New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0

Abstract

BackgroundR0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (∼40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.Methodology/Principal FindingsWe sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (∼57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6±8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).Conclusions/SignificanceIn contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.

Ancient mitochondrial lineages support the prehistoric maternal root of Basques in Northern Iberian Peninsula

“…Strikingly, with the exception of T2b, whose frequency peak is located in the North of Italy, 33 subhaplogroups H1 and U5b reach their highest frequencies in the North of the Iberian Peninsula, specifically in the region where the Franco-Cantabrian refuge was settled during the Upper Palaeolithic. 8,34,35 Two subhaplogroups found in Santimamiñe, U5a2a and U3a, are scarce in prehistoric remains and virtually absent in current European populations. However, these haplogroups of the samples S.12N and S.16G are of great interest because they are the most ancient evidence of the presence of subhaplogroups U5a2a and U3a found to date in Western Europe (Supplementary Appendix).…”

“…It preserves autochthonous subhaplogroups rarely found out of this region, some of which have been described in the last years. 15,16,34,40 With the aim of studying the presence of the ancient mitochondrial lineages from past times in the present, the control region of mtDNA was analysed in a sample of 158 autochthonous Basque individuals belonging to the population inhabiting the vicinity of the Cave of Santimamiñe, the region of Busturialdea (Figure 1 Table S2) and descriptive statistics (Supplementary Table S3) of this population can be accessed in the Supplementary Material.…”

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel

“…6,7 Amplicons were purified and sequenced using forward PCR primers. In some cases the reverse primer was also used for sequencing (due to for example, the presence of poly-C stretches between nt 16184 and 16193).…”

“…In some samples, SNP testing was analysed through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and minisequencing. 7,8 Whole genome sequencing of mtDNAs affiliated by D-loop to the haplogroup M1 was undertaken following the protocols reported elsewhere. 7,[9][10][11] For the detection of Y chromosome SNP polymorphisms, the Signet Y-SNP Identification System v 2.0 (Marligen, Rockville, MD, USA) was used.…”

“…7,8 Whole genome sequencing of mtDNAs affiliated by D-loop to the haplogroup M1 was undertaken following the protocols reported elsewhere. 7,[9][10][11] For the detection of Y chromosome SNP polymorphisms, the Signet Y-SNP Identification System v 2.0 (Marligen, Rockville, MD, USA) was used. All the samples were first analysed by A-R multiplex (polymorphisms M122, M168, M175, M207, M304, M343, M45, M89, M96 and M9), differentiating main evolutionary branches of Y chromosome phylogeny.…”