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Thread: Phylogenetic Network for European mtDNA

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    Post Phylogenetic Network for European mtDNA

    Phylogenetic Network for European mtDNA

    Phylogenetic Network for European mtDNA

    Saara Finnilä, Mervi S. Lehtonen, and Kari Majamaa

    Departments of Neurology and Medical Biochemistry, and Biocenter, University of Oulu, Oulu, Finland

    Received December 28, 2000; accepted for publication April 3, 2001; electronically published May 10, 2001.

    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.

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    Post Re: Phylogenetic Network for European mtDNA

    Geographic Patterns of mtDNA Diversity in Europe

    Geographic Patterns of mtDNA Diversity in Europe

    Lucia Simoni,1,2 Francesc Calafell,2 Davide Pettener,1 Jaume Bertranpetit,2 and Guido Barbujani3

    1Department of Evolutionary and Experimental Biology, University of Bologna, Bologna; 2Unitat de Biologia Evolutiva, Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona; and 3Department of Biology, University of Ferrara, Ferrara, Italy

    Received July 15, 1999; accepted for publication September 9, 1999; electronically published December 15, 1999.

    Summary

    Genetic diversity in Europe has been interpreted as a reflection of phenomena occurring during the Paleolithic (45,000 years before the present [BP]), Mesolithic (18,000 years BP), and Neolithic (10,000 years BP) periods. A crucial role of the Neolithic demographic transition is supported by the analysis of most nuclear loci, but the interpretation of mtDNA evidence is controversial. More than 2,600 sequences of the first hypervariable mitochondrial control region were analyzed for geographic patterns in samples from Europe, the Near East, and the Caucasus. Two autocorrelation statistics were used, one based on allele-frequency differences between samples and the other based on both sequence and frequency differences between alleles. In the global analysis, limited geographic patterning was observed, which could largely be attributed to a marked difference between the Saami and all other populations. The distribution of the zones of highest mitochondrial variation (genetic boundaries) confirmed that the Saami are sharply differentiated from an otherwise rather homogeneous set of European samples. However, an area of significant clinal variation was identified around the Mediterranean Sea (and not in the north), even though the differences between northern and southern populations were insignificant. Both a Paleolithic expansion and the Neolithic demic diffusion of farmers could have determined a longitudinal cline of mtDNA diversity. However, additional phenomena must be considered in both models, to account both for the north-south differences and for the greater geographic scope of clinal patterns at nuclear loci. Conversely, two predicted consequences of models of Mesolithic reexpansion from glacial refugia were not observed in the present study.

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