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The University of Southern Mississippi The Aquila Digital Community Dissertations Spring 5-2015 Phylogenetic Relationships of Samydaceae and Taxonomic Revision of the Species of Casearia in South-Central Asia Tharangamala Samarakoon University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Botany Commons, Plant Biology Commons, and the Systems Biology Commons Recommended Citation Samarakoon, Tharangamala, "Phylogenetic Relationships of Samydaceae and Taxonomic Revision of the Species of Casearia in South-Central Asia" (2015). Dissertations. 89. https://aquila.usm.edu/dissertations/89 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi PHYLOGENETIC RELATIONSHIPS OF SAMYDACEAE AND TAXONOMIC REVISION OF THE SPECIES OF CASEARIA IN SOUTH-CENTRAL ASIA by Tharangamala Samarakoon Abstract of a Dissertation Submitted to the Graduate School of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 ABSTRACT PHYLOGENETIC RELATIONSHIPS OF SAMYDACEAE AND TAXONOMIC REVISION OF THE SPECIES OF CASEARIA IN SOUTH-CENTRAL ASIA by Tharangamala Samarakoon May 2015 The flowering plant family Samydaceae was recently reinstated to include 14 genera and about 256 species of tropical trees and shrubs. Preliminary analyses of relationships in the family, however, indicated that the largest genus in the family, Casearia , is not monophyletic and that several smaller groups are probably misplaced. In order to affirm or refute those hypotheses, additional DNA sequence data with broader taxon sampling from the Old World were gathered for phylogenetic analysis. Phylogenetic inferences were drawn from parsimony, likelihood, and Bayesian analyses of plastid and nuclear DNA data. The results affirm the monophyly of Samydaceae and consistently recover four major clades, which are here circumscribed as four tribes. The results also affirm that Casearia is not monophyletic. Rather, several small genera (Samyda , Laetia sensu stricto, Hecatostemon , and Zuelania ) are nested within it. One previously recognized genus, Piparea , which is more closely related to Ryania and Trichostephanus , should be reinstated. Nomenclatural changes are presented here to bring generic circumscriptions in line with phylogenetic relationships within Samydaceae and with the proposed conservation of the name Casearia over Samyda and Laetia . A taxonomic revision of Casearia in south-central Asia, including the area from Pakistan to Burma and south from the Himalayas to Sri Lanka, is also presented. Thirteen species are ii recognized, nine of which are endemic to south-central Asia and four of which are more widespread, also occurring eastward into China, southeast Asia, and Malesia. Descriptions, taxonomic keys, and distributional maps are provided for the species. iii COPYRIGHT BY THARANGAMALA SAMARAKOON 2015 The University of Southern Mississippi PHYLOGENETIC RELATIONSHIPS OF SAMYDACEAE AND TAXONOMIC REVISION OF THE SPECIES OF CASEARIA IN SOUTH-CENTRAL ASIA by Tharangamala Samarakoon A Dissertation Submitted to the Graduate School of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: Dr. Mac H. Alford Committee Chair Dr. Kenneth J. Curry Dr. Micheal A. Davis Dr. Brian R. Kreiser Dr. Carl A. Reese Dr. Karen S. Coats Dean of the Graduate School May 2015 DEDICATION To my parents and family, who believe in me and deserve much credit for the success in my life. My caring husband Methil Karunanayake and my sweet little angels, Omandee, Kalana, and Selini, without whom this would not have been completed. iv ACKNOWLEDGMENTS First of all, I would like to convey my sincere gratitude to my committee chairman, Dr. Mac H. Alford for his reliable guidance, evaluation, and outstanding moral support I had continuously throughout this study. His enthusiasm is contagious and made me more spellbound for the plant world. On top of that, I thank him for the patience, kindness, and friendly support rendered not only as a mentor but also as a friend for me and my family. A special thanks to my committee members Dr. Kenneth J. Curry, who gave father-like advice and whose philosophical and sarcastic thinking made me think in different ways, and Dr. Brian R. Kreiser, Dr. Micheal A. Davis, and Dr. Carl A. Reese for their guidance, assistance, and critical review of this study. I would also like to convey my gratitude to Dr. Siril Wijesundara and Mr. Sunil Karunarathna and his family who helped me during field studies in Sri Lanka. I would also like to thank Daniel McNair and Jessica Douglas helping me to take photographs and scanning electron micrographs. Further, I wish to extend my gratitude to my loving, sister-like friend Liliana Hernández, who worked together with me long nights in the lab, helping me and giving moral support and sharing experiences together throughout this study. v TABLE OF CONTENTS ABSTRACT… .............................................................................................................. ii DEDICATION ............................................................................................................... iv ACKNOWLEDGMENTS .............................................................................................. v LIST OF TABLES ..................................................................................................... viii LIST OF ILLUSTRATIONS ......................................................................................... ix CHAPTER I. PHYLOGENETIC RELATIONSHIPS OF SAMYDACEAE (MALPIGHIALES) INFERRED FROM PLASTID AND NUCLEAR DNA SEQUENCE DATA ................................................. 1 Abstract Introduction Materials and Methods Results Discussion Taxonomic Treatment Key to Tribes and Genera of Samydaceae Acknowledgments Literature Cited Appendices II. PROPOSAL TO CONSERVE THE NAME CASEARIA AGAINST LAETIA AND SAMYDA (SAMYDACEAE) ..................... 48 Proposal Literature Cited III. NOMENCLATURAL NOVELTIES IN SAMYDACEAE ................. 51 Abstract Introduction Taxonomy Literature Cited vi IV. A TAXONOMIC REVISION OF CASEARIA (SAMYDACEAE) IN SOUTH-CENTRAL ASIA ............................................................. 62 Abstract Introduction Taxonomic History Materials and Methods Results Taxonomy Key to the Species of Casearia of South-Central Asia Discussion Literature Cited V. PROPOSAL TO REJECT THE NAME ANAVINGA OVATA (SAMYDACEAE) ............................................................................. 148 Proposal Literature cited VI. ENHANCING PCR AMPLIFICATION OF DNA FROM RECALCITRANT PLANT SPECIMENS USING A TREHALOSE-BASED ADDITIVE .................................................. 153 Abstract Introduction Taxonomic History Methods Results Conclusions Acknowledgments Literature Cited vii LIST OF TABLES Table 1.1 Primers used for PCR amplification and sequencing. References are given for previously published primer sequences. Primers for GBSSI were developed herein using the tools in Phytozome (Goodstein et al., 2012) across the Populus , Manihot , and Ricinus genomes. ………………………...……………….………10 1.2 Summary of parsimony statistics for individual plastid, nuclear, and combined matrices. Combined matrix contained plastid matK and ndhF , and nuclear EMB2765 and GBSSI . ...........................................................................................15 viii LIST OF ILLUSTRATIONS Figure 1.1 Flower diversity in Samydaceae. A. Tetrathylacium macrophyllum , with fleshy, 4-merous flowers arranged in spicate inflorescences. B. Ryania speciosa, with many stamens, intrastaminal staminodes (pink), and style divided at the apex. C. Casearia javitensis , with one whorl of stamens, intrastaminal staminodes, and style divided at the apex. D. Neoptychocarpus killipii , dioecious, with a fleshy, urceolate calyx. E. Samyda dodecandra , with fusion of androecium and lacking staminodes. F. Casearia tomentosa , with a single whorl of stamens and interstaminal staminodes. Scale bars = 1 cm. Photos A–D courtesy of Mac H. Alford; E courtesy of Jacqueline Salazar; and F courtesy of Dinesh Valke. ...........3 1.2 Fruit diversity in Samydaceae. A. Casearia obovalis , thick-walled, tardily dehiscent fruit. B. Casearia tomentosa , capsule with red arillate seed. C. Tetrathylacium macrophyllum , dry berry. Scale bars = 1 cm. Photos A, C courtesy of Mac H. Alford; photo B courtesy of Dinesh Valke. ...........................................4 1.3 A. Scanning electron micrograph of the flower of Casearia pitumba , showing hypanthium, introse anther dehiscence, and expanded glandular connective on the anther. B. Casearia corymbosa , showing pellucid dots and lines and deciduous teeth (reddish tips). C. Casearia graveolens , showing pellucid dots and lines and deciduous teeth. Scale bars = 2 mm. Photos A–B courtesy of Mac H. Alford. ......6 1.4 Strict consensus tree of 61 most parsimonious trees and Bayesian phylogram with branch lengths, constructed from combined plastid ( ndhF and matK ) and nuclear (EMB2765 and GBSSI ) data. L=1311, CI=61, RI=74. Jackknife values are above the branches; ML bootstrap values and Bayesian posterior probability values are shown below branches.

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