Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: Additional evidence from nrDNA ITS and cpDNA intron (rpl16 and rps16) sequences

Molecular Phylogenetics and Evolution

Volumn 53, Issue 1, 2009, Pages 56-68

  Zhou, Jing ^a,b   Gong, Xun ^a   Downie, Stephen R ^c   Peng, Hua ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Apiaceae subfamily Apioideae; China; cpDNA rpl16 intron; cpDNA rps16 intron; nrDNA ITS; Phylogeny

Indexed keywords

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

APIALES; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHINA; CHLOROPLAST; CLASSIFICATION; DNA SEQUENCE; GENETICS; INTRON; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENE;

APIACEAE; BAYES THEOREM; CHINA; CHLOROPLASTS; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENES, PLANT; INTRONS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ACRONEMA; APIACEAE; APIALES; APIOIDEAE; AZORELLOIDEAE; CYCLORHIZA; DICKINSIA; LIGUSTICUM; MEEBOLDIA; PEUCEDANUM; SCANDICEAE; SCANDICINAE; SELINEAE; SINODIELSIA;

EID: 67949110966     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.05.029     Document Type: Article

References (88)

1. Álvarez I., and Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29 (2003) 417-434
2. Andersson L., Kocsis M., and Eriksson R. Relationships of the genus Azorella (Apiaceae) and other hydrocotyloids inferred from sequence variation in three plastid markers. Taxon 55 (2006) 270-280
3. Barker F.K., and Lutzoni F. The utility of the incongruence length difference test. Syst. Biol. 51 (2002) 625-637
4. Bull J.J., Huelsenbeck J.P., Cunningham C.W., Swofford D.L., and Waddell P.J. Partitioning and combining data in phylogenetic analyses. Syst. Biol. 42 (1993) 384-397
5. Calviño C.I., Tilney P.M., Van Wyk B.-E., and Downie S.R. A molecular phylogenetic study of southern African Apiaceae. Am. J. Bot. 93 (2006) 1828-1847
6. Calviño C.I., and Downie S.R. Circumscription and phylogeny of Apiaceae subfamily Saniculoideae based on chloroplast DNA sequences. Mol. Phylogenet. Evol. 44 (2007) 175-191
7. Chandler G.T., and Plunkett G.M. Evolution in Apiales: nuclear and chloroplast markers together in (almost) perfect harmony. Bot. J. Linn. Soc. 144 (2004) 123-147
8. Downie S.R., and Katz-Downie D.S. A molecular phylogeny of Apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences. Am. J. Bot. 83 (1996) 234-251
9. Downie S.R., and Katz-Downie D.S. Phylogenetic analysis of chloroplast rps16 intron sequences reveals relationships within the woody southern African Apiaceae subfamily Apioideae. Can. J. Bot. 77 (1999) 1120-1135
10. Downie S.R., Ramanath S., Katz-Downie D.S., and Llanas E. Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences. Am. J. Bot. 85 (1998) 563-591
11. Downie S.R., Katz-Downie D.S., and Watson M.F. A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: towards a suprageneric classification of subfamily Apioideae. Am. J. Bot. 87 (2000) 273-292
12. Downie S.R., Watson M.F., Spalik K., and Katz-Downie D.S. Molecular systematics of Old World Apioideae (Apiaceae): relationships among some members of tribe Peucedaneae sensu lato, the placement of several island-endemic species, and resolution within the apioid superclade. Can. J. Bot. 78 (2000) 506-528
13. Downie S.R., Plunkett G.M., Watson M.F., Spalik K., Katz-Downie D.S., Valiejo-Roman C.M., Terentieva E.I., Troitsky A.V., Lee B.-Y., Lahham J., and El-Oqlah A. Tribes and clades within Apiaceae subfamily Apioideae: the contribution of molecular data. Edinb. J. Bot. 58 (2001) 301-330
14. Doyle J.J., and Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19 (1987) 11-15
15. Drude C.G.O. Umbelliferae. In: Engler A., and Prantl K. (Eds). Die natürlichen Pflanzenfamilien vol. 3 (1897), Wilhelm Engelmann, Leipzig, Germany 63-250
16. Farris J.S. The retention index and the rescaled consistency index. Cladistics 5 (1989) 417-419
17. Farris J.S., Kallersjo M., Kluge A.G., and Bult C. Constructing a significance test for incongruence. Syst. Biol. 44 (1995) 570-572
18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
19. Gielly L., and Taberlet P. The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol. Biol. Evol. 11 (1994) 769-777
20. Golenberg E.M., Clegg M.T., Durbin M.L., Doebley J., and Ma D.P. Evolution of a noncoding region of the chloroplast genome. Mol. Phylogenet. Evol. 2 (1993) 52-64
21. Hall, T., 1999. BioEdit. Biological sequence alignment editor for Win95/98/ NT/2K/XP, version 6.0.7. Available from: (accessed 19 May 2004).
22. Hiroe M., and Constance L. Umbelliferae of Japan. Univ. Calif. Publ. Bot. 30 (1958) 1-444
23. Hiroe M. Umbelliferae of World (1979), Ariake Book Company, Tokyo
24. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., and Gibson T.J. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23 (1998) 403-405
25. Jordan W.C., Courtney M.W., and Neigel J.E. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). Am. J. Bot. 83 (1996) 430-439
26. Katz-Downie D.S., Valiejo-Roman C.M., Terentieva E.I., Troitsky A.V., Pimenov M.G., Lee B., and Downie S.R. Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences. Plant Syst. Evol. 216 (1999) 167-195
27. Kelchner S.A., and Clark L.G. Molecular evolution and phylogenetic utility of the rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Mol. Phylogenet. Evol. 8 (1997) 385-397
28. Kim H.S., and Chi H.J. Studies on essential oils of plants of Angelica genus in Korea (II): essential oils of the root of Angelica tenuissima. Saengyak Hakhoechi 20 (1989) 13-20
29. Kluge A.G., and Farris J.S. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18 (1969) 1-32
30. Koso-Poljansky B.M. Sciadophytorum systematis lineamenta. Bull. Mosc. Soc. Natur. 29 (1916) 93-222
31. Leute G.H. Untersuchungen über den Verwandtschaftskreis der Gattung Ligusticum L. (Umbelliferae). Teil I. Ann. Nat. Hist. Mus. Wien A 73 (1969) 55-98
32. Mason-Gamer R.J., and Kellogg E.A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45 (1996) 524-545
33. Morton B.R., and Clegg M.T. A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae). Curr. Genet. 24 (1993) 357-365
34. Mukherjee P.K., and Constance L. New taxa and transfers in Indian Umbelliferae. Edinb. J. Bot. 48 (1991) 41-44
35. Müller K.F. SeqState-primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinform. 4 (2005) 65-69
36. Nylander, J.A.A., 2004. MrModeltest 2.2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. Available from: (accessed 15 November 2007).
37. Oh S.H., and Potter D. Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rRNA, and LEAFY. Am. J. Bot. 92 (2005) 179-192
38. Pan Z.-H., Sheh M.-L., Liu X.-T., and Yao X.-M. On karyotypes and geographical distribution of endemic genera in Umbelliferae from China. J. Plant Resour. Environ. 4 (1995) 1-8
39. Pan Z.-H., Zhuang T.-D., Yao X.-M., and Sheng N. A study on Karyotypes and geographical distribution of Angelica and related genera (Umbelliferae) in China. Acta Phytotax. Sin. 32 (1994) 419-424
40. Pan Z.-H., and Watson M.F. Angelica L. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 158-169
41. Pan Z.-H., and Watson M.F. Sinolimprichtia H. Wolff. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 55-56
42. Pimenov M.G. Systematic grouping of species of Angelica L. occurring in the USSR on the basis of coefficients of similarity. Bull. Mosc. Soc. Natur. 73 (1968) 124-139
43. Pimenov M.G., and Leonov M.V. The Genera of the Umbelliferae: A Nomenclator (1993), Royal Botanic Gardens, Kew, UK
44. Pimenov M.G., and Kljuykov E.V. New nomenclatural combinations for Chinese Umbelliferae. Feddes Repert. 110 (1999) 481-491
45. Pimenov M.G., and Kljuykov E.V. Notes on some Sino-Himalayan species of Angelica and Ostericum (Umbelliferae). Willdenowia 33 (2003) 121-137
46. Pimenov M.G., and Kljuykov E.V. Generic disposition of Vicatia bipinnata in Melanosciadium and a new species (Umbelliferae). Feddes Repert. 117 (2006) 466-475
47. Pimenov M.G., Kljuykov E.V., and Stroumova T.O. Reduction of Notopterygium to Hansenia (Umbelliferae). Willdenowia 38 (2008) 155-172
48. Plunkett G.M., Chandler G.T., Lowry II P.P., Pinney S.M., and Sprenkle T.S. Recent advances in understanding Apiales and a revised classification. S. Afr. J. Bot. 70 (2004) 371-381
49. Pu F.-D., and Peng Y.-L. Taxonomic notes on Meeboldia H. Wolff (Umbelliferae). Acta Phytotax. Sin. 43 (2005) 552-556
50. Pu F.-D., and Watson M.F. Ligusticum L. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 140-151
51. Pu F.-D., and Watson M.F. Nothosmyrnium Miq. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 113-114
52. Pu F.-D., and Watson M.F. Pimpinella L. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 93-104
53. Pu G.-Z., and Liu Q.-X. Comparative anatomical study on the genus Physospermopsis fruit from China and its systematic significance. J. Plant Resour. Environ. 14 (2005) l-6
54. Qin H.-Z., Li B.-Y., Wu Z.-J., and Pan Z.-H. On the fruit anatomy of Angelica L. (s.l.) of East Asia and North America and its evolution. Acta Bot. Boreali-Occidentalia Sin. 15 (1995) 48-54
55. Qiu Y.-X., Fu C.-X., and Wu F.-J. Analysis of population genetic structure and molecular identification of Changium smyrnioides and Chuanminshen violaceum with ISSR marker. China J. Chin. Mat. Med. 28 (2003) 598-603
56. Reeves G., Chase M.W., Goldblatt P., Rudall P., Fay M.F., Cox A.V., Lejeune B., and Souza-Chies T. Molecular systematics of Iridaceae: evidence from four plastid DNA regions. Am. J. Bot. 88 (2001) 2074-2087
57. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
58. Shan R.-H., and Sheh M.-L. Melanosciadium H. Boissieu. In: Flora Reipublicae Popularis Sinicae Editorial Committee of CAS (Ed). Flora Reipublicae Popularis Sinicae vol. 55(1) (1979), Science Press, Beijing 194
59. Shan R.-H., and Sheh M.-L. Harrysmithia L. In: Flora Reipublicae Popularis Sinicae Editorial Committee of CAS (Ed). Flora Reipublicae Popularis Sinicae vol. 55(2) (1985), Science Press, Beijing 134-137
60. Sheh M.-L., and Shan R.-H. Cyclorhiza and Chuanminshen-two newly proposed genera in Umbelliferae (Apiaceae). Acta Phytotax. Sin. 18 (1980) 45-49
61. Sheh M.-L., Shu P., and Pan Z.-H. The comparative study of pollen morphology of Angelica L. between East Asia and North America. J. Wuhan Bot. Res. 6 (1997) 41-47
62. Sheh M.-L., Pu F.-D., Pan Z.-H., Watson M.F., Cannon J.F.M., Holmes-Smith I., Kljuykov E.V., Phillippe L.R., and Pimenov M.G. Apiaceae. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 1-205
63. Sheh M.-L., and Watson M.F. Changium H. Wolff. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 37-38
64. Sheh M.-L., and Watson M.F. Harrysmithia H. Wolff. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 110
65. Sheh M.-L., and Watson M.F. Peucedanum L. In: Flora of China Editorial Committee (Ed). Flora of China vol. 14 (2005), Missouri Botanical Garden Press, St. Louis, MI, USA 182-192
66. Shu P., and Sheh M.-L. Study on pollen morphology of endemic genera in Chinese Umbellifferae. Bulletin of the Nanjing Botanical Garden Memorial of Sun Yat Sen (1990), Phenix Science Press, Nanjing 33-36
67. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
68. Spalik K., and Downie S.R. Intercontinental disjunctions in Cryptotaenia (Apiaceae, Oenantheae): an appraisal using molecular data. J. Biogeogr. 34 (2007) 2039-2054
69. * and other methods), vers. 4.0b10. Sinauer, Sunderland, MA, USA.
70. Torke B.M., and Schaal B.A. Molecular phylogenetics of the species-rich neotropical genus Swartzia (Leguminosae, Papilionoideae) and related genera of the swartzioid clade. Am. J. Bot. 95 (2008) 215-228
71. Valiejo-Roman C.M., Terentieva E.I., Samigullin T.H., and Pimenov M.G. Relationships among genera in Saniculoideae and selected Apioideae (Umbelliferae) inferred from nrITS sequences. Taxon 51 (2002) 91-101
72. Valiejo-Roman C.M., Terentieva E.I., Samigullin T.H., and Pimenov M.G. NrDNA ITS sequences and affinities (Umbelliferae) of Sino-Himalayan Apioideae (Umbelliferae). Taxon 51 (2002) 685-701
73. Vasil'eva M.G., and Pimenov M.G. Karyotaxonomic alanalysis in the genus Angelica (Umbelliferae). Plant Syst. Evol. 177 (1991) 117-138
74. 1H-NMR method in chemotaxonomy of Apioideae. J. Plant Resour. Environ. 5 (1996) 40-44
75. Wang P.-L., Pu F.-D., and Ma J.-S. Pollen morphology of the genus Ligusticum from China and its systematic significance. Acta Phytotax. Sin. 29 (1991) 235-245
76. Wang P.-L., Pu F.-D., and He X.-J. Pollen morphology of the genus Heracleum L. from China and its taxonomic and evolutionary significance. Bull. Bot. Res. 13 (1993) 276-284
77. Wang P.-L., and Pu F.-D. Pollen morphology diversity and evolution trend of the genus Physospermopsis in the Hengduan Mountains of China. Acta Bot. Yunnan. 14 (1992) 413-417
78. Watson M.F., Sheh M.-L., Pu F.-D., and Pan Z.-H. Nomenclatural novelties in the Apiaceae (Umbelliferae) for the Flora of China. Acta Phytotax. Sin. 42 (2004) 561-565
79. Wen J., and Zimmer E.A. Phylogeny and biogeography of Panax L. (the ginseng genus, Araliaceae): inferences from ITS sequences of nuclear ribosomal DNA. Mol. Phylogenet. Evol. 6 (1996) 167-177
80. White T.J., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, San Diego, CA, USA 315-322
81. Wiens J.J. Combining data sets with different phylogenetic histories. Syst. Biol. 47 (1998) 568-581
82. Xue H.-J., Yan M.-H., Lu C.-M., Wang N.-H., and Wu G.-R. Taxonomic study of Angelica from East Asia: inferences from ITS sequences of nuclear ribosomal DNA. Acta Phytotax. Sin. 45 (2007) 783-795
83. Xue H.-J., Wang N.-H., Lu C.-M., Sun M.-Y., Taniguch M., and Baba K. Phylogenetic position of Anegelica apaensis/Heracleum apaense based on evidence from ITS sequences of nuclear ribosomal DNA. J. Wuhan Bot. Res. 25 (2007) 143-148
84. Yuan C.-Q., and Shan R.-H. On the genera Angelica L. and Ostericum Hoffm. (Umbelliferae) in China. Bulletin of Nanjing Botanical Garden Mem.Sun-Yat Sen (1983), Phoenix Science Press, Nanjing 1-13
85. Yoder A.D., Irwin J.A., and Payseur B.A. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50 (2001) 408-424
86. Zhou A.-L., and Wu J.-L. Constitutes of Melanosciadium pimpinelloideum H. Boissieu. J. Plant Resour. Environ. 1 (1992) 60-61
87. Zhou J., Peng H., Downie S.R., Liu Z.-W., and Gong X. A molecular phylogeny of Chinese Apiaceae subfamily Apioideae inferred from nuclear ribosomal DNA internal transcribed spacer sequences. Taxon 57 (2008) 402-416
88. Zhou J., Pu F.-D., Peng H., Pan Y.-Z., and Gong X. Karyological studies of ten Ligusticum species (Apiaceae) from the Hengduan Mountains Region of China. Caryologia 61 (2008) 333-341