Evidence of distant hybridization within Central Asian feather grasses (Poaceae: Stipa)
Keywords:
DArTseq, feather grasses, Kazakhstan, natural hybridization, nothospecies, taxonomy
Abstract
The genus Stipa is one of the largest genera of Poaceae. The phylogeny of the genus is still poorly resolved, and one of the main problems is linked to the extensive inter and intrasectional hybridization. Disclosure of hybridization processes is a key to understanding relationships between species within the genus. During a floristic study in feathergrass steppe ecosystems of central Asia, we found challenging specimens of Stipa with an interesting combination of morphological characters suggesting their origination through hybridization between morphologically and phylogenetically distant species. To confirm our hypothesis, we applied a combination of classical morphological and genome-wide SNP genotyping methods. Using such an approach, we determined that the new taxon named Stipa × smelanskyi arose from crossing S. richteriana and S. drobovii and confirmed that it is an F1 hybrid. Moreover, we found a S. drobovii specimen with a minor admixture of S. richteriana loci that may indicate putative introgression events among these taxa.
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References
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Freitag H. 1985. The genius Stipa (Gramineae) in Southwest and South Asia. Notes R. Bot. Gard. Edinb. 42(3): 355–489.
Голоскоков В. П. Особенности видового эндемизма во флоре Казахстана (материалы к анализу «Флоры Казахстана», 1) // Ботанические материалы Гербария Института Ботаники АН КазССР, 1969. T. 6. C. 3–12.
Grant P. R., Grant B. R., Petren K. 2005. Hybridization in the recent past. Am. Nat. 166: 56–67. DOI: 10.1086/430331
Gruber B., Georges A., Berry O., Unmack P. 2021. DartR: importing and analysing SNP and Silicodart data generated by genome-wide restriction fragment analysis. URL: https://rdrr.io/cran/dartR/ (Accessed 23 April 2022).
Gruber B., Unmack P. J., Berry O. F., Georges A. 2018. Dartr: an r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol. Ecol. Resour. 18: 691–699. DOI: 10.1111/1755-0998.12745
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Kilian A., Wenzl P., Huttner E., Carling J., Xia L., Blois H., Caig V., Heller-Uszynska K., Jaccoud D., Hopper C., et al. 2012. Diversity Arrays Technology: a generic genome profiling technology on open platforms. In: F. Pompanon, A. Bonin (eds.). Data production and analysis in population genomics: methods and protocols. Methods in Molecular Biology. Totowa, NJ: Humana Press. Pp. 67–89.
Kupriyanov A.N., Gudkova P.D., Kriuchkova E.A. 2018. Endemism of the Kazakhstan flora: Poaceae Barnhart. Ukr. J. Ecol. 8(4): 393–405.
Letunic I., Bork P. 2021. Interactive Tree Of Life (ITOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49. DOI: 10.1093/nar/gkab301
Mallet J. A. 1995. Species definition for the modern synthesis. Trends Ecol. Evol. 10: 294–299. DOI: 10.1016/0169-5347(95)90031-4
Mallet J. 2005. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20: 229–237. DOI: 10.1016/j.tree.2005.02.010
Mallet J. 2007. Hybrid Speciation. Nature 446: 279–283. DOI: 10.1038/nature05706
Mayr E. 1942. Systematics and the origin of species: From the Viewpoint of a Zoologist. New York: Columbia University Press. 207 pp.
Mayr E. 1963. Animal species and evolution. Cambridge: Belknap Press of Harvard University Press. 797 pp.
Nobis M. 2014. Taxonomic revision of the Central Asian Stipa tianschanica complex (Poaceae) with particular reference to the epidermal micromorphology of the lemma. Folia Geobot. 49: 283–308. DOI: 10.1007/s12224-013-9164-2
Nobis M., Erst A., Nowak A., Shaulo D., Olonova M., Kotukhov Y., Doğru-Koca A., Dönmez A., Király G., Ebel A., et al. 2017. Contribution to the Flora of Asian and European countries: new national and regional vascular plant records, 6. Bot. Lett. 164: 23–45. DOI: 10.1080/23818107.2016.1273134
Nobis M., Gudkova P., Baiakhmetov E., Żabicka J., Krawczyk K., Sawicki J. 2019. Hybridisation introgression events and cryptic speciation in Stipa (Poaceae): a case study of the Stipa heptapotamica hybrid-complex. Perspect. Plant Ecol. Evol. Syst. DOI: 10.1016/j.ppees.2019.05.001
Nobis M., Gudkova, P., Nowak A., Sawicki J., Nobis A. 2020. A synopsis of the genus Stipa (Poaceae) in Middle Asia, including a key to species identification, an annotated checklist, and phytogeographic analyses. Ann. Missouri Bot. Gard. 105: 1–63. DOI: 10.3417/2019378
O’Brien S. J., Mayr E. 1991. Bureaucratic Mischief: recognizing endangered species and subspecies. Science 251: 1187–1188. DOI: 10.1126/science.251.4998.1187
Pagès J. 2021. Analyse factorielle de données mixtes. In: analyse factorielle multiple avec R. EDP Sciences. Pp. 65–76.
Peterson P., Romaschenko K., Soreng R., Valdés J. 2019. A key to the North American genera of Stipeae (Poaceae, Pooideae) with descriptions and taxonomic names for species of Eriocoma, Neotrinia, Oloptum, and Five New Genera: Barkworthia, × Eriosella, Pseudoeriocoma, Ptilagrostiella, and Thorneochloa launched to accelerate biodiversity research. PhytoKeys 126: 89–125. DOI: 10.3897/phytokeys.126.34096
Pritchard J., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
Romaschenko K., Peterson P., Soreng R., Garcia-Jacas N., Futorna O., Susanna A. 2012. Systematics and evolution of the needle grasses (Poaceae: Pooideae: Stipeae) based on analysis of multiple chloroplast loci, ITS, and lemma micromorphology. Taxon 61: 18–44. DOI: 10.1002/tax.611002
Рожевиц Р. Ю. Stipa L. // Флора СССР. Т. 2. Л.: АН СССР, 1934. С. 79–112, 740–741.
Sievert C., Parmer C., Hocking T., Chamberlain S., Ram K., Corvellec M. et al. 2020. Plotly: create interactive web graphics via 'plotly.js'. URL: https://rdrr.io/cran/plotly/ (Accessed 23 April 2022).
Thiers B. 2021. Index herbariorum: a global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. URL: http://sweetgum.nybg.org/science/ih/ (Accessed 23 April 2022).
Цвелев Н. Н. Злаки CCCР. Л.: Наука, 1976. 788 с.
Цвелев Н. Н. Заметки о трибе Stipeae Dumort. (Poaceae) // Новости сист. высш. раст., 2012. Т. 43. С. 20–29.
Wickham H. 2009. Ggplot2 – elegant graphics for data analysis. In: Proceedings of the Use R. Houston, Texas, USA: Springer. 212 pp.
Allendorf F. W., Leary R. F., Spruell P., Wenburg J. K. 2001. The problems with hybrids: setting conservation guidelines. Trends Ecol. Evol. 16: 613–622. DOI: 10.1016/S0169-5347(01)02290-X
Anderson E., Thompson E. 2002. A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217–1229. DOI: 10.1093/genetics/160.3.1217
Baiakhmetov E., Nowak A., Gudkova P., Nobis M. 2020. Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae). Sci. Rep. 10: 1–14. DOI: 10.1038/s41598-020-70582-1
Baiakhmetov E., Ryzhakova D., Gudkova P., Nobis M. 2021. Evidence for extensive hybridisation and past introgression events in feather grasses using genome-wide SNP genotyping. BMC Plant Biology 21. DOI: 10.1186/s12870-021-03287-w
Bor N. L. 1970. Gramineae. In: Flora Iranica. Vol. 70. Graz, Austria: Academisch Druck-u. Verlagsanstalt. 573 pp. + 72 tabl.
Cattell R. B. 1966. The scree test for the number of factors. Multivariate Behav. Res. 1: 245–276, DOI: 10.1207/s15327906mbr0102_10
Chen J., Luo M., Li S., Tao, M., Ye X., Duan W., Zhang C., Qin Q., Xiao J., Liu S. 2017. A comparative study of distant hybridization in plants and animals. Sci. China Life Sci. 61(3): 285–309. DOI: 10.1007/s11427-017-9094-2
Chhatre V., Emerson K. 2017. StrAuto: Automation and parallelization of STRUCTURE analysis. BMC Bioinformatics 18. DOI: 10.1186/s12859-017-1593-0
Earl D. A., Vonholdt B. 2012. Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4.
Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611–2620. DOI: 10.1111/j.1365-294X.2005.02553.x
Francis R. M. 2017. Pophelper: An R Package and Web App to analyse and visualize population structure. Mol. Ecol. Resour. 17: 27–32. DOI: 10.1111/1755-0998.12509
Freitag H. 1985. The genius Stipa (Gramineae) in Southwest and South Asia. Notes R. Bot. Gard. Edinb. 42(3): 355–489.
Голоскоков В. П. Особенности видового эндемизма во флоре Казахстана (материалы к анализу «Флоры Казахстана», 1) // Ботанические материалы Гербария Института Ботаники АН КазССР, 1969. T. 6. C. 3–12.
Grant P. R., Grant B. R., Petren K. 2005. Hybridization in the recent past. Am. Nat. 166: 56–67. DOI: 10.1086/430331
Gruber B., Georges A., Berry O., Unmack P. 2021. DartR: importing and analysing SNP and Silicodart data generated by genome-wide restriction fragment analysis. URL: https://rdrr.io/cran/dartR/ (Accessed 23 April 2022).
Gruber B., Unmack P. J., Berry O. F., Georges A. 2018. Dartr: an r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol. Ecol. Resour. 18: 691–699. DOI: 10.1111/1755-0998.12745
Husson F., Josse J., Lê S., Mazet J. 2014. FactoMineR: multivariate exploratory data analysis and data mining with R. FactoMineR: multivariate exploratory data analysis and data mining with R.R package version 1: 102–123.
Kassambara A., Mundt F. 2021. Factoextra: extract and visualize the results of multivariate data analyses. URL: https://rdrr.io/cran/factoextra (Accessed 23 April 2022).
Kilian A., Wenzl P., Huttner E., Carling J., Xia L., Blois H., Caig V., Heller-Uszynska K., Jaccoud D., Hopper C., et al. 2012. Diversity Arrays Technology: a generic genome profiling technology on open platforms. In: F. Pompanon, A. Bonin (eds.). Data production and analysis in population genomics: methods and protocols. Methods in Molecular Biology. Totowa, NJ: Humana Press. Pp. 67–89.
Kupriyanov A.N., Gudkova P.D., Kriuchkova E.A. 2018. Endemism of the Kazakhstan flora: Poaceae Barnhart. Ukr. J. Ecol. 8(4): 393–405.
Letunic I., Bork P. 2021. Interactive Tree Of Life (ITOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49. DOI: 10.1093/nar/gkab301
Mallet J. A. 1995. Species definition for the modern synthesis. Trends Ecol. Evol. 10: 294–299. DOI: 10.1016/0169-5347(95)90031-4
Mallet J. 2005. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20: 229–237. DOI: 10.1016/j.tree.2005.02.010
Mallet J. 2007. Hybrid Speciation. Nature 446: 279–283. DOI: 10.1038/nature05706
Mayr E. 1942. Systematics and the origin of species: From the Viewpoint of a Zoologist. New York: Columbia University Press. 207 pp.
Mayr E. 1963. Animal species and evolution. Cambridge: Belknap Press of Harvard University Press. 797 pp.
Nobis M. 2014. Taxonomic revision of the Central Asian Stipa tianschanica complex (Poaceae) with particular reference to the epidermal micromorphology of the lemma. Folia Geobot. 49: 283–308. DOI: 10.1007/s12224-013-9164-2
Nobis M., Erst A., Nowak A., Shaulo D., Olonova M., Kotukhov Y., Doğru-Koca A., Dönmez A., Király G., Ebel A., et al. 2017. Contribution to the Flora of Asian and European countries: new national and regional vascular plant records, 6. Bot. Lett. 164: 23–45. DOI: 10.1080/23818107.2016.1273134
Nobis M., Gudkova P., Baiakhmetov E., Żabicka J., Krawczyk K., Sawicki J. 2019. Hybridisation introgression events and cryptic speciation in Stipa (Poaceae): a case study of the Stipa heptapotamica hybrid-complex. Perspect. Plant Ecol. Evol. Syst. DOI: 10.1016/j.ppees.2019.05.001
Nobis M., Gudkova, P., Nowak A., Sawicki J., Nobis A. 2020. A synopsis of the genus Stipa (Poaceae) in Middle Asia, including a key to species identification, an annotated checklist, and phytogeographic analyses. Ann. Missouri Bot. Gard. 105: 1–63. DOI: 10.3417/2019378
O’Brien S. J., Mayr E. 1991. Bureaucratic Mischief: recognizing endangered species and subspecies. Science 251: 1187–1188. DOI: 10.1126/science.251.4998.1187
Pagès J. 2021. Analyse factorielle de données mixtes. In: analyse factorielle multiple avec R. EDP Sciences. Pp. 65–76.
Peterson P., Romaschenko K., Soreng R., Valdés J. 2019. A key to the North American genera of Stipeae (Poaceae, Pooideae) with descriptions and taxonomic names for species of Eriocoma, Neotrinia, Oloptum, and Five New Genera: Barkworthia, × Eriosella, Pseudoeriocoma, Ptilagrostiella, and Thorneochloa launched to accelerate biodiversity research. PhytoKeys 126: 89–125. DOI: 10.3897/phytokeys.126.34096
Pritchard J., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
Romaschenko K., Peterson P., Soreng R., Garcia-Jacas N., Futorna O., Susanna A. 2012. Systematics and evolution of the needle grasses (Poaceae: Pooideae: Stipeae) based on analysis of multiple chloroplast loci, ITS, and lemma micromorphology. Taxon 61: 18–44. DOI: 10.1002/tax.611002
Рожевиц Р. Ю. Stipa L. // Флора СССР. Т. 2. Л.: АН СССР, 1934. С. 79–112, 740–741.
Sievert C., Parmer C., Hocking T., Chamberlain S., Ram K., Corvellec M. et al. 2020. Plotly: create interactive web graphics via 'plotly.js'. URL: https://rdrr.io/cran/plotly/ (Accessed 23 April 2022).
Thiers B. 2021. Index herbariorum: a global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. URL: http://sweetgum.nybg.org/science/ih/ (Accessed 23 April 2022).
Цвелев Н. Н. Злаки CCCР. Л.: Наука, 1976. 788 с.
Цвелев Н. Н. Заметки о трибе Stipeae Dumort. (Poaceae) // Новости сист. высш. раст., 2012. Т. 43. С. 20–29.
Wickham H. 2009. Ggplot2 – elegant graphics for data analysis. In: Proceedings of the Use R. Houston, Texas, USA: Springer. 212 pp.
Published
2022-06-30
How to Cite
Gudkova P. D., Baiakhmetov E. Z., Nobis M. Evidence of distant hybridization within Central Asian feather grasses (Poaceae: Stipa) // Turczaninowia, 2022. Vol. 25, № 2. P. 75-85 DOI: 10.14258/turczaninowia.25.2.7. URL: https://turczaninowia.asu.ru/article/view/11711.
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