Different rates of molecular evolution of mitochondrial genes in Baikalian and non-Baikalian amphipods

Cover Page

Cite item

Full Text

Abstract

Rates of molecular evolution in eight protein-coding mitochondrial genes from two parallel lineages of Baikalian amphipods were compared to those in the representatives of gen. Gammarus. In six genes (Atp6, Cox2, Cox3, Nad1, Nad5, Nad6), there was a significant acceleration in the evolutionary rate of Baikalian species over those from Gammarus group. Correlation of the absolute rate of base substitution accumulation and the acceleration was insignificant, that allowed us to propose mostly adaptive reasons for the effect found.

About the authors

E. V. Romanova

Limnological Institute of the Siberian Branch of the Russian Academy of Sciences

Author for correspondence.
Email: sherb@lin.irk.ru
Russian Federation, 3, Ulan-Batorskaya St., Irkutsk, 664033

D. Yu. Sherbakov

Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Irkutsk State University

Email: sherb@lin.irk.ru
Russian Federation, 3, Ulan-Batorskaya St., Irkutsk, 664033; 1, Karl Marx St., Irkutsk, 664003

References

  1. Bromham L., Cowman P.F., Lanfear R. 2013. Parasitic plants have increased rates of molecular evolution across all three genomes. BMC Evolutionary Biology 13. doi: 10.1186/1471-2148-13-126
  2. Cock P.A., Antao T., Chang J.T. et al. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423. doi: 10.1093/bioinformatics/btp163
  3. Cormier A., Wattier R., Teixeira M. et al. 2018. The complete mitochondrial genome of Gammarus roeselii (Crustacea, Amphipoda): insights into mitogenome plasticity and evolution. Hydrobiologia 825: 197-210. doi: 10.1007/s10750-018-3578-z
  4. Ellegren H., Galtier N. 2016. Determinants of genetic diversity. Nature Reviews Genetics 17. doi: 10.1038/nrg.2016.58
  5. Fazalova V., Nevado B., Peretolchina T. et al. 2010. When environmental changes do not cause geographic separation of fauna: differential responses of Baikalian invertebrates. BMC Evolutionary Biology 10: 988-999. doi: 10.1016/j.ympev.2018.07.002
  6. Fourdrilis S., de Frias Martins A.M., Backeljau T. 2018. Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda. Scientific Reports 8: 1-12. doi: 10.1038/s41598-018-36428-7
  7. Gouy M., Guindon S., Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27: 221-224. doi: 10.1093/molbev/msp259
  8. Hou Z., Sket B. 2016. A review of Gammaridae (Crustacea: Amphipoda): the family extent, its evolutionary history, and taxonomic redefinition of genera. Zoological Journal of the Linnean Society 176: 323-348. doi: 10.1111/zoj.12318
  9. Huerta-Cepas J., Dopazo J., Gabaldón T. 2010. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 11. doi: 10.1186/1471-2105-11-24
  10. Kalyaanamoorthy S., Minh B.Q., Wong T.K. et al. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14. doi: 10.1038/nmeth.4285
  11. Kamaltynov R.M. 2009. Amfipoda: Gammaroidea in Angara and Yenisei rivers. In: Timoshkin O.A. (Ed.), Index of animal species inhabiting Lake Baikal and its catchment area. Novosibirsk, pp. 297-329. (in Russian)
  12. Katoh K., Standley D.M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780. doi: 10.1093/molbev/mst010
  13. Krebes L., Bastrop R. 2012. The mitogenome of Gammarus duebeni (Crustacea Amphipoda): a new gene order and non-neutral sequence evolution of tandem repeats in the control region. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7: 201-211. doi: 10.1016/j.cbd.2012.02.004
  14. Lanfear R., Ho S.Y., Love D. et al. 2010. Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences 107: 20423-20428. doi: 10.1073/pnas.1007888107
  15. Macdonald III K.S., Yampolsky L., Duffy J.E. 2005. Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Molecular Phylogenetics and Evolution 35: 323-343. doi: 10.1016/j.ympev.2005.01.013
  16. Macher J.N., Leese F., Weigand A.M. et al. 2017. The complete mitochondrial genome of a cryptic amphipod species from the Gammarus fossarum complex. Mitochondrial DNA Part B 2: 17-18. doi: 10.1080/23802359.2016.1275844
  17. Mann H.B., Whitney D.R. 1947. On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18: 50-60.
  18. Naumenko S.A., Logacheva M.D., Popova N.V. et al. 2017. Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Molecular Ecology 26: 536-553. doi: 10.1111/mec.13927
  19. Nguyen L.T., Schmidt H.A., von Haeseler A. et al. 2014. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268-274. doi: 10.1093/molbev/msu300
  20. Pinkster S. 1983. The value of morphological characters in taxonomy of Gammarus. Beaufortia 33: 15-28.
  21. Rabosky D.L. 2019. Phylogenies and diversification rates: variance cannot be ignored. Systematic Biology 68: 538-550. doi: 10.1093/sysbio/syy079
  22. Romanova E.V., Aleoshin V.V., Kamaltynov R.M. et al. 2016. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 17. doi: 10.1186/s12864-016-3357-z
  23. Romanova E.V., Bukin Y.S., Mikhailov K.V. et al. 2020. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Molecular Phylogenetics and Evolution 144. doi: 10.1016/j.ympev.2019.106710
  24. Shao R., Dowton M., Murrell A. et al. 2003. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Molecular Biology and Evolution 20: 1612-1619. doi: 10.1093/molbev/msg176
  25. Sun S., Wu Y., Ge X. et al. 2020. Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris. Royal Society Open Science 7. doi: 10.1098/rsos.190669
  26. Wiens J.J., Scholl J.P. 2019. Diversification rates, clade ages, and macroevolutionary methods. Proceedings of the National Academy of Sciences 116: 24400-24400. doi: 10.1073/pnas.1915908116

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2025 Romanova E.V., Sherbakov D.Y.

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Согласие на обработку персональных данных

 

Используя сайт https://journals.rcsi.science, я (далее – «Пользователь» или «Субъект персональных данных») даю согласие на обработку персональных данных на этом сайте (текст Согласия) и на обработку персональных данных с помощью сервиса «Яндекс.Метрика» (текст Согласия).