Филогения и систематика недавно дивергировавших групп на примере рода Rosa

И.А. Шанцер

Труды Зоологического института РАН, 2013, 317(Приложение 2):

Резюме

Разграничение видов и установление их родства в эволюционно молодых группах растений часто оказывается весьма затруднительным. На морфологическом уровне это связано с незначительностью межвидовых различий, параллельной изменчивостью и возможной гибридизацией; на генетическом – с той же гибридизацией, анцестральным полиморфизмом и неполной сортировкой, или, иначе, неполным расхождением линий. Одним из наиболее ярких примеров этого может быть род Rosa, в котором все перечисленные выше проблемы наблюдаются одновременно. Методы традиционной систематики, равно как и молекулярной кладистики, оказываются мало пригодными для анализа таких групп. В статье обсуждается использование генеалогий ядерных и хлоропластных гаплотипов для выявления структуры и родственных отношений в роде Rosa и сходных группах. Анализ генеалогий последовательностей ядерных ITS1 и хлоропластных trnL-trnF позволяет с разной степенью детализации выявить от 6 до 9 групп родства Rosa, в значительной степени совпадающих и географически очерченных, однако лишь отчасти соответствующих традиционно принимаемому секционному делению рода.

Ключевые слова

филогения, генеалогия, гибридизация, неполная сортировка/расхождение филогенетических линий, ITS1, trnL-trnF, Rosa

Опубликована 16 сентября 2013 г.

Литература

Абрамсон Н.И. 2007. Филогеография: итоги, проблемы, перспективы. Вестник ВОГиС, 11(2): 307–331.

Хржановский В.Н. 1958. Розы. Филогения и систематика. Спонтанные виды Европейской части СССР, Крыма и Кавказа. Опыт и перспективы использования. Советская Наука, Москва, 497 с.

Шанцер И.А. 2001. Современное состояние таксономической изученности восточноевропейских шиповников (Rosa L.). Бюллетень МОИП. Отдел биологический, 106(2): 43–48.

Шанцер И.А., Вагина А.В. и Остапко В.М. 2011. Критическое исследование шиповников (Rosa L.) заповедника “Хомутовская степь”. Бюллетень МОИП. Отдел биологический, 116(3): 38–49.

Шнеер В.С. 2005. Краткий очерк способов получения, обработки и трактовки данных по последовательности ДНК в систематике растений. Ботанический журнал, 90(3): 304–323.

Avise J.C., Arnold J., Ball R.M., Bermingham E., Lamb T., Neigel J.E., Reeb C.A. and Saunders N.C. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology, Evolution and Systematics, 18: 489–522. https://doi.org/10.1146/annurev.es.18.110187.002421

Bandelt H.-J., Forster P. and Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1): 37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036

Becker H.F. 1963. The fossil record of the genus Rosa. Bulletin of Torrey Botanical Club, 90(2): 99–110. https://doi.org/10.2307/2483008

Bruneau A., Starr J.R. and Joly S. 2007. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and an appraisal of current knowledge. Systematic Botany, 32(2): 366–378. https://doi.org/10.1600/036364407781179653

Cassens I., van Waerenbeek K., Best P.B., Crespo E.A., Reyes J. and Milinkovitch M.C. 2003. The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures. Molecular Ecology, 12(7): 1781–1792. https://doi.org/10.1046/j.1365-294X.2003.01876.x

Clement M., Posada D. and Crandall K.A. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9(10): 1657–1659. https://doi.org/10.1046/j.1365-294x.2000.01020.x

Crandall K.A. and Templeton A.R. 1993. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134: 959–969. https://doi.org/10.1093/genetics/134.3.959

Degnan J.H. and Rosenberg N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescence. Trends in Ecology and Evolution, 24(6): 332–340. https://doi.org/10.1016/j.tree.2009.01.009

Doyle J.J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany, 17(1): 144–163. https://doi.org/10.2307/2419070

Eriksson T., Donoghue M.J. and Hibbs M.S. 1998. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Systematics and Evolution, 211: 155–179. https://doi.org/10.1007/BF00985357

Fedorova A.V., Schanzer I.A. and Kagalo A.A. 2010. Local differentiation and hybridization in populations of wild roses in W Ukraine. Wulfenia, 17: 99–115.

Gurushidze M., Fritsch R.M. and Blattner F.R. 2010. Species-level phylogeny of Allium subgenus Melanocrommyum: Incomplete lineage sorting, hybridization and trnF gene duplication. Taxon, 59(3): 829–840. https://doi.org/10.1002/tax.593012

Hein J., Scheirup M.H. and Wiuf C. 2005. Gene genealogies, variation and evolution. A primer in coalescent theory. Oxford University Press, New York, 276 p.

Helfgott D.M., Francisco-Ortega J., Santos-Guerra A., Jansen R.K. and Simpson B.B. 2000. Biogeography and breeding system evolution of the woody Bencomia alliance (Rosaceae) in Macaronesia based on ITS sequence data. Systematic Botany, 25(1): 82–97. https://doi.org/10.2307/2666675

Hudson R.R. 1991. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7: 1–44.

Huson D.H. 1998. Splits Tree: A program for analyzing and visualizing evolutionary data. Bioinformatics, 14(10): 68–73. https://doi.org/10.1093/bioinformatics/14.1.68

Huson D.H. and Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23(2): 254–267. https://doi.org/10.1093/molbev/msj030

Iwata H., Kato T. and Ohno S. 2000. Triparental origin of Damask roses. Gene, 259(1–2): 53–59. https://doi.org/10.1016/S0378-1119(00)00487-X

Jacob S.S. and Blattner F.R. 2006. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Molecular Bioliology and Evolution, 23(8): 1602–1612. https://doi.org/10.1093/molbev/msl018

Joly S., Starr J.R., Lewis W.H. and Bruneau A. 2006. Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany, 93: 412–425. https://doi.org/10.3732/ajb.93.3.412

Khaitova L., Werlemark G., Nybom H. and Kovarik A. 2010. Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae). Heredity, 104(1): 113–120. https://doi.org/10.1038/hdy.2009.94

Kingman J.F.C. 1982. On the genealogy of large populations. Journal of Applied Probability, 19: 27–43. https://doi.org/10.2307/3213548

Kingman J.F.C. 2000. Origins of the coalescent: 1974–1982. Genetics, 156: 1461–1463. https://doi.org/10.1093/genetics/156.4.1461

Koopman W.J.M., Wissemann V., De Cock K., van Huylenbroeck J., De Riek J., Sabatino G.J.H., Visser D., Vosman B., Ritz C.M., Maes B., Werlemark G., Nybom H., Debener T., Linde M. and Smulders M.J.M. 2008. AFLP markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae). American Journal of Botany, 95(3): 353–366. https://doi.org/10.3732/ajb.95.3.353

Kovarik A., Werlemark G., Leitch A.R., Souckova-Skalicka K., Lim Y.K., Khaitova L., Koukalova B. and Nybom H. 2008. The asymmetric meiosis in pentaploid dogroses (Rosa sect. Caninae) is associated with a skewed distribution of rRNA gene families in the gametes. Heredity, 101(4): 359–367. https://doi.org/10.1038/hdy.2008.63

Matsumoto S., Kouchi M. and Fukui H. 2000. Phylogenetic analyses of the subgenus Eurosa using the ITS nrDNA sequence. Acta Horticulturae, 521: 193–202. https://doi.org/10.17660/ActaHortic.2000.521.21

Matsumoto S., Nishio H., Ueda Y. and Fukui H. 2001. Phylogenetic analyses of genus Rosa: polyphyly of section Pimpinellifoliae and origin of Rosa x fortuniana Lindl. Acta Horticulturae, 547: 357–363. https://doi.org/10.17660/ActaHortic.2001.547.43

McNutt P.M., Dehart M.J. and Matej L.A. 2007. Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation. Plant Cell Reports, 26(1): 47–60. https://doi.org/10.1007/s00299-006-0203-9

Mort M.E., Archibald J.K., Randle C.P., Levsen N.D., O’Leary T.R., Topalov K., Wiegand C.M. and Crawford D.J. 2007. Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci. American Journal of Botany, 94(2): 173–183. https://doi.org/10.3732/ajb.94.2.173

Page R.D. and Charleston M.A. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution, 7(2): 231–240. https://doi.org/10.1006/mpev.1996.0390

Posada D. and Crandall K.A. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16(1): 37–45. https://doi.org/10.1016/S0169-5347(00)02026-7

Potter D., Eriksson T., Evans R.C., Oh S., Smedmark J.E.E., Morgan D.R., Kerr M., Robertson K.R., Arsenault M., Dickinson T.A. and Campbell C.S. 2007. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266: 5–43. https://doi.org/10.1007/s00606-007-0539-9

Ritz C.M. and Wissemann V. 2003. Male correlated non-matroclinal character inheritance in reciprocal hybrids of Rosa section Caninae (DC.) Ser. (Rosaceae). Plant Systematics and Evolution, 241: 213–221. https://doi.org/10.1007/s00606-003-0058-2

Ritz C.M., Schmuths H. and Wissemann V. 2005. Evolution by reticulation: European dogroses originated by multiple hybridization across the genus Rosa. Journal of Heredity, 96(1): 4–14. https://doi.org/10.1093/jhered/esi011

Rosenberg N.A. and Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature reviews. Genetics, 3: 380–390. https://doi.org/10.1038/nrg795

Taberlet P., Gielly L., Pautou G. and Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17: 1105–1109. https://doi.org/10.1007/BF00037152

Templeton A.R. 1998. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7: 381–397. https://doi.org/10.1046/j.1365-294x.1998.00308.x

Templeton A.R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology, 10: 779–791. https://doi.org/10.1046/j.1365-294x.2001.01199.x

Templeton A.R. and Sing C.F. 1993. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. IV. Nested analysis with cladogram uncertainty and recombination. Genetics, 134: 659–669. https://doi.org/10.1093/genetics/134.2.659

Templeton A.R., Boerwinkle E. and Sing C.F. 1987. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117: 343–351. https://doi.org/10.1093/genetics/117.2.343

Templeton A.R., Crandall K.A. and Sing C.F. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132: 619–633. https://doi.org/10.1093/genetics/132.2.619

Wissemann V. and Ritz C. 2005. The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpB-rbcL intergenic spacer (IGS) versus conventional taxonomy. Botanical Journal of the Linnean Society, 147: 275–290. https://doi.org/10.1111/j.1095-8339.2005.00368.x

Woolley S.M., Posada D. and Crandall K.A. 2008. A comparison of phylogenetic network methods using computer simulation. PLoS ONE, 3(4): e1913. https://doi.org/10.1371/journal.pone.0001913

Wu S., Ueda Y., Nishihara S. and Matsumoto S. 2001. Phylogenetic analysis of Japanese Rosa species using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS). Journal of Horticultural Science and Biotechnology, 76: 127–132. https://doi.org/10.1080/14620316.2001.11511338

Zieliński J. 1985. Studia nad rodzajem Rosa L. – Systematyka sekcji Caninae DC. em. Christ. Arboretum Kórnickie, 30: 3–109.