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Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms

  • BIOINFORMATICS AND SYSTEMS COMPUTER BIOLOGY
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Abstract

Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand characters, the principal components were obtained. A well-known statistical method, which has not been previously used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. The subfamily level was selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p < E–5). The clear division into two groups, revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying cause for the differences between them. This requires further research.

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Funding

This study was performed within the framework of the budgetary project of the Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences no. FWNR-2022-0020 “Systems Biology and Bioinformatics: Reconstruction, Analysis, and Modeling of the Structural-Functional Organization and Evolution of Human, Animal, Plant, and Microorganism Gene Networks.”

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia

    V. M. Efimov

  2. Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, 630091, Novosibirsk, Russia

    V. M. Efimov & V. Yu. Kovaleva

  3. Novosibirsk State University, 630090, Novosibirsk, Russia

    V. M. Efimov

  4. Tomsk State University, 634050, Tomsk, Russia

    V. M. Efimov

  5. Higher School of Economics, 101000, Moscow, Russia

    K. V. Efimov

Authors
  1. V. M. Efimov
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  2. K. V. Efimov
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  3. V. Yu. Kovaleva
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Correspondence to V. M. Efimov.

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The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by M. Batrukova

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Efimov, V.M., Efimov, K.V. & Kovaleva, V.Y. Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms. Mol Biol 57, 176–181 (2023). https://doi.org/10.1134/S002689332302005X

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  • DOI: https://doi.org/10.1134/S002689332302005X

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