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Molecular Phylogenetic Studies of the Genera of Tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum

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Molecular Phylogenetic Studies of the Genera of Tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2017 Molecular phylogenetic studies of the genera of tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum. Aaron Jennings Floden University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Evolution Commons Recommended Citation Floden, Aaron Jennings, "Molecular phylogenetic studies of the genera of tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum.. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4398 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Aaron Jennings Floden entitled "Molecular phylogenetic studies of the genera of tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum.." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Edward E. Schilling, Major Professor We have read this dissertation and recommend its acceptance: Brian O'meara, Randy Small, Sally Horn Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Molecular phylogenetic studies of the genera of tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum. A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Aaron Jennings Floden May 2017 Copyright © 2017 by Aaron J. Floden. All rights reserved. ii Acknowledgements I cannot thank my wife, Heather Floden, or express my gratitude sufficiently to her. She has helped throughout and endured my absence during my fieldwork ‘vacations’ and allowed the cultivation of some 400+ accessions of Polygonatum and relatives in the home garden all while being essentially the sole provider for us and numerous poodle rescues. I also thank family and friends for encouragement. I thank my parents for partial funding for a trip to India. Amongst my botanically and/or horticulture inclined friends I am grateful for discussions on taxonomy of numerous genera that facilitate a more inclusive understanding or species relationships, and also for comments on growth habits observed in shared divisions of the cultivated collection of Polygonatum. Foremost thanks goes to those individuals that shared discussion, field experience where I could not visit during this brief period, an interest in the genera of “Ruscaceaous” monocots, and/or for providing living material or DNA samples that led to so much confusion - some of which still exists - and clarity at once. I believe I have listed all individuals who have helped immensely though I regret some may not be listed, though their aid is gratefully acknowledged: Tony Avent and Zac Hill at Juniper Level Botanic Garden; Dr. Leonid Averyanov; Sergey Banketov; Sean Barton; Cedric Basset; Wim Boens; Pascal Bruggeman; Clint and Robin Callens; Chris Chadwell; Anne Chambers; Kelly Dodson and Sue Milliken at Far Reaches Farm; Alan Galloway; Michael Goetz; Roy Herold; Daniel Hinkley; Ellen Hornig; Josef Jurasek; Jim Kee; Karl Kristensen; Jerry Lehman; Dr. John Lonsdale; Nick Macer, Dr. J.F. Maxwell; Dr. Jamie Minnaert-Grote (Collections Manager Herbarium University of Illinois); Dr. Tom Mitchell; Johan Nilsson, Dr. William Norris (WNMU); Momjir Pavelka; Vlastimil Pilous; Koen van Poucke; Giorgio Pozzi; Kevin Pratt; David Preshler; Darrell Probst; David Scherberich; Dr. Lena Strowe; Jim Waddick; Yijia Wang; Mark Weathington at JC Rauslton Arboretum; Paige Woodward; Bleddyn and Sue Wynn-Jones; Chen Yi; Peter Zale; and especially Bjørnar Olsen for assistance in getting much of the plant material cultivated used in this study. I thank the curators of the following herbaria for digitization of specimens or for specimen loans: BM; CAS; CBD; E; HUH; K; KUN; MI; MO; NY; P; PE; US. At the University of Tennessee I thank Dr. Wofford for use of the TENN herbarium and Dr. McFarland for use of greenhouse space in seed germination studies and cultivation of samples for cytological examination. I extend my thanks to several individuals who have aided me in one way or another in accessing material, data on specimens, or in searching herbaria for additional specimens of otherwise unknown taxa – many of which are still in need of names. I thank the Hesler Fund for financial support of fieldwork in Vietnam and India. Special thanks go to Darrell Probst who funded fieldwork in China. Additionally, grateful thanks are warranted for the Chancellors Fund which provided partial funding for travel India and to China. I extend my thanks to Joe May and Veronica Brown at the University of Tennessee Molecular Biology Resource Facility for sequencing, help with resolving issues with some sequence data, and also for assistance with next-generation sequencing on the Ion Torrent platform. iii “Common experience teacheth, that in the world there is not to be found another herbe comparable to it." John Gerard, 1597. Gerard's Herball - Or, Generall Historie of Plantes, London: John Norton 1975. iv Abstract The Polygonateae (Asparagaceae) are a subtribe of the Nolinoideae that is redefined here to include three genera which are investigated here: Disporopsis; Heteropolygonatum, and Polygonatum. This group of genera, characterized by their axillary-flowered habit, are closely related but differ greatly in their morphology, cytology, and diversity. A molecular phylogeny is presented to show their relationships to one another and to closely related outgroups based on data from whole chloroplast genomes with low taxonomic sampling. The results show that the genera of the Polygonateae are each monophyletic, and also show that a fourth genus, Maianthemum, that was traditionally included in Polygonateae is not accurately placed there and should be excluded. A second set of analyses was based on an expanded dataset with high taxonomic sampling using a few selected loci from the chloroplast, mitochondrial, and nuclear genomes. The results confirmed the revised delimitation of Polygonateae that excludes Maianthemum and the respective monophyly of Disporopsis, Heteropolygonatum, and Polygonatum. Species-level relationships within each individual genus were analyzed, in part to allow assessment of the placement of many novel or obscure species that have been described (or resurrected) recently. Finally, the phylogenetic results from the expanded dataset were used to test various hypotheses regarding cytological evolution in the subtribe, and the results showed a pattern of descending (or in a few cases ascending) dysploidy that underlies the observed variation in chromosome numbers. v Table of Contents Introduction ............................................................................................................................1 References ...........................................................................................................................6 Chapter 1 The chloroplast genomes of Disporopsis, Heteropolygonatum, and Polygonatum (Asparagaceae) and comparative analysis of two widely disjunct Polygonatum species .....9 Abstract ...............................................................................................................................10 References ...........................................................................................................................28 Appendix A .........................................................................................................................36 Appendix B .........................................................................................................................36 Appendix C .........................................................................................................................37 Chapter 2 Resolving Polygonatum (Asparagaceae); a phylogeny based on molecular data from the nuclear and plastid genomes ...................................................................................41 Abstract ...............................................................................................................................42 References ...........................................................................................................................62 Appendix D .........................................................................................................................66 Chapter 3 Cytological evolution in the Polygonateae (Asparagaceae: Nolinoideae) ............86 Abstract ...............................................................................................................................87 References ...........................................................................................................................94 Appendix E .........................................................................................................................97
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