A new species in the genus Nomocharis Franchet (Liliaceae): Evidence that brings the genus Nomocharis into Lilium

Plant Systematics and Evolution

Volumn 298, Issue 1, 2012, Pages 69-85

  Gao, Yun Dong ^a   Hohenegger, Markus ^c   Harris, A J ^b   Zhou, Song Dong ^a   He, Xing Jin ^a   Wan, Juan ^a  

^a SICHUAN UNIVERSITY   (China)

^b OKLAHOMA STATE UNIVERSITY   (United States)

^c NONE

Author keywords

ITS; Lilium Nomocharis complex; Nomocharis gongshanensis Y. D. Gao et X. J. He; psbA trnH

Indexed keywords

LILIACEAE; LILIUM; NOMOCHARIS; NOMOCHARIS SALUENENSIS;

EID: 84855327550     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-011-0524-1     Document Type: Article

References (70)

1. Akaike H (1974) A new look at the statistical model identification. IEEE T Automat Contr 19: 716-723.
2. Baker JG (1871) A new synopsis of all the known lilies. Gard Chron 104: 1650.
3. Balfour B (1918) The genus Nomocharis. Bot J Scot 27: 273-300.
4. Baranova MV (1988) A synopsis of the system of the genus Lilium (Liliaceae). Bot Zurn 73: 1319-1329.
5. Brock RD (1954) Fertility in Lilium hybrids. Heredity 8: 409-420.
6. Chen FB (1992) Hengduan event: an important tectonic event of the late Cenozoic in Eastern Asia. Mt Res 10: 195-202.
7. Chen FB (1996) Second discussion on the Hengduan movement. Volcanol Miner Resour 17: 14-22.
8. Chung SL, Lo CH, Lee TY, Zhang YQ, Xie YW, Li XH, Wang KL, Wang PL (1998) Diachronous uplift of the Tibetan plateau starting 40 Myr ago. Nature 394: 769-773.
9. Comber HF (1949) A new classification of genus Lilium. R Hort Soc Lily Year Book 13: 85.
10. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
11. Dubouzet JD, Shinoda K (1999) Phylogenetic analysis of the internal transcribed spacer region of Japanese Lilium species. Theor Appl Genet 98: 954-960.
12. Evans WE (1925) A revision of the genus Nomocharis. Notes Roy Bot Gard Edinb 15: 1-46.
13. Fay MF, Chase MW, Rønsted N et al (2006) Phylogenetics of Liliales: summarized evidence from combined analyses of five plastid and one mitochondrial loci. In: Columbus JT, Friar EA, Porter JM, Prince LM, Simpson MG (eds) Monocots: comparative biology and evolution (excluding Poales). Rancho Santa Ana Botanic Garden, Claremont, CA, pp 559-565.
14. Franchet AR (1889) Nomocharis Franchet. J Bot (Morot) 3: 113.
15. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, cause and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol S 34: 397-423.
16. Hamilton MB (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol 8: 521-523.
17. Harrison TM, Copeland P, Kidd WSF, Yin A (1992) Raising Tibet. Science 255: 1663-1670.
18. Haw SG (1986) The lilies of China. Timber Press, Portland.
19. Hayashi K, Kawano S (2000) Molecular systematics of Lilium and allied genera (Liliaceae): phylogenetic relationships among Lilium and related genera based on the rbcL and matK gene sequence data. Plant Spec Biol 15: 73-93.
20. Holder MT, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Gene 4: 275-284.
21. Holderegger R, Abbott RJ (2003) Phylogeography of the Arctic-Alpine Saxifraga oppositifolia (Saxifragaceae) and some related taxa based on cpDNA and ITS sequence variation. Am J Bot 90: 931-936.
22. İkinci N, Oberprieler C, Güner A (2006) On the origin of European lilies: phylogenetic analysis of Lilium section Liriotypus (Liliaceae) using sequences of the nuclear ribosomal transcribed spacers. Willdenowia 36: 647-656.
23. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding psbA-trnH spacer region. PLoS One 6: e508.
24. Kress WJ, Wurdack KJ, Zimmer EA, Weight LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102: 8369-8374.
25. Kumar S, Tamura K, Nei M (1993) MEGA: Molecular Evolutionary Genetics Analysis, version 1. 01. The Pennsylvania State University, University Park, PA. http://evolgen. biol. metro-u. ac. jp/MEGA/manual/default. html. Accessed 8 Aug 2011.
26. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 105: 2923-2928.
27. Liang SY (1980) Flora Reipublicae Popularis Sinicae, vol. 14, Anagiospermae, Monocotyledoneae Liliaceae (I). Science Press, Beijing, pp 116-157.
28. Liang SY (1984) Studies on the genus Nomocharis (Liliaceae). Bull Bot Res 4: 163-178.
29. Liang SY (1995) Chorology of Liliaceae (S. Str.) and its bearing on the Chinese Flora. Acta Phytotax Sin 33: 27-51.
30. Liang SY, Tamura M (2000) Lilium L.; Nomocahris Franchet. In: Wu ZY, Raven PH (eds) Flora of China, vol 24. Science Press, Beijing; Missouri Botanical Garden Press, St. Louis, pp 135-159.
31. Liang SY, Zhang WX (1985) Pollen morphology of the genus Nomocharis and its delimitation with Lilium. Acta Phytotax Sin 23: 405-417.
32. Liu JQ, Wang YJ, Wang AL, Hideakic O, Abbott RJ (2006) Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 38: 31-49.
33. McRae EA (1998) Lilies: a guide for growers and collectors. Timber Press, Portland, pp 17-26.
34. Morrell PL, Rieseberg LH (1998) Molecular tests of the proposed diploid hybrid origin of Gilia achilleifolia (Polemoniaceae). Am J Bot 85: 1439-1453.
35. Morrison DA (2009) A framework for phylogenetic sequence alignment. Plant Syst Evol 282: 127-149.
36. Newmaster SG, Ragupathy S (2009) Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Mol Ecol Res 9(Suppl 1): 172-180.
37. Nishikawa T, Okazaki K, Uchino T, Arakawa K, Nagamine T (1999) A molecular phylogeny of Lilium in the internal transcribed spacer region. J Mol Evol 49: 238-249.
38. Nishikawa T, Okazaki K, Arakawa K, Nagamine T (2001) Phylogenetic analysis of section Sinomartagon in genus Lilium using sequences of the internal transcribed spacer region in nuclear ribosomal DNA. Breed Sci 51: 39-46.
39. Nylander JAA (2004) MrModeltest 2. 0. Department of Systematic Zoology, EBC, Uppsala University, Uppsala (available from the author).
40. Patterson TB, Givnish TJ (2002) Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data. Evolution 56: 233-252.
41. Peruzzi L, Leitch IJ, Caparelli KF (2009) Chromosome diversity and evolution in Liliaceae. Ann Bot (Oxford) 103: 459-475.
42. Rambaut A, Drummond AJ (2007) Tracer v1. 4. http://beast. bio. ed. ac. uk/Tracer. Accessed 5 Aug 2011.
43. Rešetnik I, Liber Z, Satovic Z, Cigić P, Nikolić T (2007) Molecular phylogeny and systematics of the Lilium carniolicum group (Liliaceae) based on nuclear ITS sequences. Plant Syst Evol 265: 45-58.
44. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
45. Rønsted N, Law S, Thornton H, Fay MF, Chase MW (2005) Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria. Mol Phylogenet Evol 35: 509-527.
46. Royden LH, Burchfiel BC, van der Hilst RD (2008) The geological evolution of the Tibetan Plateau. Science 321: 1054-1058.
47. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot 84: 1120-1136.
48. Sass C, Little DP, Stevenson DW, Specht CD (2007) DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2: e1154.
49. Sealy JR (1950) Nomocharis and Lilium. Kew Bull 5: 273-297.
50. Sealy JR (1978) Nomocharis pardanthina Franchet f. punctulata Sealy. Notes Roy Bot Gard Edinb 36: 295.
51. Sealy JR (1983) A revision of the genus Nomocharis Franchet. Bot J Linn Soc 87: 285-323.
52. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genomes to choose non-coding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94: 275-288.
53. Siripun KC, Schilling EE (2006) Molecular confirmation of the hybrid origin of Eupatorium godfreyanum (Asteraceae). Am J Bot 93: 319-325.
54. Song J, Yao H, Li Y, Li X, Lin Y, Liu C, Han J, Xie C, Chen S (2009) Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique. J Ethnopharmacol 124: 434-439.
55. Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA.
56. Tamura MN, Yamashita J, Fuse S, Haraguchi M (2004) Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences. J Plant Res 117: 109-120.
57. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
58. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
59. Trewick SA (2008) DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 24: 240-254.
60. Tuyl JM, van Diën MP, van Creij MGM, van Kleinwee TCM, Franken J (1991) Application of in vitro pollination, ovary culture, ovule culture and embryo rescue for overcoming incongruity barriers in interspecific Lilium crosses. Plant Sci 74: 115-126.
61. Vinnersten A, Bremer K (2001) Age and biogeography of major clades in Liliales. Am J Bot 88: 1695-1703.
62. Vischi M, Arzenton F, De Paoli E, Paselli S, Tomat E, Olivieri AM (2006) Identification of wild species of sunflower by a specific plastid DNA sequence. Helia 29: 11-18.
63. Wang FZ, Tang J (1980) Lilium L. In: Flora Reipublicae Popularis Sinicae, vol 14. Science Press, Beijing, pp 116-157.
64. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Shinsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315-322.
65. Wilson EH (1925) The Lilies of Eastern Asia: a monograph. Dulau, London.
66. Xie XY, Gu ZJ, Wu QA (1992) Cytological studies of the genus Nomocharis and its related genera. Acta Phytotax Sin 30: 487-497.
67. Yao H, Song JY, Ma XY, Liu C, Li Y, Xu HX, Han JP, Duan LS, Chen SL (2009) Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Med 75: 667-669.
68. Zhang DF, Li FQ, Bian JM (2000) Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China. Environ Geol 39: 1352-1358.
69. Zhang JM, Wang JX, Xia T, Zhou SL (2009) DNA barcoding: species delimitation in tree peonies. Sci China Ser C 52: 568-578.
70. Zhang YH, Volis S, Sun H (2010) Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions. Mol Phylogenet Evol 57: 1162-1172.