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Sawai Mattapha Sawai Mattapha The Systematics of tribe Millettieae (Leguminosae-Papilionoideae) A Thesis submitted by Sawai Mattapha For the degree of Doctor of Philosophy School of Biological Sciences The University of Reading January 2017 to my parents i Declaration I confirm that this is my own work and the use of all material from other sources has been properly and fully acknowledged. Sawai Mattapha ii Abstract The tribe Millettieae belongs to the family Leguminosae. As traditionally circumscribed it comprises approximately 45 genera and over 900 species distributed pantropically and in subtropical regions. Previous phylogenetic studies revealed that many genera in the tribe are not monophyletic. The most problematic genus is the massive genera Millettia. Various authors have attempted to clarify generic circumscription since the genus was established in 1834. This thesis attempts to clarify the phylogenetic relationships of doubtfully placed genera of the tribe Millettieae, with the emphasis on the polyphyletic genus Millettia and its closed allies. Forty-five genera placed in the Millettioid s.l. were sampled for phylogeny reconstruction, representing 22 genera putatively part of the Core Millettieae, 17 genera from the Basal millettioid & phaseoloid group (BMP) of the Millettioid s.str. Group, and six genera from the IRLC Clade. Phylogenetic relationships are reconstructed in this study using Maximum Likelihood and Bayesian analysis. Three DNA markers were used in the study, which included published and newly-generated sequence data. In total, there were 361 sequences of the ribosomal nuclear DNA (nrDNA) ITS region; a combined chloroplast (matK+trnL-F) included 306 individuals, and the total evidence analysis (ITS+matK+trnL-F) included 436 individuals. The Maximum Likelihood and Bayesian analyses which produced comparable phylogenies are largely congruent. The total evidence phylogeny supported the monophyly of genera in Millettioid s.str. Group, namely Antheroporum, Apurimacia, Chadsia, Leptoderris, Mundulea, Philenoptera, Piscidia, Platysepalum, Pongamiopsis, Pyranthus, Solori, Sylvichadsia and Tephrosia, while others were not monophyletic and need to be re-evaluated, namely Dahlstedtia, Deguelia, Derris, Fordia, Lonchocarpus, Millettia, Muellera, Ptycholobium and Requienia. Genera with uncertain placement that now more robustly placed are: Antheroporum and Disynstemon in the Basal Millettioid and phaseoloid group (BMP), and Deguelia, Fordia, Leptoderris, Platysepalum and Sylvichadsia in the Core Millettieae. In case of genus Millettia, all sequences were distributed between Group 1 and Group 2 of the Millettioid s.str. Group, groups which correspond with the Canavanine Group and the Non-canavanine Group. Within these groups eleven subgroups were recognized. iii The distribution of canavanine, a Non-Protein Amino Acid Accumulating (NPAAA), is explored by means of a literature review, in the light of the new phylogenetic hypothesis. The investigation found three species without canavanine in the Canavanine Group, and two species with canavanine in the Non-canavanine Group. Consequently, these groups are considered whether to retain old names or proposed possible alternative names. In order to retain the monophyletic Derris, a need for a new combination and a new name for Millettia pachycarpa Benth. was identified. Here Derris lithocarpa (Benth.) Mattapha & Hawkins, com.nov. et nom.nov. is proposed. In relation to this, a new species of Derris from Thailand is newly described as Derris constricta Mattapha & Hawkins, sp.nov. Furthermore, three new species Millettia are also newly described, two species from Thailand namely M. calcicola Mattapha & Hawkins, sp.nov. and M. khaoyaiensis Mattapha & Hawkins, sp.nov. and another species from Vietnam, M. fulva Mattapha, Forest & Hawkins, sp.nov. However, the generic placement for these new species might yet prove to be provisional, since generic limits remain unsatisfactory. iv Acknowledgements I would like to express deepest thankfulness to my advisors professor Julie Hawkins and Dr. Felix Forest for their kind encouragement and valuable guidance extended to me. Professor Pranom Chantaranothai, my master degree supervisor at Khon Kaen University in Thailand, Brian Schrire at Kew, UK, and Frits Adema at Leiden, the Netherlands, are gratefully acknowledged to for their inspiration to work on family Leguminosae, particularly tribe Millettieae, before starting to the PhD study at University of Reading. I am highly indebt to Biological School of University of Reading, UK, for the facilities providing in the laboratory. I also grateful thank to staff and curator of BK, BKF, BM, E, K, KKU, L P and QBG for allowing me to observe and loan specimens. My thanks and appreciations go to my technician and colleagues, namely Steve Ansell, Rhama Alshamrani for kindly assisting me in molecular laboratory Biological School, University of Reading and to Edith Kapinos Jodrell Laboratory, Royal Botanic Gardens, Kew, for aiding the DNA extraction. Special thanks to BKF herbarium staff, Arthit Kamgamnerd and Sukid rueangruea who are skillfully rendered for the beautiful illustrations in Chapter 5. Yotsawate Sirichamorn is sincerely thanked for dry samples of Millettia spp. and specimens on loan to Reading herbarium (RNG) and for sharing his DNA sequences of genera Afgekia, Callerya, Derris and Wisteria. Additionally, I would like to thank Sue Mott at Reading herbarium (RNG), Odile Poncy at Paris herbarium (P), Gwilym Lewis, Ruth Clark, Lulu Rico at Kew herbarium (K) for their help the facilities in various ways. Fieldwork in Thailand was undertaken with the help of Dr. Somran Suddee and his staff of Bangkok herbarium (BKF), and PhD students under supervision of Professor Pranom Chantaranothai. This PhD study was financially funded by Udon Thani Rajabhat University, Thailand which provided me great opportunities to study at University of Reading. Ultimately, I wish to express my deepest gratitude to my family, my wife, daughter and parents who encourage, motivate and support various ways to complete this thesis without any condition. v TABLE OF CONTENTS Contents Page Declaration…………………………………………………………………………………………………… i Abstract…………………………………………………………………………….…………………………. ii Acknowledgements……………………………………………………………………………………... iv Table of contents………………………………………………………………….………………………. v List of Tables……………………………….………………………………………….……………………. ix List of Figures………………………………….……………………………………………………………. xi Appendices ………………………………………………………………………………………………….. xiv The Electronic Supplementary Data……………………………………………………………… xv Chapter 1 Introduction…………………………………………………………………………………. 1 1.1 An overview of the family Leguminosae………………………….……….. 1 1.1.1 The Leguminosae…………………………………………………………………. 1 1.1.2 Ecology and Distribution………………………………………………………. 8 1.1.3 Economic Botany………..……………………………………………………….. 9 1.2 Delimitation and subdelimitation of tribe Millettieae………………. 10 1.2.1 Historical taxonomic delimitation of tribe Millettieae………….. 10 1.2.2 Phylogenetic insights into the delimitation and subdivision of tribe Milletieae………………………………………………………………… 14 1.3 Infrageneric classification & regional treatment of the genus Millettia s.l………………………………………………………………………………… 28 1.3.1 Global treatments…..…………………………………………………………… 28 1.3.2 African and Madagascan treatments……..……………………………. 30 1.3.3 Asian treatments………………………….…………………………………….. 31 1.3.3.1 The British Indian and Burmese regions………………….…. 31 1.3.3.2 Malesian region………………………………………………………… 31 1.3.3.3 Indo-Chinese and Chinese regions…………………………….. 32 1.4 Studies of genera, other than Millettia, in the Millettieae………… 34 1.5 Structure of this thesis work……..……………………………………………… 36 Chapter 2 A new phylogenetic hypothesis for the Millettioids and allies to investigate the circumscription of genus Millettia………………………… 38 2.1 Introduction…………………………………………………………………………..… 38 vi 2.2 Materials and Methods………………………………………………………….. 39 2.2.1 Taxonomic sampling……………………………………………………………. 39 2.2.2 Molecular methods…………………………………………………………….. 40 2.2.3 Sequence handling and phylogenetic analysis…………………….. 40 2.3 Results….…………………………………………………………………………………. 41 2.3.1 Alignment statistics…………………………………………………………….. 41 2.3.2 The phylogenies………………………………………………………………….. 42 2.4 Description of phylogenies and comparison to existing hypotheses of relationships…………………………………………………….. 43 2.4.1 Higher-level relationships……………………………………………………. 43 2.4.2 Genera outwith the Millettioid s.str. clade………………………….. 60 2.4.3 The Core Millettieae comprises two sister clades……………….. 61 2.4.4. The Core Millettieae: genera other than Millettia………………. 62 2.4.5 The Millettioid clade: placement of Millettia species …………. 78 2.5 Conclusions……………………………………………………………………………… 86 2.5.1 Future perspectives for the tribe Millettieae ……………………… 86 2.5.2 Taxonomic implications for the future classification of 86 Millettia……………………………………………………………………………… 2.5.3 Integrating the new phylogenetic hypothesis presented here with other data sets……………………………………………………. 88 Chapter 3 Informal groups in the “Core Millettieae”: a review of the occurrence of the non-protein amino acid canavanine in the light of a new phylogenetic hypothesis………………………………………………… 89 3.1 Introduction……………………………………………………………………………… 89 3.2 Materials and Methods…..………………………………………………………… 92 3.2.1 Phylogenetic tree…………………………………………………………………. 92 3.2.2 Survey of literature………….…………………………………………………… 92 3.2.3 Ancestral state reconstruction……………................................. 92 3.3 Results……………………….…………………………………………………………….
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