Phylogenetic Network for European mtDNA

Abstract

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms.

The maternal aborigine colonization of La Palma (Canary Islands)

“…5,14 To improve the reading of each HVRI fragment sequence, the M13 forward primer (Promega) was added, as a tail, at the 5 0 end of all the seven forward primers used. In addition, two new RFLP analyses, that characterise subhaplogroups H1 15 and H3, 16 were performed. The first was typed amplifying a fragment of 50 bp, using the forward primer L3005 5 0 -CTCGATGTTG GATCAGGACA-3 0 and a modified reverse primer H3011 5 0 -GAACCTTTAATAGCGGCTGCACAAT-3 0 that creates a Tsp509I site when the derived A is present, giving fragments of 24 and 26 bp.…”

The link between mitochondrial DNA hypervariable segment I heteroplasmy and ageing among genetically unrelated Latvians

“…Classification of haplogroups was based on Torroni et al, (1996), Richards et al, (1998), Macaulay et al, (1999), Finnila et al, (2001), Kivisild et al, (2002).…”

“…The wide range of nucleotide positions, in which heteroplasmy appeared, are characterized by a diverse substitution rate, from fast-to slowly-mutated nucleotide positions. Transitions at nps 16093, 16129, 16189, 16311 and 16362 in HVS-I are considered as mutational "hotspots" and are often observed in different phylogenetic branches of mtDNA (Hasegawa et al, 1993;Finnila et al, 2001). Among…”

Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic

“…Extensive search with more than 1,000 published complete mtDNA sequences (Ingman et al 2000;Finnila¨et al 2001;Maca-Meyer et al 2001;Torroni et al 2001;Derbeneva et al 2002;Herrnstadt et al 2002;Kivisild et al 2002 and references therein;Ingman and Gyllensten 2003;Mishmar et al 2003) revealed two additional cases with the T12338C variation, with one in a P type (Ingman and Gyllensten 2003) and another in a H1 type (Herrnstadt et al 2002). To further clarify whether the T12338C variation is characteristic of haplogroup F2 or not, 32 samples were selected from our collection described in Table 2 so as to include at least one sample from respective sub-clades, and subjected to PCR amplification and subsequent direct sequencing for detecting the variation.…”