Plant Diversity ›› 2022, Vol. 44 ›› Issue (05): 455-467.DOI: 10.1016/j.pld.2022.02.002
• Research paper • Previous Articles Next Articles
Ting-Shen Hana,b,c, Zheng-Yan Hua,d, Zhi-Qiang Dua,d, Quan-Jing Zhenga,d, Jia Liua,b, Thomas Mitchell-Oldsc, Yao-Wu Xinga,b
Received:
2022-01-18
Revised:
2022-02-22
Online:
2022-09-25
Published:
2022-10-14
Supported by:
Ting-Shen Han, Zheng-Yan Hu, Zhi-Qiang Du, Quan-Jing Zheng, Jia Liu, Thomas Mitchell-Olds, Yao-Wu Xing. Adaptive responses drive the success of polyploid yellowcresses (Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot[J]. Plant Diversity, 2022, 44(05): 455-467.
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[1] Al-Shehbaz, I.A. 2016. Brassicaceae. In:Hong D-Y ed. Flora of the Pan-Himalaya. Cambridge University Press, Cambridge, UK. pp. 275-288 [2] Alonso-Blanco, C., Andrade, J., Becker, C., et al., 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481-491 [3] An, Z., Clemens, S.C., Shen, J., et al., 2011. Glacial-interglacial Indian summer monsoon dynamics. Science 333, 719-723 [4] Arnold, B.J., Lahner, B., DaCosta, J.M., et al., 2016. Borrowed alleles and convergence in serpentine adaptation. Proc. Natl. Acad. Sci. U.S.A. 113, 8320-8325 [5] Arrigo, N., Barker, M.S. 2012. Rarely successful polyploids and their legacy in plant genomes. Curr. Opin. Plant Biol. 15, 140-146 [6] Baniaga, A.E., Marx, H.E., Arrigo, N., et al., 2020. Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives. Ecol. Lett. 23, 68-78 [7] Barker, M.S., Arrigo, N., Baniaga, A.E., et al., 2016. On the relative abundance of autopolyploids and allopolyploids. New Phytol. 210, 391-398 [8] Bleeker, W., Weber-Sparenberg, C., Hurka, H. 2002. Chloroplast DNA variation and biogeography in the genus Rorippa scop.(Brassicaceae). Plant Biol. 4, 104-111 [9] Blischak, P.D., Latvis, M., Morales-Briones, D.F., et al., 2018. Fluidigm2PURC:automated processing and haplotype inference for double-barcoded PCR amplicons. Appl. Plant Sci. 6, 1-6 [10] Bomblies, K. 2020. When everything changes at once:finding a new normal after genome duplication. Proc. Royal Soc. B. 287, 1-14 [11] Brochmann, C., Brysting, A.K., Alsos, I.G., et al., 2004. Polyploidy in arctic plants. Biol. J. Linn. Soc. Lond. 82, 521-536 [12] Cai, L., Ma, H. 2016. Using nuclear genes to reconstruct angiosperm phylogeny at the species level:a case study with Brassicaceae species. J. Systemat. Evol. 54, 438-452 [13] Cauvy-Fraunie, S., Dangles, O. 2019. A global synthesis of biodiversity responses to glacier retreat. Nat. Ecol. Evol. 3, 1675-1685 [14] Certner, M., Sudova, R., Weiser, M., et al., 2019. Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae). New Phytol. 221, 1117-1127 [15] Chalk, T.B., Hain, M.P., Foster, G.L., et al., 2017. Causes of ice age intensification across the Mid-Pleistocene Transition. Proc. Natl. Acad. Sci. U.S.A. 114, 13114-13119 [16] Chao, D.-Y., Dilkes, B., Luo, H., et al., 2013. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 341, 658-659 [17] Clement, M., Posada, D., Crandall, K.A. 2000. TCS:a computer program to estimate gene genealogies. Mol. Ecol. 9, 1657-1659 [18] Comai, L. 2005. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6, 836-846 [19] Crawley, M.J. 2013. The R Book (2nd). John Wiley&Sons, [20] Dolezel, J., Greilhuber, J., Suda, J. 2007. Estimation of nuclear DNA content in plants using flow cytometry. Nat. Protoc. 2, 2233-2244 [21] Doyle, J.J., Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15 [22] Drummond, A.J., Suchard, M.A., Xie, D., et al., 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973 [23] Fawcett, J.A., Van de Peer, Y. 2010. Angiosperm polyploids and their road to evolutionary success. Trends Ecol. Evol. 2, 13-21 [24] Fick, S.E., Hijmans, R.J. 2017. WorldClim 2:new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302-4315 [25] Folk, R.A., Siniscalchi, C.M., Soltis, D.E. 2020. Angiosperms at the edge:extremity, diversity, and phylogeny. Plant Cell Environ. 43, 2871-2893 [26] Gadgil, M., Solbrig, O.T. 1972. The concept of r-and K-selection:evidence from wild flowers and some theoretical considerations. Am. Nat. 106, 14-31 [27] Gamisch, A. 2019. Oscillayers:a dataset for the study of climatic oscillations over Plio-Pleistocene time-scales at high spatial-temporal resolution. Global Ecol. Biogeogr. 28, 1552-1560 [28] Guo, X., Liu, J., Hao, G., et al., 2017. Plastome phylogeny and early diversification of Brassicaceae. BMC Genom. 18, 1-9 [29] Han, T.-S., Wu, Q., Hou, X.-H., et al., 2015. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd's purse (Capsella bursa-pastoris). Mol. Plant 8, 427-438 [30] Han, T.-S., Zheng, Q.-J., Onstein, R.E., et al., 2020. Polyploidy promotes species diversification of Allium through ecological shifts. New Phytol. 225, 571-583 [31] Hegarty, M.J., Hiscock, S.J. 2008. Genomic clues to the evolutionary success of polyploid plants. Curr. Biol. 18, R435-R444 [32] Hijmans, R.J., Guarino, L., Mathur, P. 2012. DIVA-GIS Version 7.5 [33] Hu, Z., Zheng, Q., Mu, Q., et al., 2021. The mating system and reproductive assurance of Rorippa elata (Brassicaceae) across latitude. Biodivers. Sci. 29, 712-721 [34] Huynh, S., Broennimann, O., Guisan, A., et al., 2020. Eco-genetic additivity of diploids in allopolyploid wild wheats. Ecol. Lett. 23, 663-673 [35] Jonsell, B. 1968. Studies in the North-West European Species of Rorippa S. Str. Uppsala, Sweden:Acta Universitatis Upsaliensis. 1-221 [36] Kearse, M., Moir, R., Wilson, A., et al., 2012. Geneious Basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649 [37] Kellogg, E.A. 2016. Has the connection between polyploidy and diversification actually been tested? Curr. Opin. Plant Biol. 30, 25-32 [38] Koch, M.A., Haubold, B., Mitchell-Olds, T. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17, 1483-1498 [39] Koenig, D., Weigel, D. 2015. Beyond the thale:comparative genomics and genetics of Arabidopsis relatives. Nat. Rev. Genet. 16, 285-298 [40] Korner, C. 2020. Plant adaptations to alpine environments. In:Goldstein MI, DellaSala DA eds. Encyclopedia of the World's Biomes. Elsevier, Oxford. pp. 355-361 [41] Leitch, A., Leitch, I. 2008. Genomic plasticity and the diversity of polyploid plants. Science 320, 481-483 [42] Les, D.H. 2018. Core Eudicots:Dicotyledons IV:"Rosid" Tricolpates:Malvid Rosids (Eurosids II):Order 9:Brassicales:Family 2:Brassicaceae:7. Rorippa. Aquatic Dicotyledons of North America:Ecology, Life History, and Systematics. CRC Press. pp. 398-406 [43] Levin, D.A. 2019. Why polyploid exceptionalism is not accompanied by reduced extinction rates. Plant Systemat. Evol. 305, 1-11 [44] Li, J., Feng, Z., Zhou, S. 1996. The vestiges of Quaternary glaciation in the Hengduan Mountains region. In:Li J, Su Z eds. Glacier in the Hengduan Mountains. Science Press, Beijing, China. pp. 157-173 [45] Li, Z., McKibben, M.T.W., Finch, G.S., et al., 2021. Patterns and processes of diploidization in land plants. Annu. Rev. Plant Biol. 72, 387-410 [46] Liu, S., Kruse, S., Scherler, D., et al., 2021. Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity. Nat. Commun. 12, 1-9 [47] Madlung, A. 2013. Polyploidy and its effect on evolutionary success:old questions revisited with new tools. Heredity 110, 99-104 [48] Mandakova, T., Marhold, K., Lysak, M.A. 2014. The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. New Phytol. 201, 982-992 [49] Mao, K.-S., Wang, Y., Liu, J.-Q. 2021. Evolutionary origin of species diversity on the Qinghai-Tibet plateau. J. Systemat. Evol. 42, 1142-1158 [50] Matzke, N.J. 2018. BioGeoBEARS:BioGeography with Bayesian (And Likelihood) Evolutionary Analysis with R Scripts. Version 1.1.1 [51] Mayrose, I., Zhan, S.H., Rothfels, C.J., et al., 2011. Recently formed polyploid plants diversify at lower rates. Science 333, 1257-1257 [52] Molau, U. 1993. Relationships between flowering phenology and life history strategies in tundra plants. Arctic Antarct. Alpine Res. 25, 391-402 [53] Muellner-Riehl, A.N. 2019. Mountains as evolutionary arenas:patterns, emerging approaches, paradigm shifts, and their implications for plant phylogeographic research in the Tibeto-Himalayan region. Front. Plant Sci. 10, 1-18 [54] Nakayama, H., Fukushima, K., Fukuda, T., et al., 2014. Molecular phylogeny determined using chloroplast DNA inferred a new phylogenetic relationship of Rorippa aquatica (Eaton) EJ Palmer&Steyermark (Brassicaceae)-lake cress. Am. J. Plant Sci. 5, 48-54 [55] Nie, Z.-L., Wen, J., Gu, Z.-J., et al., 2005. Polyploidy in the flora of the Hengduan Mountains hotspot, southwestern China. Ann. Mo. Bot. Gard. 92, 275-306 [56] Novikova, P.Y., Hohmann, N., Van de Peer, Y. 2018. Polyploid Arabidopsis species originated around recent glaciation maxima. Curr. Opin. Plant Biol. 42, 8-15 [57] Otto, S.P. 2007. The evolutionary consequences of polyploidy. Cell 131, 452-462 [58] Phillips, S.J., Anderson, R.P., Schapire, R.E. 2006. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231-259 [59] R Core Team. 2018. R:A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria [60] Rahbek, C., Borregaard, M.K., Antonelli, A., et al., 2019. Building mountain biodiversity:geological and evolutionary processes. Science 365, 1114-1119 [61] Ramsey, J. 2011. Polyploidy and ecological adaptation in wild yarrow. Proc. Natl. Acad. Sci. U.S.A. 108, 7096-7101 [62] Rice, A., Smarda, P., Novosolov, M., et al., 2019. The global biogeography of polyploid plants. Nat. Ecol. Evol. 3, 265-273 [63] Roman-Palacios, C., Molina-Henao, Y.F., Barker, M.S. 2020. Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae. Proc. Royal Soc. B. 287, 1-9 [64] Rothfels, C.J. 2021. Polyploid phylogenetics. New Phytol. 230, 66-72 [65] Rothfels, C.J., Pryer, K.M., Li, F.W. 2017. Next-generation polyploid phylogenetics:rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytol. 213, 413-429 [66] Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J.C., et al., 2017. DnaSP 6:DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299-3302 [67] Santos, A.M., Cabezas, M.P., Tavares, A.I., et al., 2015. tcsBU:a tool to extend TCS network layout and visualization. Bioinformatics 32, 627-628 [68] Schmickl, R., Yant, L. 2021. Adaptive introgression:how polyploidy reshapes gene flow landscapes. New Phytol. 230, 457-461 [69] Selmecki, A.M., Maruvka, Y.E., Richmond, P.A., et al., 2015. Polyploidy can drive rapid adaptation in yeast. Nature 519, 349-352 [70] Slotte, T., Hazzouri, K.M., Agren, J.A., et al., 2013. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat. Genet. 45, 831-835 [71] Soltis, D.E., Segovia-Salcedo, M.C., Jordon-Thaden, I., et al., 2014. Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al.(2011). New Phytol. 202, 1105-1117 [72] Soltis, P.S., Soltis, D.E. 2000. The role of genetic and genomic attributes in the success of polyploids. Proc. Natl. Acad. Sci. U.S.A. 97, 7051-7057 [73] Spoelhof, J.P., Keeffe, R., McDaniel, S.F. 2020. Does reproductive assurance explain the incidence of polyploidy in plants and animals? New Phytol. 227, 14-21 [74] Stanford, A.M., Harden, R., Parks, C.R. 2000. Phylogeny and biogeography of Juglans (Juglandaceae) based on matK and ITS sequence data. Am. J. Bot. 87, 872-882 [75] Stebbins, G.L. 1971. Chromosomal Evolution in Higher Plants. Edward Arnold, London, UK [76] Stebbins, G.L. 1985. Polyploidy, hybridization, and the invasion of new habitats. Ann. Mo. Bot. Gard. 72, 824-832 [77] Stinchcombe, J.R., Caicedo, A.L., Hopkins, R., et al., 2005. Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae):the effects of latitude and FLC variation. Am. J. Bot. 92, 1701-1707 [78] Stockenhuber, R., Zoller, S., Shimizu-Inatsugi, R., et al., 2015. Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing. PLoS One 10, 1-19 [79] Sun, H., Zhang, J., Deng, T., et al., 2017. Origins and evolution of plant diversity in the Hengduan Mountains, China. Plant Divers. 39, 161-166 [80] Sun, Y., Abbott, R.J., Li, L., et al., 2014. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau:homoploid hybrid origin and Pleistocene expansion. Mol. Ecol. 23, 343-359 [81] Sun, Y., McManus, J.F., Clemens, S.C., et al., 2021. Persistent orbital influence on millennial climate variability through the Pleistocene. Nat. Geosci. 14, 812-818 [82] Taberlet, P., Gielly, L., Pautou, G., et al., 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17, 1105-1109 [83] te Beest, M., Le Roux, J.J., Richardson, D.M., et al., 2012. The more the better? The role of polyploidy in facilitating plant invasions. Ann. Bot. 109, 19-45 [84] Thomas, G.W.C., Ather, S.H., Hahn, M.W. 2017. Gene-tree reconciliation with MUL-trees to resolve polyploidy events. Syst. Biol. 66, 1007-1018 [85] Van de Peer, Y., Ashman, T.-L., Soltis, P.S., et al., 2021. Polyploidy:an evolutionary and ecological force in stressful times. Plant Cell 33, 11-26 [86] Van de Peer, Y., Mizrachi, E., Marchal, K. 2017. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411-424 [87] Van Drunen, W.E., Husband, B.C. 2019. Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms. New Phytol. 224, 1266-1277 [88] Wallis, G.P., Waters, J.M., Upton, P., et al., 2016. Transverse alpine speciation driven by glaciation. Trends Ecol. Evol. 31, 916-926 [89] Wang, J.-J., Peng, Z.-B., Sun, H., et al., 2017. Cytogeographic patterns of angiosperms flora of the Qinghai-Tibet plateau and hengduan mountains. Biodivers. Sci. 25, 218-225 [90] Wang, Z., Jiang, Y., Bi, H., et al., 2021. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. Mol. Plant 14, 208-222 [91] Wen, J., Zhang, J., Nie, Z.-L., et al., 2014. Evolutionary diversifications of plants on the Qinghai-Tibetan plateau. Front. Genet. 5, 1-16 [92] White, T.J., Bruns, T., Lee, S., et al.,. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In:Sninsky JJ, Gelfand DH, White TJ, Innis MA eds. PCR Protocols:a Guide to Methods and Applications. Academic Press, San Diego, California, USA. pp. 315-322 [93] Wu, S., Han, B., Jiao, Y. 2020. Genetic contribution of paleopolyploidy to adaptive evolution in angiosperms. Mol. Plant 13, 59-71 [94] Wu, S., Wang, Y., Wang, Z., et al., 2022. Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau. New Phytol., 10.1111/nph.17956 [95] Yang, R., Folk, R., Zhang, N., et al., 2019. Homoploid hybridization of plants in the Hengduan mountains region. Ecol. Evol. 9, 8399-8410 [96] Ye, C.-Y., Wu, D., Mao, L., et al., 2020. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298-1310 [97] Yu, H., Favre, A., Sui, X., et al., 2019. Mapping the genetic patterns of plants in the region of the Qinghai-Tibet Plateau:implications for conservation strategies. Divers. Distrib. 25, 310-324 [98] Zhang, D.C., Boufford, D.E., Ree, R.H., et al., 2009. The 29°N latitudinal line:an important division in the Hengduan Mountains, a biodiversity hotspot in southwest China. Nord. J. Bot. 27, 405-412 [99] Zhang, L., Wu, S., Chang, X., et al., 2020. The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. Plant Cell Environ. 43, 2847-2856 [100] Zhang, Y., Qian, L., Spalink, D., et al., 2021. Spatial phylogenetics of two topographic extremes of the Hengduan Mountains in southwestern China and its implications for biodiversity conservation. Plant Divers. 43, 181-191 [101] Zhao, Y., Tzedakis, P.C., Li, Q., et al., 2020. Evolution of vegetation and climate variability on the Tibetan Plateau over the past 1.74 million years. Sci. Adv. 6, 1-12 [102] Zheng, Q.-J., Yu, C.-C., Xing, Y.-W., et al., 2021. A new Rorippa species (Brassicaceae), R. hengduanshanensis, from the hengduan mountains in China. Phytotaxa 480, 210-222 |
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