TY - JOUR

T1 - Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms

AU - Efimov, V. M.

AU - Efimov, K. V.

AU - Kovaleva, V. Yu

N1 - 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. FWNR2022-0020 “Systems Biology and Bioinformatics: Reconstruction, Analysis, and Modeling of the Structural-Functional Organization and Evolution of Human, Animal, Plant, and Microorganism Gene Networks.” Публикация для корректировки.

PY - 2023/4

Y1 - 2023/4

N2 - 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.

AB - 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.

KW - Euclidean distances

KW - Rodentia

KW - cluster analysis

KW - cytochrome b

KW - geographic coordinates

KW - orthogonal decomposition

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85153717584&origin=inward&txGid=814a75d63ac4b2939ecfcdb38ea1316a

UR - https://www.mendeley.com/catalogue/37473e57-5970-3b7d-b2db-10aeb55ca3f1/

U2 - 10.1134/S002689332302005X

DO - 10.1134/S002689332302005X

M3 - Article

VL - 57

SP - 176

EP - 181

JO - Molecular Biology

JF - Molecular Biology

SN - 0026-8933

IS - 2

ER -