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

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Abstract

The paleotropical woody bamboo subtribe Bambusinae has not been satisfactorily circumscribed and remains a major taxonomic problem. Genera such as Holttumochloa, Mullerochloa and Temburongia have not been confidently assigned to this subtribe. The phylogenetic relationships among genera hitherto placed in or near the Bambusinae, together with the related subtribes Racemobambosinae and Melocanninae, were investigated using three chloroplast DNA markers (rps16-trnQ, trnC-rpoB and trnD-T intergenic spacers) and a nuclear DNA marker (granule-bound starch synthase I, GBSSI) for a sample of 51 ingroup species and 2 outgroup species. Phylogenetic analyses revealed four distinct lineages among the members of the currently recognized Bambusinae: (1) the Bambusa-Dendrocalamus-Gigantochloa (BDG) complex, (2) the Holttumochloa-Kinabaluchloa clade, (3) the Dinochloa-Mullerochloa-Neololeba-Sphaerobambos (DMNS) clade and (4) Temburongia simplex. The BDG complex, which comprises the core of the Bambusinae, appears to have a complex evolutionary history as indicated by incongruence between the cpDNA and the nuclear gene topologies. Introgressive hybridization and incomplete lineage sorting are possible underlying causes for this complexity. The distinction of the climbing-scrambling bamboo lineages from the core Bambusinae and Racemobambosinae suggests directions for investigating the possible existence of further subtribes with increased taxon and geographical sampling. Possible biogeographic scenarios associated with the Holttumochloa-Kinabaluchloa clade and the DMNS clade are discussed.

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Acknowledgments

This work would have been impossible without the generous help and interest of many who helped make available the diverse array of samples used: Forest Research Centre, Sabah; Rimba Ilmu Botanical Garden, University of Malaya; South China Botanical Garden; South West Forestry College, Kunming; the Kunming World Expo; Kinabalu Park, Sabah; Brunei Forestry Department; David Bowman, Nicholas Hogarth, Shingo Kaneko, Lin Rushun, Y.W. Low, Janna Nilsson, Joan Pereira, M. Sugumaran, Cliff Sussman, Tran Van Tien and Zheng Chaohan. We are likewise grateful for comments and constructive suggestions from Lynn G. Clark (Iowa State University), Koichi Kamiya (Ehime University) and Scot A. Kelchner (Idaho State University) during the preparation of this paper. WLG was supported by a Postgraduate Fellowship of the University of Malaya. This work received funding from University of Malaya research grants FS275/2008C, PS151/2008B and PS293/2009C, and the H.M. Burkill Research Fellowship of the Singapore Botanic Gardens. This paper is dedicated to Len Muller, whose huge enthusiasm for unraveling the many mysteries of Southeast Asian and Australian bamboos has been a constant encouragement.

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Authors and Affiliations

  1. Center for Research in Biotechnology for Agriculture, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia

    W. L. Goh & S. Chandran

  2. Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia

    D. C. Franklin

  3. Laboratory of Forest Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan

    Y. Isagi

  4. Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram, 695562, Kerala, India

    K. C. Koshy

  5. Department of Forest Biology, Faculty of Forestry, Kasetsart University, Lad-Yao Jatujak, Bangkok, 10900, Thailand

    S. Sungkaew

  6. Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, Yunnan, China

    H. Q. Yang

  7. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China

    N. H. Xia

  8. Singapore Botanic Gardens, 1 Cluny Road, Singapore, 259569, Singapore

    K. M. Wong

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  1. W. L. Goh
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Corresponding author

Correspondence to W. L. Goh.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1. (DOC 27 kb)

606_2012_718_MOESM2_ESM.jpg

Supplementary material 2. Phylogram of the 50% majority-rule consensus tree from the Bayesian analyses based on the cpDNA (rps16-trnQ+trnC-rpoB+trnD-T) data (JPEG 463 kb)

606_2012_718_MOESM3_ESM.jpg

Supplementary material 3. Phylogram of the 50% majority-rule consensus tree from the Bayesian analyses based on the partial GBSSI data (JPEG 514 kb)

Appendix

Appendix

Species and GenBank accession numbers of the DNA sequences used in this paper (rps16-trnQ; trnC-rpoB; trnD-T; GBSSI). Details about the voucher reference numbers, the herbaria where deposited and the collection localities are available in GenBank.

Bambusa arnhemica F.Muell.; JN033886; JN033913; JN033941; JN033997. Bambusa bambos (L.) Voss, accession 1; FJ416342; GU390912; GU390939; GU390987. Bambusa bambos (L.) Voss, accession 2; JN033887; JN033914; JN033942; JN033998. Bambusa blumeana J.A. & J.H.Schultes; GU390903; GU390913; GU390940; GU390988. Bambusa boniopsis McClure; JN033888; JN033915; JN033943; JN033999. Bambusa burmanica Gamble; JN033889; JN033916; JN033944; JN034000. Bambusa distegia (Keng & P.C.Keng) L.C. Chia & H.L. Fung; GU390904; GU390914; GU390941; GU390966. Bambusa eutuldoides var. viridivittatta (W.T. Lin) L.C. Chia; JN033890; JN033917; JN033945; JN034001. Bambusa farinacea K.M. Wong, accession 1; FJ416341; GU390915; GU390942; GU390967. Bambusa farinacea K.M. Wong, accession 2; JN033891; JN033918; JN033946; JN034002. Bambusa gibba McClure; GU390906; GU390917; GU390944; GU390986. Bambusa grandis (Q.H. Dai & X.L. Tao) Ohrnberger; JN033892; JN033919; JN033947; JN034003. Bambusa intermedia Hsueh & T.P. Yi; JN033893; JN033920; JN033948; JN034004. Bambusa multiplex (Lour.) Raeuschel ex J.A. & J.H. Schultes; FJ416351; GU390918; GU390945; GU390969. Bambusa oldhamii Munro; JN033894; JN033921; JN033949; JN034005. Bambusa polymorpha Munro; JN033895; JN033922; JN033950; JN034006. Bambusa sinospinosa McClure; FJ416352; GU390919; GU390946; GU390970. Bambusa textilis McClure; JN033896; JN033923; JN033951; JN034007. Bambusa tuldoides Munro; GU390907; GU390920; GU390947; GU390989. Bambusa valida (Q.H. Dai) W.T. Lin; GU390908; GU390921; GU390948; GU390990. Dendrocalamus elegans (Ridl.) Holttum; FJ416344; GU390922; GU390949; GU390971. Dendrocalamus hirtellus Ridl.; FJ416362; JN033924; JN033952; JN034008. Dendrocalamus khoonmengii Sungkaew, Teerawat & Hodk.; JN033897; JN033925; JN033953; JN034009. Dendrocalamus pendulus Ridl., accession 1; HQ697855; HQ697866; HQ697877; HQ697890. Dendrocalamus pendulus Ridl., accession 2; HQ697856; HQ697867; HQ697878; HQ697889. Dendrocalamus strictus (Roxb.) Nees, accession 1; FJ416364; GU390923; GU390950; GU390972. Dendrocalamus strictus (Roxb.) Nees, accession 2; JN033898; JN033926; JN033954; JN034010. Dinochloa malayana S. Dransfield; FJ416343; GU390924; GU390951; GU390973. Dinochloa scabrida S. Dransf.; GU390910; GU390926; GU390953; GU390975. Dinochloa sp.; GU390909; GU390925; GU390952; GU390974. Dinochloa trichogona S. Dransf.; JN033899; JN033927; JN033955; JN034011. Gigantochloa apus (J.A. & J.H. Schultes) Kurz; JN033900; JN033928; JN033956; JN034012. Gigantochloa atter (Hassk.) Kurz; JN033901; JN033929; JN033957; JN034013. Gigantochloa balui K.M. Wong; FJ416359; GU390927; GU390954; GU390976. Gigantochloa latifolia Ridl.; FJ416361; GU390929; GU390956; GU390978. Gigantochloa ligulata Gamble; FJ416360; GU390928; GU390955; GU390977. Gigantochloa scortechinii Gamble, accession 1; HQ697861; HQ697872; HQ697883; HQ697897. Gigantochloa scortechinii Gamble, accession 2; HQ697864; HQ697875; HQ697886; HQ697899. Gigantochloa wrayi Gamble; FJ416365; GU390930; GU390957; GU390979. Guadua cf. chacoensis (Rojas) Londoño & Peterson; JN033902; JN033930; JN033958; JN034014. Holttumochloa magica (Ridl.) K.M. Wong; FJ416348; GU390931; GU390958; GU390980. Kinabaluchloa nebulosa (Stapf) K.M. Wong; FJ416356; GU390932; GU390959; GU390981. Kinabaluchloa wrayi (Stapf.) K.M. Wong; JN033903; JN033931; JN033959; JN034015. Maclurochloa montana (Ridl.) K.M. Wong; FJ416349; GU390933; GU390960; GU390982. Melocanna baccifera (Roxb.) Kurz; FJ416347; GU390934; GU390961; GU390983. Mullerochloa moreheadiana (F.M. Bailey) K.M. Wong; JN033904; JN033932; JN033960; JN034016. Neololeba atra (Lindl.) Widjaja; JN033905; JN033933; JN033961; JN034017. Phuphanochloa speciosa Sungkaew & Teerawat; JN033906; JN033934; JN033962; JN034018. Racemobambos gibbsiae (Stapf.) Holttum; JN033907; JN033935; JN033963; JN034019. Racemobambos hepburnii S. Dransf., accession 1; JN033908; JN033936; JN033964; JN034020. Racemobambos hepburnii S. Dransf., accession 2; JN033909; JN033937; JN033965; JN034021. Schizostachyum gracile (Munro) Holttum; FJ416353; GU390937; GU390964; GU390991. Schizostachyum zollingeri Steud.; FJ416354; GU390938; GU390965; GU390992. Soejatmia ridleyi (Gamble) K.M. Wong; FJ416355; GU390936; GU390963; GU390984. Sphaerobambos hirsuta S. Dransf.; GU390911; GU390935; GU390962; GU390985. Temburongia simplex S. Dransf. & K.M. Wong; JN033910; JN033938; JN033966; JN034022. Thyrsostachys siamensis Gamble; JN033911; JN033939; JN033967; JN034023. Yushania tessellata (Holttum) S. Dransf.; JN033912; JN033940; JN033968; JN034024.

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Goh, W.L., Chandran, S., Franklin, D.C. et al. Multi-gene region phylogenetic analyses suggest reticulate evolution and a clade of Australian origin among paleotropical woody bamboos (Poaceae: Bambusoideae: Bambuseae). Plant Syst Evol 299, 239–257 (2013). https://doi.org/10.1007/s00606-012-0718-1

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