The “evolution” of the mitochondrial genome of the (Phylloscopus borealis sensu lato) occurs in its nuclear genome

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Sequencing of a partial fragment of the ND5–cytb mithochondrial genes (1553 bp) and its nuclear copies was carried out to Phylloscopus borealis sensu lato, belonging to individual taxonomic groups from different parts of the range. It was shown that the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms were identical to those in nuclear copies of borealis mtDNA. Differences between mitochondrial haplotypes of examinandus and nuclear copies of mtDNA borealis were low (p = 0.02), at the same time the mtDNA genetic divergence in borealis–examinandus, borealis–xanthodryas and examinandus–xanthodryas significantly exceeded this value (p = 0.035, 0.044 and 0.046, respectively). A nuclear copy of the mitochondrial haplotype of the easternmost form of xanthodryas was first discovered in the nuclear genome of one borealis individual in the western part of the breeding range (Komi Republic). Alongside this, it was shown at the first time, the nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were close to the mitochondrial haplotypes of borealis from Kytlym (Sverdlovsk region) (p = 0.018). Thus, the mutations emerging in the nuclear copies of mitochondrial genes are the source of most substitutions in the mitochondrial DNA of the studied forms. The origin of the mitochondrial haplotypes examinandus and xanthodryas from nuclear copies of mtDNA borealis and the close similarity of their nuclear genomes gives grounds to consider the mitogenomes of these forms as variants of the haplotype of the single species Ph. borealis sensu lato. With a high degree of probability, it can be argued that the divergence time of the haplotypes of the analyzed forms is significantly less than 2.5-3 million years, as previously assumed by a number of authors [Saitoh et al. 2010; Alström et al. 2011], and the “molecular clock” that do not take into account recombination events between the nuclear and mitochondrial genomes cannot be used in this case.

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Sobre autores

L. Spiridonova

Federal Scientific Center for Biodiversity of Terrestrial Biota of Eastern Asia Far Eastern Branch of the Russian Academy of Sciences

Autor responsável pela correspondência
Email: spiridonova@biosoil.ru
Rússia, 690022, Vladivostok

O. Valchuk

Federal Scientific Center for Biodiversity of Terrestrial Biota of Eastern Asia Far Eastern Branch of the Russian Academy of Sciences

Email: spiridonova@biosoil.ru
Rússia, 690022, Vladivostok

Ya. Red’kin

Moscow State University; Institute of Biological Problems of the Cryolithozone, Siberian Branch of the Russian Academy of Sciences

Email: spiridonova@biosoil.ru

Zoological Museum

Rússia, 125009, Moscow; 677000, Moscow

Bibliografia

  1. Гребельный С.Д., Иванова Н.Ю., Нефедова Е.А. Обмен между ядерным и митохондриальными геномами (по результатам анализа ядерных и цитоплазматических копий митохондриальных генов – numts и cymts ) // Цитология. 2018. Т. 60. № 11. С. 899–902. https://doi.org/10.1134/S004137711811007X
  2. Sorenson M.D., Quinn T.W. Numts: A challenge for avian systematics and population biology. Auk. 1998. V. 115. P. 214–221.
  3. Спиридонова Л.Н., Вальчук О.П., Редькин Я.А., Крюков А.П. Ядерные копии митохондриальных генов – источник новых гаплотипов гена цитохрома b мтДНК Luscinia calliope (Muscicapidae, Aves) // Генетика. 2016. Т. 52. № 9. С. 1069–1080. https://doi.org/10.7868/S0016675816090137
  4. Спиридонова Л.Н., Вальчук О.П., Редькин Я.А. Новый случай рекомбинации между ядерным и митохондриальным геномами в роде Calliope Gould, 1836 (Muscicapidae, Aves): гипотеза происхождения Calliope pectoralis Gould, 1837 // Генетика. 2019. Т. 55. № 1. С. 81–93. https://doi.org/10.1134/S0016675819010132.
  5. Спиридонова Л.Н., Вальчук О.П. Полный митохондриальный геном Phylloscopus examinandus и гипотеза его происхождения // Генетика. 2022. Т. 58. № 3. С. 362–366. https://doi.org/10.31857/S0016675822030146
  6. Triant D.A., DeWoody J.A. Demography and phylogenetic utility of numt pseudogenes in the southern red-backed // J. Mammalogy. 2009. V. 90. № 3. P. 561–570. https://doi.org/10.1644/08-MAMM-A-149R1.1
  7. Романов Д.А., Андрианов Б.В. Митохондриальные последовательности в ядерном геноме животных // Успехи соврем. биологии. 2013. Т. 133. № 3. С. 254–268.
  8. Спиридонова Л.Н., Вальчук О.П., Редькин Я.А. и др. Филогеография и демографическая история соловья-красношейки Luscinia calliope // Генетика. 2017. Т. 53. № 8. С. 933–951. https://doi.org/10.7868/S0016675817080100
  9. Волков В.А., Григорьева Е.А., Лебедева М.В., Потокина Е.К. Гетероплазмия и ядерные копии митохондриальных генов (NUMTs), выявленные в зоне интрогрессивной гибридизации ели европейской и ели сибирской // Тр. Санкт-Петербургского науч.-исслед. ин-та лесного хозяйства. 2022. № 1. C. 4–19. doi: 10.21178/2079-6080.2022.1.4
  10. Fok K.W., Wade C.M., Parkin D.T. Inferring the phylogeny of disjunct populations of the azurewinged magpie Cyanopica cyanus from mitochondrial control region sequences // Proc. R. Soc. Lond. B. 2002. V. 269. P. 1671–1679. https://doi.org/10.1098/rspb.2002.2057
  11. Kryukov A., Iwasa M.A., Kakizawa R. еt al. Synchronic east-west divergence in azure-winged magpies (Cyanopica cyanus) and magpies (Pica pica) // J. Zool. Syst. Evol. Res. 2004. V. 42. P. 342–351. https://doi.org/10.1111/j.1439-0469.2004.00287.x
  12. Kryukov A., Spiridonova L., Mori S. et al. Deep phylogeographic breaks in magpie Pica pica across the Holarctic: concordance with bioacoustics and phenotypes // Zool. Sci. 2017. V. 34. P. 185–200. https://doi.org/10.2108/ zs160119
  13. Zhang D., Tang L, Cheng Y., Hao Y., et al. “Ghost introgression” as a cause of deep mitochondrial divergence in a bird species complex // Mol. Biol. Evol. 2019. V. 36. № 11. P. 2375–2386. https://doi.org/10.1093/molbev/msz170
  14. Коблик Е.А., Редькин Я.А., Архипов В.Ю. Список птиц Российской Федерации. М.: Тов-во науч. изданий КМК, 2006. 281 c.
  15. Глущенко Ю.Н., Нечаев В.А., Редькин Я.А. Птицы Приморского края: краткий фаунистический обзор. М.: Тов-во науч. изданий КМК, 2016. 523 с.
  16. Reeves A.B., Drovetski S.V., Fadeev I.V. Mitochondrial DNA data imply a stepping-stone colonizaiton of Beringia by arctic warbler Phylloscopus borealis // J. Avian Biol. 2008. V. 39. P. 567–575. https://doi.org/10.1111/j.0908-8857.2008.04421.x
  17. Saitoh T., Shigeta Y., Ueda K. Morphological differences among populations of the Arctic Warbler with some intraspecific taxonomic notes // Ornith. Sci. 2008. V. 7 (2). P. 135–142. https://doi.org/10.2326/1347-0558-7.2.135
  18. Saitoh T., Alström P., Nishiumi I. et al. Old divergences in a boreal bird supports long-term survival through the Ice Ages // BMC Evol. Biology. 2010. V. 10 (1). № 35. https://doi.org/10.1186/1471-2148-10-35
  19. Saitoh T., Nishiumi I., Shigeta Y., Ueda K. Re-examination of the taxonomy of the Arctic Warbler Phylloscopus borealis (Blasius): Three separate species withing the Phylloscopus [borealis] subspecies // Japan. J. Ornithol. 2011. V. 61 (1). P. 46–59. https://doi.org/10.3838/jjo.61.46
  20. Alström P., Saitoh T. et al. The Arctic Warbler Phylloscopus borealis – three anciently separated cryptic species revealed // Ibis. 2011. V. 153. P. 395–410.
  21. Dickinson E.C., Christidis L. The Howard & Moore Complete Checklist of the Birds of the World: Passerines. 4th ed. V. 2. Eastbourne: Aves Press, 2014. 752 p.
  22. Назаренко А.А. К орнитофауне Хэнтэй-Чикойского нагорья, Южное Забайкалье // Сб. Экология и зоогеография некоторых позвоночных суши Дальнего Востока. Владивосток, 1978. С. 40–56.
  23. Лобков Е.Г. Гнездящиеся птицы Камчатки. Владивосток: ДВНЦ АН СССР, 1986. 290 с.
  24. Red’kin Ya.A. Geographic variation and reproductive isolation in the eastern populations of arctic warbler // Avian migrants in the Northern Pacific: Breeding and Stopover sites in changing Earth. Scientific conf. Institute of Marine Geology and Geophysics FEB RAS: Abstracts. Yuzhno-Sakhalinsk, September 3–7, 2013. P. 11. /
  25. Del Hoyo J., Collar N.J. (Eds). HBW and BirdLife International Illustrated Checklist of the Birds of the World: Passerines. Barcelona, Spain: Lynx Edicions, 2016. V. 2. 1013 p.
  26. Bonfield J.K., Smith K.F., Staden R. A New DNA Sequence Assembly Program // Nucl. Acids Res. 1995. V. 23. P. 4992–4999.
  27. Kumar S., Stecher G., Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets // Mol Biol Evol. 2016. V. 33 №7. P. 1870–1874. https://doi.org/10.1093/molbev/msw054
  28. Nei M., Kumar S. Molecular Evolution and Phylogenetics. N. Y.: Oxford Univ. Press, 2000. 333 p.
  29. Librado P., Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data // Bioinformatics. 2009. V. 25. P. 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
  30. Goldman N. Statistical tests of models of DNA substitution // J. Mol. Evol. 1993. V. 36. P. 182–198.
  31. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees // Bioinformatics. 2001. V. 17. P. 754–755. https://doi.org/10.1093/bioinformatics/17.8.754
  32. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap // Evolution. 1985. V. 39. P. 783–791.
  33. Rambaut A., Drummond A.J., Xie D., Baele G., Suchard M.A. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7 // Systematic Biology. 2018. V. 67 (5). P. 901–904. https://doi.org/10.1093/ sysbio/syy032
  34. Bandelt H.J., Forster P., Rohl A. Median-Joining networks for inferring intraspecific phylogenies // Mol. Biol. Evol. 1999. V. 16. P. 37–48.
  35. Van den Burg M.P., Vieites D.R. Bird genetic databases need improved curation and error reporting to NCBI // Ibis. 2022. https://doi.org/10.1111/ibi.13143
  36. Cтрижикова С.В., Стрижиков В.К., Житенко Н.В. Гистогенез яичников у птиц в пренатальном периоде онтогенеза // Успехи соврем. естествознания. 2002. Т. 4. С. 77–78.
  37. Triant D.A., DeWoody J.A. Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents // Genetica. 2008. V. 132. № 1. P. 21–33. https://doi.org/10.1007/s10709-007-9145-6
  38. Hazkani-Covo E., Graur D. A comparative analysis of numt evolution in human and chimpanzee // Mol. Biol. Evol. 2007. V. 24. № 1. P. 13–18. https://doi.org/10.1093/molbev/msl149
  39. Hazkani-Covo E. Nuclear sequences of mitochondrial origin as phylogenetic markers // Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester, 2010. https://doi.org/10.1002/9780470015902.a0022877
  40. Андрианов Б.В., Романов Д.А., Горелова Т.В. и др. Перенос митохондриальной ДНК в ядерный геном клеток пересеваемой клеточной линии Drosophila virilis // Генетика. 2013. Т. 49. № 6. С. 788–792. https://doi.org/10.7868/S0016675813060027
  41. Martens J., Sun Y.-H., Packert M. Intraspecific differentiation of Sino-Himalayan bish-dwelling Phylloscopus leaf warblers, with description of two new taxa (P. fuscatus, P. fuligiventer, P. affinis, P.armandii, P. subaffinis) // Vertebrate Zool. 2008. V. 58. № 2. P. 233–265. https://doi.org/10.3897/vz.58.e30935
  42. Alström P., Rheindt F.E., Zhang R. et al. Complete species–level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation // Mol. Phylogenet. Evol. 2018. V. 126. P. 141–152. https://doi.org/10.1016/j.ympev.2018.03.0311

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2. Fig. 1. Areal and collection sites of Ph. borealis s. l. Point numbers correspond to the materials presented in Table 1.

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3. Fig. 2. ND5 mtDNA gene region of Ph. borealis s. l.: 1 - xanthodryas (Genbank AB362465), 2 - xanthodryas (IH17880), 3 - borealis (R-34870), 4 - examinandus (Genbank AB362424), 5 - examinandus (VF57191), 6 - examinandus (RYA-3202), 7 - borealis (Genbank AB362462). Sites differing from the xanthodryas sequence are marked in red. Sites with double peaks are shown in yellow, with transitions (R, Y) and transversions (D, M, S, W) lettered.

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4. Fig. 3. Polymorphic sites of the ND5-cytb fragment and its nuclear copies of Ph. borealis s. l.: borealis (a), examinandus (b) and NUMT (the line separates phylogroups NUMT II (top) and NUMT I (bottom)) (в).

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5. Figure 4. Phylogenetic tree of mtDNA sequences of the ND5-cytb fragment and its nuclear copies of Ph. borealis s. l., constructed using the ML method. Support values (ML/BI ≥ 50%) are indicated at the branching nodes. The scale at the top of the tree is indicated with the branch length measured by the number of substitutions per site.

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6. Fig. 5. Phylogenetic network of mtDNA sequences of the ND5-cytb fragment of Ph. borealis s. l. and its nuclear copies, constructed using the Median Joining method. The number of substitutions (≥10) is indicated on the branches in red. The green dashed arrow indicates the mt-haplotype, and the yellow arrow indicates the nuclear copy of mtDNA.

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