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. 2014 Feb 4;9(2):e87612.
doi: 10.1371/journal.pone.0087612. eCollection 2014.

Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade Within the Broadly Distributed Human Haplogroup C1

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Free PMC article

Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade Within the Broadly Distributed Human Haplogroup C1

Clio Der Sarkissian et al. PLoS One. .
Free PMC article

Abstract

The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined "C1f". We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.

Conflict of interest statement

Competing Interests: The authors declare having received funding from a commercial partner (IBM). This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Approximate geographical distribution of the C1 sub-clades in modern and Mesolithic Yuzhnyy Oleni Ostrov populations.
Figure 2
Figure 2. Network representation of C1 HVR-I sequences in Mesolithic Yuzhnyy Oleni Ostrov and modern Eurasian populations.
Each haplotype is represented by a circle, the area of which is proportional to the number of individuals that were found to carry this haplotype in the literature. The haplotypes are colour-coded according to their geographical location: India (black), Asia (dark grey), Lebanon (light grey), and Europe (white). Each section of the circles represents individuals sampled from a same population. Mutations are all substitutions and are reported according to the Reconstructed Sapiens Reference Sequence minus 16000. The star represents the hypervariable region-I haplotype that characterizes the root of the C1 clade. The haplotype labeled ‘UZOO’ is the hypervariable region-I haplotype sequenced from individuals of the archaeological site of Yuzhnyy Oleni Ostrov. All the other haplotypes were found in modern populations.
Figure 3
Figure 3. Median joining phylogenetic tree of haplogroup C1 complete mitochondrial genomes.
A haplogroup sequence L3 sequence was chosen as the root of the tree. Mutations are reported according to the Reconstructed Sapiens Reference Sequence. “d” represents deletions. “i” represents insertions.

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