The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers

Molecular Phylogenetics and Evolution

Volumn 68, Issue 2, 2013, Pages 340-356

  Yang, Hong Mei ^a,b,c   Zhang, Yu Xiao ^a,b   Yang, Jun Bo ^b   Li, De Zhu ^a,b  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b Plant Germplasm and Genomics Center   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Chimonocalamus; GBSSI; Incongruence; LEAFY; Phylogeny; Plastid DNA

Indexed keywords

GRANULE BOUND STARCH SYNTHASE I; GRANULE-BOUND STARCH SYNTHASE I; STARCH SYNTHASE; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; ENZYMOLOGY; GENE DOSAGE; GENETIC MARKER; GENETICS; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PLANT GENE; PLASTID; POACEAE; STATISTICAL MODEL;

BAYES THEOREM; CELL NUCLEUS; GENE DOSAGE; GENES, PLANT; GENETIC MARKERS; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE ANNOTATION; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PLANT PROTEINS; PLASTIDS; POACEAE; STARCH SYNTHASE; TRANSCRIPTION FACTORS;

AMPELOCALAMUS; BAMBUSA; BAMBUSOIDEAE; BASHANIA; CHIMONOCALAMUS; DREPANOSTACHYUM; FARGESIA; HIMALAYACALAMUS; POACEAE; THAMNOCALAMUS; YUSHANIA;

EID: 84878106037     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.04.002     Document Type: Article

References (73)

1. Acosta M.C., Premoli A.C. Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae). Mol. Phylogenet. Evol. 2010, 54:235-242.
2. Alvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 2003, 29:417-434.
3. Archambault A., Bruneau A. Phylogenetic utility of the LEAFY/FLORICAULA gene in the Caesalpinioideae (Leguminosae): gene duplication and a novel insertion. Syst. Bot. 2004, 29:609-626.
4. Avise J.C., Robinson T.J. Hemiplasy: a new term in the lexicon of phylogenetics. Syst. Biol. 2008, 57:503-507.
5. Bamboo Phylogeny Group, 2012. An updated tribal and subtribal classification for the Bambusoideae (Poaceae). In: Gielis, J., Potters, G. (Eds.), Proceedings of the 9th World Bamboo Congress, Antwerp, Belgium: World Bamboo Organization, pp. 3-27.
6. Barker F.K., Lutzoni F.M. The utility of the incongruence length difference test. Syst. Biol. 2002, 51:625-637.
7. Bouchenak-Khelladi Y., Salamin N., Savolainen V., Forest F., van der Bank M., Chase M.W., Hodkinson T.R. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol. Phylogenet. Evol. 2008, 47:488-505.
8. Bouchenak-Khelladi Y., Verboom G.A., Savolainen V., Hodkinson T.R. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Bot. J. Linn. Soc. 2010, 162:543-557.
9. Buckley T.R., Cordeiro M., Marshall D.C., Simon C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst. Biol. 2006, 55:411-425.
10. Chao C., Renvoize S. A revision of the species described under Arundinaria (Gramineae) in Southeast Asia and Africa. Kew Bull. 1989, 349-367.
11. 4 photosynthesis in grasses. Curr. Biol. 2008, 18:37-43.
12. Darlington C.D., Ammal E.K.J. Chromosome Atlas of Cultivated Plants 1945, George Allen and Unwin, Ltd., London.
13. Darlu P., Lecointre G. When does the incongruence length difference test fail?. Mol. Biol. Evol. 2002, 19:432-437.
14. Dolphin K., Belshaw R., Orme C.D.L., Quicke D.L.J. Noise and incongruence: interpreting results of the incongruence length difference test. Mol. Phylogenet. Evol. 2000, 17:401-406.
15. Dowton M., Austin A.D. Increased congruence does not necessarily indicate increased phylogenetic accuracy: the behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 2002, 51:19-31.
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. Dransfield S., Widjaja E.A. Plant resources of South-East Asia. No. 7: Bamboos 1995, Backhuys Publishers, Leiden.
18. Edwards C.E., Lefkowitz D., Soltis D.E., Soltis P.S. Phylogeny of Conradina and related southeastern scrub mints (Lamiaceae) based on GapC gene sequences. Int. J. Plant Sci. 2008, 169:579-594.
19. Edwards C.E., Soltis D.E., Soltis P.S. Molecular phylogeny of Conradina and other scrub mints (Lamiaceae) from the southeastern USA: evidence for hybridization in Pleistocene refugia?. Syst. Bot. 2006, 31:193-207.
20. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1994, 10:315-319.
21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
22. Fortune P.M., Schierenbeck K.A., Ainouche A.K., Jacquemin J., Wendel J.F., Ainouche M.L. Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae). Mol. Phylogenet. Evol. 2007, 43:1040-1055.
23. Gould F.W. Chromosome numbers in southwestern grasses. II. Am. J. Bot. 1960, 47:873-877.
24. Grob G.B.J., Gravendeel B., Eurlings M.C.M. Potential phylogenetic utility of the nuclear FLORICAULA/LEAFY second intron: comparison with three chloroplast DNA regions in Amorphophallus (Araceae). Mol. Phylogenet. Evol. 2004, 30:13-23.
25. Guo Z.H., Chen Y.Y., Li D.Z. Phylogenetic studies on the Thamnocalamus group and its allies (Gramineae: Bambusoideae) based on ITS sequence data. Mol. Phylogenet. Evol. 2002, 22:20-30.
26. Guo Z.H., Li D.Z. Phylogenetics of the Thamnocalamus group and its allies (Gramineae: Bambusoideae): inference from the sequences of GBSSI gene and ITS spacer. Mol. Phylogenet. Evol. 2004, 30:1-12.
27. Hilu K.W. Phylogenetics and chromosomal evolution in the Poaceae (grasses). Aust. J. Bot. 2004, 52:13-22.
28. Hodkinson T.R., Chonghaile G.N., Sungkaew S., Chase M.W., Salamin W., Salamin N., Stapleton C.M.A. Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae). Plant Ecol. Divers. 2010, 3:109-120.
29. Hsueh C.J., Yi T.P. Two new genera of Bambusoideae from S.W. China, 1: Chimonocalamus Hsueh et Yi. Acta Bot. Yunnanica 1979, 1:74-92.
30. Hsueh C.J., Yi T.P. A new species of Chimonocalamus from China. Acta Phytotax. Sin. 1985, 23:236-237.
31. Jakob S.S., Blattner F.R. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol. Biol. Evol. 2006, 23:1602-1612.
32. Karthikeyan, S., Jain, S.K., Nayar, M.P., Sanjappa, M., 1989. Florae Indicae Enumeratio: Monocotyledonae. Botanical Survey of India, Calcutta, p. 276.
33. Keng P.C., Wang C.P. Flora Reipublicae Popularis Sinicae 1996, vol. 9. Science Press, Beijing.
34. Le V.L., Xia N.H., Deng Y.F. Chimonocalamus baviensis, a new combination in Vietnamese Bambusoideae (Poaceae). Ann. Bot. Fenn. 2009, 46:148-150.
35. Li D.Z. Notes on Bambusoideae (Gramineae) in Yunnan and adjacent Sichuan and Burma. Acta Bot. Yunnanica 1994, 16:39-42.
36. Li D.Z. The Flora of China Bambusoideae Project-Problems and Current Understanding of Bamboo Taxonomy in China 1997, Academic Press, London.
37. Li, D.Z., 1999. Taxonomy and biogeography of the Bambuseae (Gramineae: Bambusoideae). In: Rao, A.N., Rao, V.R. (Eds.), Bamboo-Conservation, Diversity, Ecogeography, Germplasm, resource Utilization and Taxonomy. Proceeding of training course cum workshop, Kunming & Xishuangbanna, Yunnan, China. IPGRI-APO, Serdagn, Malaysia, pp. 14-23.
38. Li D.Z., Stapleton C.M.A., Xue J.R. A new combination in Ampelocalamus and notes on A. patellaris (Gramineae: Bambusoideae). Kew Bull. 1996, 51:809-813.
39. Li D.Z., Wang Z.P., Zhu Z.D., Xia N.H., Jia L.Z., Guo Z.H., Yang G.Y., Stapleton C.M.A. Bambuseae (Poaceae). Flora of China 2006, vol. 22:103-105. Science Press, St. Louis: Missouri Botanical Garden Press, Beijing.
40. Li S.F., Wang Z.P. A new species of Chimonocalamus (Poaceae) from Yunnan. China. Acta Phytotax. Sin. 1995, 33:614-615.
41. Ma L.S., Yi T.P., Shi J.Y., Li B.X. Chimonocalamus peregrinus Yi et L.S. Ma-A new species of Chimonocalamus Huseh et Yi. Bull. Bot. Res. 2010, 30:390-393.
42. Maizel A., Busch M.A., Tanahashi T., Perkovic J., Kato M., Hasebe M., Weigel D. The floral regulator LEAFY evolves by substitutions in the DNA binding domain. Science 2005, 308:260-263.
43. Maruyama I., Okamura H., Murata G. On a new hybrid genus Hibanobambusa. Acta Phytotax. Geobot. 1979, 30:148-152.
44. Moyroud E., Kusters E., Monniaux M., Koes R., Parcy F. LEAFY blossoms. Trends Plant Sci. 2010, 15:346-352.
45. Moyroud E., Tichtinsky G., Parcy F. The LEAFY floral regulators in angiosperms: conserved proteins with diverse roles. J. Plant Biol. 2009, 52:177-185.
46. Oh S.H., Potter D. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Mol. Phylogenet. Evol. 2003, 29:203-215.
47. Oh S.H., Potter D. Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rDNA, and LEAFY. Am. J. Bot. 2005, 92:179-192.
48. Ohrnberger D. The Bamboos of the World: Annotated Nomenclature and Literature of the Species and the Higher and Lower Taxa 1999, Elsevier Science, Amsterdam and New York, pp. 126-128.
49. Peng S., Yang H.Q., Li D.Z. Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): evidence from GBSSI and ITS sequences. Taxon 2008, 57:799-810.
50. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
51. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
52. Ruiz-Sanchez E. Biogeography and divergence time estimates of woody bamboos: insights in the evolution of neotropical bamboos. Bol. Soc. Bot. Mex. 2011, 88:67-75.
53. Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
54. Small R.L., Cronn R.C., Wendel J.F. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 2004, 17:145-170.
55. Soderstrom T.R. Some evolutionary trends in the Bambusoideae (Poaceae). Ann. Missouri Bot. Gard. 1981, 68:15-47.
56. Soderstrom T.R., Ellis R.P. The position of bamboo genera and allies in a system of grass classification. Grass Systematics and Evolution 1987, Smithsonian Institution Press, Washington, DC. T.R. Soderstrom, K.W. Hiu, C.S. Campbell, M.F. Barkworth (Eds.).
57. Sota T., Vogler A.P. Reconstructing species phylogeny of the carabid beetles Ohomopterus using multiple nuclear DNA sequences: heterogeneous information content and the performance of simultaneous analyses. Mol. Phylogenet. Evol. 2003, 26:139-154.
58. Sungkaew S., Stapleton C.M.A., Salamin N., Hodkinson T.R. Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. J. Plant Res. 2009, 122:95-108.
59. Swofford, D.L., 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0 b10. Sinauer Associates, Sunderland.
60. Taylor W.C., Lekschas A.R., Wang Q.F., Liu X., Napier N.S., Hoot S.B. Phylogenetic relationships of Isoëtes (Isoëtaceae) in China as revealed by nucleotide sequences of the nuclear ribosomal ITS region and the second intron of a LEAFY homolog. Am. Fern J. 2004, 94:196-205.
61. Triplett J.K., Clark L.G. Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies. Syst. Bot. 2010, 35:102-120.
62. Triplett J.K., Oltrogge K.A., Clark L.G. Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria). Am. J. Bot. 2010, 97:471-492.
63. Wang X.S., Ma D.Q., Jiang D.H. Geology of Hainan Island III: Tectonic Geology 1991, Science Press, Beijing.
64. Wolfe A.D., Elisens W.J. Evidence of chloroplast capture and pollen-mediated gene flow in Penstemon sect. Peltanthera (Scrophulariaceae). Syst. Bot. 1995, 20:395-412.
65. Yang H.Q., Yang J.B., Peng Z.H., Gao J., Yang Y.M., Li D.Z. A molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trnL-F DNA sequences. Mol. Phylogenet. Evol. 2008, 48:809-824.
66. Yi T.P. New taxa of Bambusoideae from Xizang (Tibet), China. J. Bamboo Res. 1983, 2:38.
67. Yi T.P., Shi J.Y., Ma L.S., Wang H.T., Yang L. Iconographia Bambusoidearum Sinicarum 2008, Science Press, Beijing.
68. Yi T.P., Shi J.Y., Ma L.S., Yang L., Yao J. A new species of Chimonocalamus Huseh et Yi on west Yunnan China. Bull. Bot. Res. 2008, 28:133-135.
69. Zeng C.X., Zhang Y.X., Triplett J.K., Yang J.B., Li D.Z. Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Mol. Phylogenet. Evol. 2010, 56:821-839.
70. Zhang G.C. Studies on chromosome number of some sympodial bamboos. Guangdong Forest. Sci. Technol. 1985, 4:16-21.
71. Zhang Y.J., Ma M.F., Li D.Z. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS ONE 2011, 6(5):e20596.
72. Zhang Y.X., Zeng C.X., Li D.Z. Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol. Phylogenet. Evol. 2012, 63:777-797.
73. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation. The University of Texas at Austin.