Evolutionary relationships in the medicinally important genus Fritillaria L. (Liliaceae)

Molecular Phylogenetics and Evolution

Volumn 80, Issue 1, 2014, Pages 11-19

  Day, Peter D ^a,b   Berger, Madeleine ^a,c,e   Hill, Laurence ^d   Fay, Michael F ^a   Leitch, Andrew R ^b   Leitch, Ilia J ^a   Kelly, Laura J ^a,b  

^a JODRELL LABORATORY   (United Kingdom)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c DURHAM UNIVERSITY   (United Kingdom)

^d Petersham Lodge River Lane Richmond   (United Kingdom)

^e ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

Genome size; Incomplete concerted evolution; Low copy nuclear gene; Medicinal species; Species non monophyly; Traditional Chinese medicine (TCM)

Indexed keywords

PLANT DNA;

BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; FRITILLARIA; GENETICS; LILIACEAE; PHYLOGENY; PLASTID;

BAYES THEOREM; BIOLOGICAL EVOLUTION; DNA, PLANT; FRITILLARIA; LILIACEAE; MODELS, GENETIC; PHYLOGENY; PLASTIDS; SEQUENCE ANALYSIS, DNA;

EID: 84906706978     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.07.024     Document Type: Article

References (62)

1. Altekar G., Dwarkadas S., Huelsenbeck J.P., Ronquist F. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 2004, 20:407-415.
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Álvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 2003, 29:417-434.
4. Ambrožová K., Mandáková T., Bureš P., Neumann P., Leitch I.J., Koblížková A., Macas J., Lysak M.A. Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies. Ann. Bot. 2011, 107:255-268.
5. Atta-ur-Rahman A.F., Choudhary M.I., Gilani A.H., Shaheen F., Ali R.A., Noor-e-ain F., Sener B. A new anticholinergic steroidal alkaloid from Fritillaria imperialis of Turkish origin. Planta Med. 1994, 60:377-379.
6. Bartolucci F., Caparelli K.F., Peruzzi L. A biometric study of Fritillaria montana Hoppe ex W.D.J. Koch s.l. (Liliaceae) shows a single polymorphic species, with no infraspecific taxa. Plant Biosyst. 2009, 143:516-527.
7. Bennett, M.D. Leitch, I.J., 2012. Plant DNA C-values database (release 6.0, December 2012) <>.http://www.kew.org/cvalues/.
8. Bennett M.D., Leitch I.J., Price H.J., Johnston J.S. Comparisons with Caenorhabditis (~100Mb) and Drosophila (~175Mb) using flow cytometry show genome size in Arabidopsis to be ~157Mb and thus ~25% larger than the Arabidopsis Genome Initiative estimate of ~125Mb. Ann. Bot. 2003, 91:547-557.
9. Chinese Herbal Medicine: Materia Medica 2004, Eastland Press, Vista, California. third ed. D. Bensky, S. Clavey, E. Stöger, A. Gamble (Eds.).
10. Buntaine M.T., Mullen R.B., Lassoie J.P. Human use and conservation planning in Alpine areas of northwest Yunnan, China. Environ. Dev. Sustain. 2007, 9:305-324.
11. Chen, S., 2005. Sustaining herbal supplies: China. In: Sharing Innovative Experience, vol. 10, Examples of the Development of Pharmaceutical Products from Medicinal Plants. United Nations Office for South-South Cooperation, pp. 157-163.
12. Chen S.-C., Hsia K.-C. A taxonomic study of the Chinese drug bei-mu (Fritillaria). Acta Phytotaxonomica Sinica 1977, 15:31-46.
13. Comber H.F. A new classification of the genus Lilium. Lily Yearbook Roy. Hort. Soc. 1949, 13:86-105.
14. DeWoody, J., Hipkins, V., 2012. Genetic differentiation among species and populations of Fritillaria in northern California: identification of a possible hybrid swarm. National Forest Genetics Laboratory Report for Project Number 251, Forest Service, United States Department of Agriculture.
15. Douglas N.A., Wall W.A., Xiang Q.-Y., Hoffmann W.A., Wentworth T.R., Gray J.B., Hohmann M.G. Recent vicariance and the origin of the rare, edaphically specialized Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from phylogenetic and coalescent analyses. Mol. Ecol. 2011, 20:2901-2915.
16. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
17. Fay M.F., Chase M.W. Modern concepts of Liliaceae, with a focus on the relationships of Fritillaria. Curtis's Bot. Mag. 2000, 17:146-149.
18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 63:783-791.
19. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes and consequences with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Evol. Syst. 2003, 34:397-423.
20. Gao Y.-D., Hohenegger M., Harris A.J., Zhou S.-D., He X.-J., Wan J. A new species in the genus Nomocharis Franchet (Liliaceae): evidence that brings the genus Nomocharis into Lilium. Plant Syst. Evol. 2012, 298:69-85.
21. Gao Y.-D., Zhou S.-D., Wan J. Chromosome diversity and evolution in tribe Lilieae (Liliaceae) with emphasis on Chinese species. J. Plant. Res. 2012, 125:55-69.
22. Gao Y.-D., Harris A.J., Zhou S.-D., He X.-J. Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q-T Plateau and the Hengduan Mountains. Mol. Phylogenet. Evol. 2013, 68:443-460.
23. Hao D.-D., Gu X.-J., Xiao P.-G., Peng Y. Phytochemical and biological research of Fritillaria medicinal resources. Chin. J. Natl. Med. 2013, 11:330-344.
24. Hill L. A taxonomic history of Japanese endemic Fritillaria (Liliaceae). Kew. Bull. 2011, 66:227-240.
25. Hill, L., 2013. Fritillaria: A List of Published Names. v4.0. <>. (last accessed 26.11.13). http://www.fritillariaicones.com/info/names/frit.names.pdf.
26. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
27. Ikinci N. Molecular phylogeny and divergence times estimates of Lilium section Liriotypus (Liliaceae) based on plastid and nuclear ribosomal ITS sequence data. Turkish J. Bot. 2011, 35:319-330.
28. Keller K., Chintauan-Marquier I.C., Veltsos P., Nichols R.A. Ribosomal DNA in the Grasshopper Podisma pedestris: escape from concerted evolution. Genetics 2006, 174:863-874.
29. Kelly L.J., Leitch I.J. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Res. 2011, 19:939-953.
30. Kelly L.J., Leitch A.R., Fay M.F., Renny-Byfield S., Pellicer J., Macas J., Leitch I.J. Why size really matters when sequencing plant genomes. Plant Ecol. Divers. 2012, 5:415-425.
31. Kelly L.J., Leitch A.R., Clarkson J.J., Knapp S., Chase M.W. Reconstructing the complex evolutionary origin of wild allopolyploid tobaccos (Nicotiana section Suaveolentes). Evolution 2013, 67:80-94.
32. Konchar K., Li X.-L., Yang Y.-P., Emshwiller E. Phytochemical variation in Fritillaria cirrhosa D. Don (Chuan Bei Mu) in relation to plant reproductive stage and timing of harvest. Econ. Bot. 2011, 65:283-294.
33. Leitch I.J., Beaulieu J.M., Cheung K., Hanson L., Lysak M.A., Fay M.F. Punctuated genome size evolution in Liliaceae. J. Evol. Biol. 2007, 20:2296-2308.
34. Li H.-J., Jiang Y., Li P., Ye W.C. Puqienine F, a novel veratramine alkaloid from the bulbs of Fritillaria puqiensis. Chem. Pharm. Bull. 2006, 54:722-724.
35. Lin G., Li P., Li S.-L., Chan S.-W. Chromatographic analysis of Fritillaria isosteroidal alkaloids, the active ingredients of beimu, the antitussive traditional Chinese medicinal herb. J. Chromatogr. A 2001, 935:321-338.
36. Löytynoja A., Goldman N. WebPrank: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 2010, 11:579-585.
37. Maddison, D.R., Maddison, W.P., 2005. MacClade 4: Analysis of Phylogeny and Character Evolution, Version 4.08 OS X. Sinauer Associates, Sunderland, Massachusetts.
38. Muratović E., Hidalgo O., Garnatje T., Siljak-Yakovlev S. Molecular phylogeny and genome size in European Lilies (Genus Lilium, Liliaceae). Adv. Sci. Lett. 2010, 3:180-189.
39. Muratović E., Odil R., Bogunić F., Šoljan D., Siljak-Yakovlev S. Karyotype evolution and speciation of European lilies from Lilium sect. Liriotypus. Taxon 2010, 59:165-175.
40. Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
41. Nylander J.A.A. MrModeltest v2. Program Distributed by the Author 2004, Evolutionary Biology Centre, Uppsala University.
42. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
43. Parkin E.J., Butlin R.K. Within- and between-individual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion. Mol. Biol. Evol. 2004, 21:1595-1601.
44. Pharmacopoeia of the People's Republic of China, 2010. vol. 1: Chinese Pharmacopoeia Commission. China Science Medical Press, Beijing.
45. Rambaut, A., Drummond, A.J., 2009. Tracer v1.5, <>.http://tree.bio.ed.ac.uk/software/tracer.
46. Rix E.M. Plate 396. Fritillaria crassifolia subsp. kurdica. Curtis's Bot. Mag. 2000, 17:173-175.
47. Rix E.M. Fritillaria: A Revised Classification Together with an Updated List of Species 2001, Publication of the Fritillaria Group of the Alpine Garden Society, UK.
48. Ronquist F., Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
49. Rønsted N., Law S., Thornton H., Fay M.F., Chase M.W. Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria. Mol. Phylogenet. Evol. 2005, 35:509-527.
50. Saslis-Lagoudakis C.H., Savolainen V., Williamson E.M., Forest F., Wagstaff S.J., Baral S.R., Watson M.F., Pendry C., Hawkins J.A. Phylogenies reveal predictive power of traditional medicine in bioprospecting. Proc. Natl. Acad. Sci. USA 2012, 109:15835-15840.
51. Schlumpberger B.O., Renner S.S. Molecular phylogenetics of Echinopsis (Cactaceae): polyphyly at all levels and convergent evolution of pollination modes and growth forms. Am. J. Bot. 2012, 99:1335-1349.
52. Shang Z.J., Liu X.L. The history of medicinal use of beimu and investigation of its original plants. Chin. J. Med. History 1994, 25:38-42.
53. * Implementation of the Parsimony Ratchet (Beta Software, version 1). Distributed by the Authors 2001, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, USA.
54. Sun Y., Wang A., Wan D., Wang Q., Liu J. Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits. Mol. Phylogenet. Evol. 2010, 63:150-158.
55. Swofford, D.L., 2003. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Mass.
56. Türktaş M., Aslay M., Kaya E., Ertugǧrul F. Molecular characterization of phylogenetic relationships in Fritillaria species inferred from chloroplast trnL-trnF sequences. Turkish J. Bot. 2012, 36:552-560.
57. WCSP, 2014. World Checklist of Selected Plant Families. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; <>. (last accessed 21.03.14). http://apps.kew.org/wcsp/.
58. Wietsma W., van den Berg R.G. Cultivating Fritillaria eduardii. The Plantsman 2012, 11:222-225.
59. Xiao P.-G., Jiang Y., Li P., Luo Y.-B., Liu Y. The botanical origin and pharmacophylogenetic treatment of Chinese materia medica beimu. Acta Phytotaxonomica Sinica 2007, 45:473-487.
60. Xinqi, C., Mordak, H.V., 2000. Fritillaria. In: Wu Z.Y., Raven P.H. (Eds.), Flora of China, vol. 24 (Flagellariaceae through Marantaceae). Science Press, Beijing, and Missouri Botanical Garden Press, St. Louis., pp. 127-133.
61. Yan Z.H., Yan L., Ding W.G. Studies on the chemical constituents of Fritillaria Cirrhosa D. Don. Acta Universitatis Medicinalis Secondae Shanghai 1999, 19:487-489.
62. Zhang D.-Q., Gao L.-M., Yang Y.-P. Genetic diversity and structure of a traditional Chinese medicinal plant species, Fritillaria cirrhosa (Liliaceae), in southwest China and implications for its conservation. Biochem. Syst. Ecol. 2010, 38:236-242.