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Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels

  • Theoretical Papers and Reviews
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Abstract

Algorithms of nucleotide diversity measures and other measures of genetic divergence at the molecular level are analyzed. Based on a database of p-distances, we have compared genetic divergence of populations (1) and taxa of different rank, such as sibling species (2), species within a genus (3), and species from different genera within a family (4). Based on the theory and algorithms of distance calculation from the primary DNA sequences, as well as the actual distances estimated from literature, it is recommended to use in analysis of experimental data a specific model selected from the eight available ones. The empirical data for more than 24 000 vertebrate and invertebrate species demonstrate that the data series are realistic and interpretable when p-distance or its various estimates are used. This testifies to the applicability of p-distance for most interspecies and intraspecies comparisons of genetic divergence up to the family level by two genes compared. Data on p-distances revealed various and increasing levels of genetic divergence of the sequences of genes Cyt-b and Co-1 in four groups compared. Mean unweighted scores of distances for the four groups were as follows: Cyt-b (1) 1.55 ± 0.56, (2) 5.52 ± 1.34, (3) 10.69 ± 1.34, (4) 18.51 ± 2.09 and Co-1 (1) 0.55 ± 0.19, (2) 4.91 ± 0.83, (3) 9.66 ± 0.72, (4) 14.69 ± 1.02. Differences in divergence between the genes themselves at the four levels were also found, although the total mean distances for the two genes did not show statistically significant differences. This conforms to the ample evidence showing different and nonuniform evolution rates of these and other genes and their various regions. The results of the analysis of the nucleotide and allozyme divergence within species and higher taxa of animals, first, are in a good agreement with these results, including data on protein gene markers, and, second, this evidence suggests that in animals, phyletic evolution is likely to prevail at the molecular level, and speciation mainly corresponds to the type D1 (geographic model). The prevalence of the D1 speciation mode does not mean that the other modes are absent. There are at least seven various modes of speciation. Recognition of speciation modes is a task that seems to require construction of a quantitative genetic model (theory) of speciation. Although, in view of a vast diversity of the possible causes of reproductive isolating barriers (RIBs) and speciation initiation, as well as the “empirical nature” of the formalized approach, proposed in the present work, some newly arising questions may be left without an answer. Their solution probably lied in increasing the number of descriptors and members of equations, proposed in this study, on the basis of DNA markers and other genomic characteristics.

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  1. Institute of Marine Biology, Russian Academy of Sciences, Vladivostok, 690041, Russia

    Y. P. Kartavtsev

  2. Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul, 133791, Republic of Korea

    J. -S. Lee

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Original Russian Text © Y.P. Kartavtsev, J.-S. Lee, 2006, published in Genetika, 2006, Vol. 42, No. 4, pp. 437–461.

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Kartavtsev, Y.P., Lee, J.S. Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels. Russ J Genet 42, 341–362 (2006). https://doi.org/10.1134/S1022795406040016

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