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

• Published in: Molekuliarnaia biologiia Vol. 57; no. 2; p. 178
• Main Authors: Efimov, V M, Efimov, K V, Kovaleva, V Yu
• Format: Journal Article
• Language: Russian
• Published: Russia (Federation) 01.03.2023
• Subjects: Animals; Cytochromes b - genetics; Cytochromes b - metabolism; Molecular Biology; Phylogeny; Phylogeography; Rodentia - metabolism; orthogonal decomposition; geographic coordinates; Euclidean distances; cluster analysis; Rodentia; cytochrome b
• DOI: 10.31857/S0026898423020052
• ISSN: 0026-8984

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.