Multi-gene region phylogenetic analyses suggest reticulate evolution and a clade of Australian origin among paleotropical woody bamboos (Poaceae: Bambusoideae: Bambuseae)

Plant Systematics and Evolution

Volumn 299, Issue 1, 2013, Pages 239-257

  Goh, W L ^a   Chandran, S ^a   Franklin, D C ^b   Isagi, Y ^c   Koshy, K C ^d   Sungkaew, S ^e   Yang, H Q ^f   Xia, N H ^g   Wong, K M ^h  

^a UNIVERSITY OF MALAYA   (Malaysia)

^b CHARLES DARWIN UNIVERSITY   (Australia)

^c KYOTO UNIVERSITY   (Japan)

^d JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE   (India)

^e KASETSART UNIVERSITY   (Thailand)

^f RESEARCH INSTITUTE OF FORESTRY   (China)

^g SOUTH CHINA INSTITUTE OF BOTANY   (China)

^h SINGAPORE BOTANIC GARDENS   (Singapore)

Author keywords

Australia; Bambusinae; Biogeography; Incomplete lineage sorting; Incongruent gene topologies; Introgressive hybridization; Paleotropical bamboos; Racemobambosinae; Reticulate evolution; Southeast Asia

Indexed keywords

BAMBUSA; BAMBUSEAE; BAMBUSOIDEAE; DENDROCALAMUS; DINOCHLOA; GIGANTOCHLOA; PHYLLOSTACHYS ACUTA; POACEAE; TEMBURONGIA; TEMBURONGIA SIMPLEX;

EID: 84871926926     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-012-0718-1     Document Type: Article

References (112)

1. Armstrong KC (1991) Chromosome evolution of Bromus. In: Armstrong KC, Tsuchiya T, Gupta P (eds) Chromosome engineering in plants: genetics, breeding, evolution, part B. Elsevier Science Publ, The Netherlands, pp 366-377.
2. Avise JC, Arnold J, Ball RM, Birmingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann Rev Ecol Syst 18: 489-522.
3. Bahadur KN, Jain SS (1981) Rare bamboos of India. Indian J For 4: 280-286.
4. Bamboo Phylogeny Group (2005) L. G. Clark Lab: Sequencing primers and PCR protocols. http://www. eeob. iastate. edu/research/bamboo/pdf/PCR_protocols. pdf.
5. Bamboo Phylogeny Group (2012) An updated tribal classification for the Bambusoideae (Poaceae). In: Proceedings of the 9th World Bamboo Congress, Antwerp, Belgium, 10-12 April 2012.
6. Bänfer G, Moog U, Fiala B, Mohamed M, Weising K, Blattner FR (2006) A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersal. Mol Ecol 15: 4409-4424.
7. Batchelor BC (1979) Discontinuously rising Late Cainozoic eustatic sea-levels, with special reference to Sundaland, southeast Asia. Geologie en Mijnbouw 58: 1-20.
8. Borchsenius F (2009) FastGap 1. 1. Department of Biological Sciences, University of Aarthus, Denmark, http://www. aubot. dk/fb/FastGap_home. htm.
9. Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, Bank M, Chase MW, Hodkinson TR (2008) Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol 47: 488-505.
10. Bouchenak-Khelladi Y, Verboom A, Savolainen V, Hodkinson TR (2010) Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Bot J Linn Soc 162: 543-557.
11. Bowden WM (1959) Chromosome numbers and taxonomic notes on northern grasses: I Tribe Triticeae. Can J Bot 37: 1143-1145.
12. Bowden WM (1960a) Chromosome numbers and taxonomic notes on northern grasses: II Tribe Festuceae. Can J Bot 38: 117-131.
13. Bowden WM (1960b) Chromosome numbers and taxonomic notes on northern grasses: III Twenty-five genera. Can J Bot 38: 541-557.
14. Bowden WM (1961) Chromosome numbers and taxonomic notes on northern grasses: IV. Tribe Festuceae: Poa and Puccinellia. Can J Bot 39: 123-138.
15. Bremer K (2002) Gondwanan evolution of the grass alliance of families (Poales). Evolution 56: 1374-1387.
16. Cannon CH, Manos PS (2003) Phylogeography of the Southeast Asian stone oaks (Lithocarpus). J Biogeogr 30: 211-226.
17. Chen R, Li X, Song W, Liang G, Zhang P, Lin R, Zong W, Chen C, Fung H (2004) Chromosome atlas of major economic plants genome in China (Tomus IV). Chromosome atlas of various bamboo species. Science Press, Beijing.
18. Clark LG, Davidse G, Ellis RP (1989) Natural hybridization in bamboos: evidence from Chusquea sect. Swallenochloa (Poaceae: Bambusoideae). Nat Geo Res 5: 459-476.
19. Clark LG, Zhang W, Wendel JF (1995) A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst Bot 20: 436-460.
20. Clark LG, Dransfield S, Triplett J, Sánchez-Ken JG (2007) Phylogenetic relationships among the one-flowered, determinate genera of Bambuseae (Poaceae: Bambusoideae). Aliso 23: 315-332.
21. Cotton R, Stace CA (1976) Taxonomy of the genus Vulpia (Gramineae). I Chromosome numbers and geographical distribution of the old world species. Genetica 46: 235-255.
22. Devos KM et al (2010) Grass genome organization and evolution. Curr Opin Plant Biol 13: 139-145.
23. Döring E, Schneider J, Hilu KW, Röser M (2007) Phylogenetic relationships in the Aveneae/Poaceae complex (Pooideae, Poaceae). Kew Bull 62: 407-424.
24. Dransfield S (1981) The genus Dinochloa (Gramineae-Bambusoideae) in Sabah. Kew Bull 36: 613-633.
25. Dransfield S (1983) The genus Racemobambos (Gramineae-Bambusoideae). Kew Bull 37: 661-679.
26. Dransfield S (1989) Sphaerobambos, a new genus of bamboo (Gramineae-Bambusoideae) from Malesia. Kew Bull 44: 425-434.
27. Dransfield S (1992) The bamboos of Sabah. Sabah Forest Records, No. 14. Sabah Forestry Department, Malaysia.
28. Dransfield S, Widjaja EA (1995) Plant resources of South-East Asia No. 7: Bamboos. Backhuys Publishers, Leiden.
29. Dransfield S, Wong KM (1996) Temburongia, a new genus of bamboo (Gramineae: Bambusoideae) from Brunei. Sandakania 7: 49-58.
30. Franklin DC (2003) Morphology and taxonomy of the Top End Bamboo Bambusa arnhemica F. Muell., a little-known bamboo from northern Australia. Bamboo Sci Cult 17: 44-54.
31. Franklin DC (2008) Taxonomic interpretations of Australian native bamboos (Poaceae: Bambuseae) and their biogeographic implications. Telopea 12: 179-191.
32. Goh WL, Chandran S, Xia NH, Lin RS, Wong KM (2010) Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex. Biochem Syst Ecol 38: 764-773.
33. Goh WL, Chandran S, Kamiya K, Wong KM (2011) A natural hybrid between Dendrocalamuspendulus and Gigantochloascortechinii (Poaceae: Bambsoideae: Bambuseae) in Peninsular Malaysia. Gard Bull Sing 62: 223-238.
34. GPWG (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Missouri Bot Gard 88: 373-457.
35. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
36. Hall R (2009) Southeast Asia's changing palaeogeography. Blumea 54: 148-161.
37. Harlan JR, deWet JMJ (1975) On Ö. Winge and a prayer: the origins of polyploidy. Bot Rev 41: 361-390.
38. Heaney LR (1991) A synopsis of climatic and vegetational change in Southeast Asia. Climate Change 19: 53-61.
39. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42: 182-192.
40. Hilu KW (1985) Trends of variation and systematics of Poaceae. Taxon 34: 102-114.
41. Hilu KW (2004) Phylogenetics and chromosomal evolution in the Poaceae (grasses). Aust J Bot 52: 13-22.
42. Holttum RE (1956) The classification of bamboos. Phytomorphology 6: 73-90.
43. Holttum RE (1958) The bamboos of the Malay Peninsula. Gard Bull Sing 16: 1-135.
44. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
45. Hunziker JH, Wulff AF, Soderstrom TR (1982) Chromosome studies on the Bambusoideae (Gramineae). Brittonia 34: 30-35.
46. Ishiyama H, Inomata N, Yamazaki T, Shukor NAA, Szmidt AE (2008) Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions. Can J For Res 38: 996-1007.
47. Kamiya K, Gan YY, Lum SKY, Khoo MS, Chua SC, Faizu NNH (2011a) Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae). Tree Genet Genomes 7: 297-306.
48. Kamiya K, Nanami S, Kenzo T, Yoneda R, Diway B, Chong L, Azani MA, Majid NM, Lum SKY, Wong KM, Harada K (2011b) Demographic history of Shoreacurtisii (Dipterocarpaceae) inferred from chloroplast DNA sequence variations. Biotropica. doi: 10. 1111/j. 1744-7429. 2011. 00834. x.
49. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application plant systematics. Ann Missouri Bot Gard 87: 482-498.
50. Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Mol Phylogenet Evol 8: 385-397.
51. Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 30: 259-262.
52. Kellogg EA (2009) The evolutionary history of Ehrhartoideae, Oryzeae, and Oryza. Rice 2: 1-14.
53. Kellogg EA, Appels R, Mason-Gamer RJ (1996) When genes tell different stories: the diploid genera of Triticeae (Gramineae). Syst Bot 21: 321-347.
54. Koshy KC, Jee G (2001) Studies on the absence of seed set in Bambusa vulgaris. Curr Sci 8: 375-378.
55. Levin RA, Watson K, Bohs L (2005) A four-gene study of evolutionary relationships in Solanum section Acanthophora. Am J Bot 92: 603-612.
56. Li XL, Lin RS, Fung HL, Qi ZX, Song WQ, Chen RY (2001) Chromosome numbers of some bamboos native in or introduced to China. Acta Phytotax Sinica 39: 433-442 (in Chinese).
57. Maruyama I, Okamura H, Murata G (1979) On a new hybrid genus Hibanobambusa. Acta Phytotax Geobot 30: 148-152 (in Japanese).
58. Mason-Gamer RJ (2004) Reticulate evolution, introgression and intertribal gene capture in an allohexaploid grass. Syst Biol 53: 25-37.
59. Mason-Gamer RJ, Weil CF, Kellogg EA (1998) Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 15: 1658-1673.
60. Mason-Gamer RJ, Burns MM, Naum M (2010) Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: analyses of three nuclear gene trees. Mol Phylogenet Evol 54: 10-22.
61. McClure FA (1966) The Bamboos: A fresh perspective. Harvard University Press, Cambridge, pp 1-347.
62. McKenna MCC (1973) Sweepstakes, filters, corridors, Noah's Arks, and beached Viking funeral ships in palaeogeography. In: Tarling DH, Runcorn SK (eds) Implications of continental drift to the earth sciences. Academic Press, London, pp 291-304.
63. Meijaard E, Groves CP (2006) The geography of mammals and rivers in mainland Southeast Asia. In: Lehman SM, Fleagle JG (eds) Primate biogeography. Springer, New York, pp 305-329.
64. Morley RJ (2000) Origin and evolution of tropical rainforest. John Wiley & Sons, Chichester.
65. Morley RJ (2003) Interplate dispersal paths for megathermal angiosperms. Persp Pl Ecol Evol Syst 6: 5-20.
66. Muller L (1998) Flowering and fruiting of a Gigantochloa ridleyi clone, seed germination and growth. Amer Bamboo Soc Newslett 19: 8-11.
67. Munro W (1868) A monograph of the Bambusaceae, including descriptions of all species. Trans Linn Soc Lond 26: 1-157.
68. Muramatsu M (1981) Hybridization among Bambuseae species. In: Higuchi T (ed) Bamboo production and utilization. Proceedings of the 17th IUFRO World Congress, Kyoto, Sept 6-17, 1981.
69. Ní Chonghaile G (2002) Systematics of the woody bamboos (Tribe Bambuseae). PhD thesis, University of Dublin, Trinity College, Ireland.
70. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
71. Ohrnberger D (1999) The bamboos of the world: annotated nomenclature and literature of the species and the higher and lower taxa. Elsevier Science, Amsterdam.
72. Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5: 568-583.
73. Pohl RW, Clark LG (1992) New chromosome counts for Chusquea and Aulonemia (Poaceae: Bambusoideae). Am J Bot 79: 478-480.
74. Rieseberg LH, Brunsfield SJ (1992) Molecular evidence and plant introgression. In: Soltis DE, Soltis PS, Doyle JJ (eds) Plant molecular systematics. Chapman and Hall Inc., New York, pp 151-176.
75. Rieseberg LH, Wendel JF (1993) Introgression and its consequences in plants. In: Harrison RG (ed) Hybrid zones and evolutionary process. Oxford University Press, New York, pp 70-109.
76. Roodt R, Spies JJ (2003) Chromosome studies in the grass subfamily Chloridoideae II. An analysis of polyploidy. Taxon 52: 736-746.
77. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogeny inference. Mol Biol Evol 16: 1114-1116.
78. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49: 369-381.
79. Soderstrom TR (1981) Some evolutionary trends in the Bambusoideae (Poaceae). Ann Missouri Bot Gard 68: 15-47.
80. Soderstrom TR, Ellis RP (1987) The position of bamboo genera and allies in a system of grass classification. In: Soderstrom TR, Hilu KW, Campbell CS, Barkworth ME (eds) Grass systematics and evolution. Smithsonian Institution, Washington DC, pp 225-238.
81. Soderstrom TR, Young SM (1983) A guide to collecting bamboos. Ann Missouri Bot Gard 70: 128-136.
82. Soreng RJ, Davis JI, Voionmaa MA (2007) A phylogenetic analysis of Poaceae tribe Poeae sensu lato based on morphological characters and sequence data from three plastid-encoded genes: evidence for reticulation, and a new classification for the tribe. Kew Bull 62: 425-454.
83. Stapleton CMA (1994) The bamboos of Nepal and Bhutan Part III: Drepanostachyum, Himalayacalamus, Ampelocalamus, Neomicrocalamus and Chimonobambusa (Gramineae: Poaceae, Bambusoideae). Edinburgh J Bot 51: 301-330.
84. Stapleton CMA (1997) The morphology of woody bamboos. In: Chapman GP (eds) The bamboos, vol 19. Linnean Soc Symposium Series, pp 251-267.
85. Stebbins GL (1981) Chromosomes and evolution in the Genus Bromus (Gramineae). Bot Jahrb Syst 102: 359-379.
86. Stebbins GL (1983) Cytogenetics and phylogeny in the family Poacae. Am J Bot 70: 96-97.
87. Sun Y, Xia NH, Lin RS (2005) Phylogenetic analysis of Bambusa (Poaceae: Bambusoideae) based on internal transcribed spacer sequences of nuclear ribosomal DNA. Biochem Genet 43: 603-612.
88. Sun Y, Xia NH, Stapleton CMA (2006) Relationships between Bambusa species (Poaceae, Bambusoideae) revealed by random amplified polymorphic DNA. Biochem Syst Ecol 34: 417-423.
89. Sungkaew S, Stapleton CMA, Salamin N, Hodkinson TR (2009) Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s. s. J Plant Res 122: 95-108.
90. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
91. Takahashi K, Watano Y, Shimizu T (1994) Allozyme evidence for intersectional and intergeneric hybridization in the genus Sasa and its related genera (Poaceae: Bambusoideae). J Phytogeogr Taxon 42: 49-60.
92. Taylor DJ, Piel WH (2004) An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol Biol Evol 21: 1534-1537.
93. Thompson JD (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25: 4876-4882.
94. Tran VT, Xia N, Nguyen HN, Diep MH (2012) Kinabaluchloa wrayi (Poaceae: Bambusoideae), a new bamboo record for Vietnam and a new synonym. Nordic J Bot (in press).
95. Triplett JK, Clark LG (2010) Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies. Syst Bot 35: 102-120.
96. Triplett JK, Oltrogge KA, Clark LG (2010) Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria). Am J Bot 97: 1-22.
97. Voris HK (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J Biogeogr 27: 1153-1167.
98. Widjaja EA (1987) A revision of Malesian Gigantochloa (Poaceae-Bambusoideae). Reinwardtia 10: 291-380.
99. Widjaja EA (1997) New taxa in Indonesian bamboos. Reinwardtia 11: 57-152.
100. Wong KM (1993) Four new genera of bamboos (Gramineae: Bambusoideae) from Malesia. Kew Bull 48: 517-532.
101. Wong KM (1995) The morphology, anatomy, biology and classification of Peninsular Malaysian bamboos. University of Malaya botanical monographs No. 1. University of Malaya, Kuala Lumpur.
102. Wong KM (2005) Mullerochloa, a new genus of bamboo (Poaceae: Bambusoideae) from north-east Australia and notes on the circumscription of Bambusa. Blumea 50: 425-441.
103. Wong KM (2011) A biogeographic history of Southeast Asian rainforests. In: Wickneswari R, Cannon C (eds) Managing the future of Southeast Asia's valuable tropical rainforests, Advances in Asian human-environmental research 2. Springer, Dordrecht, pp 21-55.
104. Xia NH, Jia LZ, Li DZ, Stapleton CMA (2007) Bambusa Schreber. In: Wu Z, Raven PH, Hong D (eds) Flora of China, vol 22. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, pp 9-38.
105. Yamane K, Kawahara T (2005) Intra- and interspecific phylogenetic relationships among diploid Triticum-Aegilops species (Poaceae) based on base-pair substitutions, indels and microsatellites in chloroplast noncoding sequences. Am J Bot 92: 1887-1898.
106. Yang HQ, Peng S, Li DZ (2007) Generic delimitations of Schizostachyum and its allies (Gramineae: Bambusoideae) inferred from GBSSI and trnL-F sequence phylogenies. Taxon 56: 45-54.
107. Yang HQ, Yang JB, Peng ZH, Gao J, Yang YM, Peng S, Li DZ (2008) 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 48: 809-824.
108. Yang JB, Yang HQ, Li DZ, Wong KM, Yang YM (2010) Phylogeny of Bambusa and its allies (Poaceae: Bambusoideae) inferred from nuclear GBSSI gene and plastid psbA-trnH, rpl32-trnL and rps16 intron DNA sequences. Taxon 59: 1102-1110.
109. Zeng CX, Zhang YX, Triplett JK, Yang JB, Li DZ (2010) Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Mol Phylogenet Evol 56: 821-839.
110. Zhang GZ (1985) Studies on chromosome number of some sympodial bamboos. Bamboo Research 2: 1-7.
111. Zhang GC, Chen FS (1980) No. 1 of Chenmaqing, a good bamboo hybrid. Forest Sci Technol Gansu 16(Suppl 1): 124-126 (in Chinese).
112. Zhang YX, Zeng CX, Li DZ (2012) Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol Phylogenet Evol 63: 777-797.