植物生命之树重建的现状、问题和对策建议

doi:10.17520/biods.2019373

摘要/Abstract

摘要：

生命之树的概念源自1859年达尔文的《物种起源》, 但利用分子数据重建植物生命之树的研究则在20世纪90年代才开始兴起。近年来, 随着测序技术、分析方法和计算能力的快速发展, 植物生命之树重建研究取得了显著成果。本文首先概述了当前以及未来很长一段时间内植物生命之树重建工作的重点, 包括植物属级和种级水平的系统发育研究、植物系统发育基因组学研究、分子和形态数据联合分析、包括灭绝与现存植物类群的生命之树重建, 以及超大植物生命之树重建等5个方面; 然后简要概括国内植物生命之树重建研究的现状, 指出了我国在植物生命之树重建领域发展中所存在的问题, 并从“类群研究体系、学科评价体系、国家顶层设计, 以及拓展国际合作”等方面对学科未来的发展提出了一些对策建议。

关键词: 分子系统学, 系统发育基因组学, 形态学, 超大树, 生命之树

Abstract

In 1859, Charles Darwin put forward the concept of the tree of life (TOL), a metaphor for charting relationships between organisms in space and time in his The Origin of Species. The TOL is a cornerstone in evolutionary theory and makes sense of all biology. Decades of research in plant molecular systematics has led to substantial progress in understanding many aspects of the plant TOL. Here, we summarized five major aspects of reconstructing the plant TOL, which are being studied at the present day and will continue to be goals moving forward. These include: (1) constructing genus- and species-level phylogenies for plant groups; (2) resolving deep-time and/or rapidly divergent phylogenetic relationships using genomic approaches; (3) updating classification systems by combining morphological and molecular data; (4) integrating fossil taxa into phylogenies derived from extant taxa; and (5) building big trees using supermatrix methods. We then outlined the current state of plant molecular systematics and highlight existing problems in the field, specifically in regard to China. Finally, we propose the corresponding guidelines and policy suggestions for the continued study of China’s reconstruction of the plant TOL.

Key words: molecular systematics, phylogenomics, morphology, big tree, tree of life

王伟, 刘阳 (2020) 植物生命之树重建的现状、问题和对策建议. 生物多样性, 28, 176-188. DOI: 10.17520/biods.2019373.

Wei Wang, Yang Liu (2020) The current status, problems, and policy suggestions for reconstructing the plant tree of life. Biodiversity Science, 28, 176-188. DOI: 10.17520/biods.2019373.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019373

https://www.biodiversity-science.net/CN/Y2020/V28/I2/176

参考文献 92

[1]	APG (1998) An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden, 85, 531-553.
[2]	Atkinson BA (2018) The critical role of fossils in inferring deep-node phylogenetic relationships and macroevolutionnary patterns in Cornales. American Journal of Botany, 105, 1401-1411. DOI URL PMID
[3]	Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Duruflé L, Gaasterland T, Lopez P, Müller M, Philippe H (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proceedings of the National Academy of Sciences, USA, 99, 1414-1419.
[4]	Benton MJ, Ayala FJ (2003) Dating the tree of life. Science, 300, 1698-1700. DOI URL PMID
[5]	Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price R, Hills HG, Qiu YL, Kron KA, Retting JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH, Graham S, Barrett SCH, Dayanandan S, Albert VA (1993) Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden, 80, 528-580. DOI URL PMID
[6]	Chen ZD, Wang XQ, Sun HY, Han Y, Zhang ZX, Zou YP, Lu AM (1998) Systematic position of the Rhoipteleaceae: Evidence from nucleotide sequences of the rbcL gene. Acta Phytotaxonomica Sinica, 36, 1-7.
[7]	Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM, Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham SW, Soltis PS, Liu X, Xu X, Wong GK (2018) 10KP: A phylodiverse genome sequencing plan. GigaScience, 7, giy013. DOI URL PMID
[8]	Cox CJ, Li B, Foster PG, Embley TM, Civán P (2014) Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Systematic Biology, 63, 272-279. DOI URL PMID
[9]	Cronquist A (1981) An Integrated System of Classification of Flowering Plants. Columbia University Press, New York.
[10]	Darwin C (1859) The Origin of Species by Means of Natural Selection. Murray, London.
[11]	Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics, 6, 362-375.
[12]	Doyle JA, Endress PK (2000) Morphological phylogenetic analysis of basal angiosperms: Comparison and combination with molecular data. International Journal of Plant Sciences, 161(Suppl.), 121-153.
[13]	Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE (2014) Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology, 63, 368-382. DOI URL PMID
[14]	Eisen JA, Fraser CM (2003) Phylogenomics: Intersection of evolution and genomics. Science, 300, 1706-1707. DOI URL PMID
[15]	Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, Pokorny L, Rahbek C, Sandel B, Smith SA, Stamatakis A, Vos RA, Warnow T, Baker WJ (2018) A roadmap for global synthesis of the plant tree of life. American Journal of Botany, 105, 614-622. DOI URL PMID
[16]	Folk RA, Sun M, Soltis PS, Smith SA, Soltis DE, Guralnick RP (2018) Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids. American Journal of Botany, 105, 433-445. DOI URL PMID
[17]	Friis EM, Pedersen KR, Crane PR (2016) The emergence of core eudicots: New floral evidence from the earliest Late Cretaceous. Proceedings of the Royal Society B: Biological Sciences, 283, 20161325.
[18]	Gitzendanner MA, Yang Y, Wickett NJ, McKain M, Beaulieu JM (2018) Methods for exploring the plant tree of life. Applications in Plant Sciences, 6, e1039.
[19]	Glenner H, Hansen AJ, Sørensen MV, Ronquist F, Huelsenbeck JP, Willerslev E (2004) Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach. Current Biology, 14, 1644-1649. DOI URL PMID
[20]	Goremykin VV, Nikiforova SV, Biggs PJ, Zhong B, Delange P, Martin W, Woetzel S, Atherton RA, McLenachan PA, Lockhart PJ (2013) The evolutionary root of flowering plants. Systematic Biology, 62, 50-61. DOI URL PMID
[21]	Haeckel E (1866) Generelle Morphologie der Organismen: Allgemeine Grundzüge der Organischen Formen-Wissenschaft, Mechanisch Begründet durch die von Charles Darwin Reformirte Descendenz-Theorie. Georg Reimer, Berlin. (in German)
[22]	Hamilton JP, Buell CR (2012) Advances in plant genome sequencing. The Plant Journal, 70, 177-190. DOI URL PMID
[23]	Hennnig W (1950) Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin. (in German)
[24]	Hennnig W (1966) Phylogenetic Systematics. University of Illinois Press, Urbana, IL.
[25]	Hinchliff CE, Smith AS, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD 4th, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, USA, 112, 12764-12769.
[26]	Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences, USA, 104, 19369-19374.
[27]	Kadereit JW, Albach DC, Ehrendorfer F, Galbany-Casals M, Garcia-Jacas N, Gehrke B, Kadereit G, Kilian N, Klein JT, Koch MA, Kropf M, Oberprieler C, Pirie MD, Ritz CM, Roser M, Spalik K, Susanna A, Weigend M, Welk E, Wesche K, Zhang LB, Dillenberger MS (2016) Which changes are needed to render all genera of the German flora monophyletic? Willdenowia, 46, 39-91.
[28]	Kerkhoff AJ, Moriarty PE, Weiser MD (2014) The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis. Proceedings of the National Academy of Sciences, USA, 111, 8125-8130.
[29]	Lavoué S (2016) Was Gondwanan breakup the cause of the intercontinental distribution of Osteoglossiformes? A time-calibrated phylogenetic test combining molecular, morphological, and paleontological evidence. Molecular Phylogenetetics and Evolution, 99, 34-43. DOI URL PMID
[30]	Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R (2011) A functional phylogenomic view of the seed plants. PLoS Genetics, 7, e1002411. DOI URL PMID
[31]	Lehtonen S (2011) Towards resolving the complete fern tree of life. PLoS ONE, 6, e24851. DOI URL PMID
[32]	Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G (2018) Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences, USA, 115, 4325-4333.
[33]	Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, van der Bank M, Zhang SD, Wang QF, Wang J, Zhang ZR, Fu CN, Yang J, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Li DZ (2019) Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants, 5, 461-470. DOI URL PMID
[34]	Liu L, Wu S, Yu L (2015) Coalescent methods for estimating species trees from phylogenomic data. Journal of Systematics and Evolution, 53, 380-390. DOI URL
[35]	Liu Y, Cox CJ, Wang W, Goffinet B (2014) Mitochondrial phylogenomics of early land plants: Mitigating the effects of saturation, compositional heterogeneity, and codon usage bias. Systematic Biology, 63, 862-878. DOI URL
[36]	Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenäs L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B (2019) Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications, 10, 1485. DOI URL PMID
[37]	Lu LM, Mao LF, Yang T, Ye JF, Liu B, Li HL, Sun M, Miller JT, Mathews S, Hu HH, Niu YT, Peng DX, Chen YH, Smith SA, Chen M, Xiang KL, Le CT, Dang VC, Lu AM, Soltis PS, Soltis DE, Li JH, Chen ZD (2018) Evolutionary history of the angiosperm flora of China. Nature, 554, 234-238. DOI URL PMID
[38]	Lu Y, Ran JH, Guo DM, Yang ZY, Wang XQ (2014) Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes. PLoS ONE, 9, e107679. DOI URL PMID
[39]	Maddison DR (2013) The tree of life. Systematic Biology, 62, 179. DOI URL
[40]	Maddison WP, Midford PE, Otto SP (2007) Estimating a binary character’s effect on speciation and extinction. Systematic Biology, 56, 701-710. DOI URL PMID
[41]	McKain MR, Johnson MG, Uribe-Convers S, Eaton D, Yang Y (2018) Practical considerations for plant phylogenomics. Applications in Plant Sciences, 6, e1038. DOI URL PMID
[42]	Medina R, Johnson M, Liu Y, Wilding N, Hedderson TA, Wickett N, Goffinet B (2018) Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae. Molecular Phylogenetetics and Evolution, 120, 240-247. DOI URL PMID
[43]	Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proceedings of the National Academy of Sciences, USA, 104, 19363-19368.
[44]	Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biology, 6, 17. DOI URL PMID
[45]	Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proceedings of the National Academy of Sciences, USA, 107, 4623-4628.
[46]	Morales-Briones DF, Liston A, Tank DC (2018) Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). New Phytologist, 218, 1668-1684. DOI URL PMID
[47]	Moreira D, Le Guyader H, Philippe H (2000) The origin of red algae and the evolution of chloroplasts. Nature, 405, 69-72. DOI URL PMID
[48]	Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O’Brien SJ (2001) Molecular phylogenetics and the origins of placental mammals. Nature, 409, 614-618. DOI URL PMID
[49]	Nandi O, Chase MW, Endress PK (1998) A combined cladistic analysis of angiosperms using rbcL and non-molecular data sets. Annals of the Missouri Botanical Garden, 79, 249-265.
[50]	Nixon KC (1996) Paleobotany in cladistics and cladistics in paleobotany: Enlightenment and uncertainty. Review of Palaeobotany and Palynology, 90, 361-373.
[51]	One Thousand Plant Transcriptomes Initiative (2019) One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574, 679-685. DOI URL PMID
[52]	O’Reilly JE, Puttick MN, Pisani D, Donoghue PCJ (2018) Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data. Palaeontology, 61, 105-118. DOI URL PMID
[53]	Palmer JD, Soltis DE, Chase MW (2004) The plant tree of life: An overview and some points of view. American Journal of Botany, 91, 1437-1445. DOI URL PMID
[54]	Pennisi E (2017) Sequencing all life captivates biologists. Science, 355, 894-895. DOI URL PMID
[55]	Pyron RA (2011) Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466-481. DOI URL PMID
[56]	Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Zimmer EA, Chen Z, Savolainen V, Chase MW (1999) The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes. Nature, 402, 404-407. DOI URL PMID
[57]	Rothwell GW, Escapa IH, Tomescu AMF (2018a) Tree of death: The role of fossils in resolving the overall pattern of plant phylogeny. American Journal of Botany, 105, 1239-1242. DOI URL PMID
[58]	Rothwell GW, Millay MA, Stockey RA (2018b) Resolving the overall pattern of marattialean fern phylogeny. American Journal of Botany, 105, 1304-1314. DOI URL PMID
[59]	Schneider H, Schuettpelz E (2016) Systematics and evolution of lycophytes and ferns. Journal of Systematics and Evolution, 54, 561-562. DOI URL
[60]	Schrago CG, Aguiar BO, Mello B (2018) Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data. Journal of Evolutionary Biology, 31, 1477-1484. DOI URL PMID
[61]	Smith SA, Beaulieu JM, Donoghue MJ (2009) Mega-phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches. BMC Evolutionary Biology, 9, 37. DOI URL PMID
[62]	Smith SA, Brown JW, Yang Y, Bruenn R, Drummond CP, Brockington SF, Walker JF, Last N, Douglas NA, Moore MJ (2018) Disparity, diversity, and duplications in the Caryophyllales. New Phytologist, 217, 836-854. DOI URL PMID
[63]	Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science, 322, 86-89. DOI URL PMID
[64]	Soltis DE, Moore MJ, Burleigh G, Soltis PS (2009) Molecular markers and concepts of plant evolutionary relationships: Progress, promise and future prospects. Critical Reviews in Plant Sciences, 28, 1-15. DOI URL
[65]	Soltis DE, Moore MJ, Sessa EB, Smith SA, Soltis PS (2018) Using and navigating the plant tree of life. American Journal of Botany, 105, 287-290. DOI URL PMID
[66]	Stull GW, Schori M, Soltis DE, Soltis PS (2018) Character evolution and missing (morphological) data across Asteridae. American Journal of Botany, 105, 470-479. DOI URL PMID
[67]	Su JX, Wang W, Zhang LB, Chen ZD (2012) Phylogenetic placements of two enigmatic genera, Borthwickia and Stixis, based on molecular and pollen data and description of a new family of Brassicales, Borthwickiaceae. Taxon, 61, 601-611.
[68]	Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology, 50, 525-539. URL PMID
[69]	Takhtajan AL (1969) Flowering Plants: Origin and Dispersal. Oliver and Boyd, Edinburgh.
[70]	Takhtajan AL (2009) Flowering Plants, 2nd edn. Springer, Heidelberg.
[71]	Thornhill AH, Baldwin BG, Freyman WA, Nosratinia S, Kling MM, Morueta-Holme N, Madsen TP, Ackerly DD, Mishler BD (2017) Spatial phylogenetics of the native California flora. BMC Biology, 15, 96. DOI URL PMID
[72]	Twyford AD (2018) The road to 10,000 plant genomes. Nature Plants, 4, 312-313. DOI URL PMID
[73]	Wagner WH (1952) The fern genus Diellia: Structure, affinities, and taxonomy. University of California Publications in Botany, 26, 1-212. URL PMID
[74]	Wang Q, Wu S, Su X, Zhang L, Xu X, Lyu L, Cai H, Shrestha N, Liu Y, Wang W, Wang Z (2018) Niche conservatism and elevated diversification shape species diversity in drylands: Evidence from Zygophyllaceae. Proceedings of the Royal Society B: Biological Sciences, 285, 20181742.
[75]	Wang W, Liu Y, Yu SX, Gao TG, Chen ZD (2013) Gymnaconitum, a new genus of Ranunculaceae endemic to the Qinghai-Tibetan Plateau. Taxon, 62, 713-722. DOI URL
[76]	Wang W, Lu AM, Ren Y, Endress ME, Chen ZD (2009) Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data. Perspectives in Plant Ecology, Evolution and Systematics, 11, 81-110.
[77]	Wang W, Ortiz RDC, Jacques FMB, Liu Y, Xiang XG, Yu SX, Chen ZD (2017) New insights into the phylogeny of Burasaieae (Menispermaceae) with the recognition of a new genus and emphasis on the southern Taiwanese and mainland Chinese disjunction. Molecular Phylogenetetics and Evolution, 109, 11-20. DOI URL PMID
[78]	Wang W, Zhang XX, Chen ZD, Lu AM (2017) Comments on the APG’s classification of angiosperms. Biodiversity Science, 25, 418-426. (in Chinese with English abstract) DOI URL PMID
	[ 王伟, 张晓霞, 陈之端, 路安民 (2017) 被子植物APG分类系统评论. 生物多样性, 25, 418-426.]
[79]	Warburg O, Reiche K (1895) Balsaminaceae. In: Die Natürlichen Pflanzenfamilien (eds Engler HGA, Prantl KAE), pp. 383-392. Wilhelm Engelmann, Leipzig. (in German)
[80]	Wen J, Liu J, Ge S, Xiang QY (Jenny), Zimmer EA (2015) Phylogenomic approaches to deciphering the tree of life. Journal of Systematics and Evolution, 53, 369-370.
[81]	Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA, 111, E4859-E4868.
[82]	Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, USA, 74, 5088-5090.
[83]	Wu SD, Zhang LJ, Lin L, Yu SX, Chen ZD, Wang W (2018) Insights into the historical assembly of global dryland floras: the diversification of Zygophyllaceae. BMC Evolutionary Biology, 18, 166. DOI URL PMID
[84]	Xi Z, Ruhfel BR, Schaefer H, Amorim AM, Sugumaran M, Wurdack KJ, Endress PK, Matthews ML, Stevens PF, Mathews S, Davis CC (2012) Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences, USA, 109, 17309-17310.
[85]	Xiang XG, Xiang KL, Ortiz RDC, Jabbour F, Wang W (2019) Integrating palaeontological and molecular data reveals ancient and recent dispersal patterns in the pantropical Hamamelidaceae. Journal of Biogeography, 46, 1622-1631.
[86]	Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Kohno N, Nishida S, Wu J, Jin H, Adachi J, Kishino H, Kurokawa K, Nogi Y, Tanabe H, Mukoyama H, Yoshida K, Rasoamiaramanana A, Yamagishi S, Hayashi Y, Yoshida A, Koike H, Akishinonomiya F, Willerslev E, Hasegawa M (2017) Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the Ratites. Current Biology, 27, 68-77. DOI URL PMID
[87]	Yu SX, Janssens SB, Zhu XY, Lidén M, Gao TG, Wang W (2016) Phylogeny of Impatiens (Balsaminaceae): Integrating molecular and morphological evidence into a new classification. Cladistics, 32, 179-197.
[88]	Yu XQ, Gao LM, Soltis DE, Soltis PS, Yang JB, Fang L, Yang SX, Li DZ (2017) Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. New Phytologist, 215, 1235-1248. DOI URL PMID
[89]	Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O’Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM (2014) Three keys to the radiation of angiosperms into freezing environments. Nature, 506, 89-92. DOI URL PMID
[90]	Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB (2018) Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods, 14, 43. DOI URL PMID
[91]	Zhang YJ, Li DZ (2011) Advances in phylogenomics based on complete chloroplast genomes. Plant Diversity and Resources, 33, 365-375. (in Chinese with English abstract)
	[ 张韵洁, 李德铢 (2011) 叶绿体系统发育基因组学的研究进展. 植物分类与资源学报, 33, 365-375.]
[92]	Zhong B, Liu L, Yan Z, Penny D (2013) Origin of land plants using the multispecies coalescent model. Trends in Plant Science, 18, 492-495. DOI URL PMID