Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe

Abstract

R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario.

Mitochondrial DNA haplogroups influence the risk of incident knee osteoarthritis in OAI and CHECK cohorts. A meta-analysis and functional study

“…The haplogroup J is characterised by a set of uncoupling mitochondrial polymorphisms,9 10 preferentially non-synonymous SNPs,39 acquired during its evolutionary history. These aspects make this haplogroup to be biochemically different from other mitochondrial variants, specially the haplogroup H 40 41…”

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

“…However, the discrepancies were not that substantial and did not affect our conclusions. To confirm the age estimation of a lineage, we compared the results with the published literature16171829 and showed little difference.…”

Molecular evolution and the latitudinal biodiversity gradient

“…Given the metabolic role of mitochondria, the mitochondrial genome could be implicated in climate adaptation, and thus far from neutral in the context of the LBG. This idea has been mooted for human mitochondrial genetics (Ruiz-Pesini et al, 2004;Wallace, 2005;Das, 2006;Pierron et al, 2011), but remains controversial given suggestions that available methods to detect selection within populations are flawed (Kryazhimskiy and Plotkin, 2008). Nuclear 'loci' such as ITS are far from ideal given their complex and poorly understood process of sequence evolution (Elder and Turner, 1995).…”