaks in the Chinese sample.




Note also the extreme behavior of many of the samples on the PCA plot below and the bloated genetic distances between them and others in the Fst table. Again, that's mostly due to genetic drift.





Khrunin AV, Khokhrin DV, Filippova IN, Esko T, Nelis M, et al. (2013) A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. PLoS ONE 8(3): e58552. doi:10.1371/journal.pone.0058552