Verbenaceae), a Molecular
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The Systematics and Evolution of Lantaneae (Verbenaceae), a Molecular Phylogenetic Approach Patricia Lu-Irving A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Richard G. Olmstead, Chair Harvey D. (Toby) Bradshaw Caroline A. E. Stromberg Program Authorized to Offer Degree: Department of Biology ©Copyright 2013 Patricia Lu-Irving University of Washington Abstract The systematics and evolution of Lantaneae (Verbenaceae), a molecular phylogenetic approach Patricia Lu-Irving Chair of the Supervisory Committee: Professor Richard G. Olmstead Department of Biology Lantaneae are a morphologically variable group of 300-400 species, representing the largest tribe within Verbenaceae. They are widespread and diverse in the new world tropics and subtropics; some members are native to Africa, and others, most notably the Lantana camara complex, have spread across the globe as noxious weeds. Complex patterns of morphological parallelism have hindered taxonomic efforts within Lantaneae, and previous molecular phylogenetic studies have failed to resolve relationships within the tribe. The lack of variability among loci commonly used to infer phylogeny at the species level in plants suggests that Lantaneae are recently radiated. With growing interest in the taxonomy of this difficult group, and growing recognition of the worldwide ecological and economic impacts of Lantana camara, there is a clear need for a well resolved phylogenetic hypothesis for Lantaneae. Species-level phylogenetic reconstruction in taxonomically complex, recently radiated lineages is a major challenge in plant systematics, and represents an opportunity to test the limitations of the molecular methods that are currently prevalent in modern systematic biology. Here, I have taken a multi-locus approach to resolve the pattern of diversification among a broad representative sample of the morphological, taxonomic, and geographic diversity of Lantaneae, demonstrating the effectiveness of the PPR gene family as phylogenetic tools. The results reveal that major genera are not monophyletic, with Lantana species belonging to two main clades, derived within a background of Lippia species. The small African genus Coelocarpum is the sister group to the tribe. Different loci reconstruct the species of Aloysia, and its affiliated genera, differently: either in a paraphyletic grade to the Lantana-Lippia complex, or as its sister group. A species tree reconstruction supports the hypothesis of sister clades. Within the Lantana-Lippia complex, fleshy fruits have evolved four times independently from dry-fruited ancestors, and are associated with higher speciation rates. At a broad scale, there is no clear pattern suggesting that fleshy fruits confer a dispersal advantage over dry fruits. My results place the origin of core Lantaneae in the Miocene, in subtropical South America, with different lineages subsequently migrating independently throughout the neotropics, into North America, and twice to Africa. University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Patricia Lu-Irving and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: ____________________________________________________ Richard G. Olmstead Reading Committee: ____________________________________________________ Harvey D. (Toby) Bradshaw ____________________________________________________ Caroline A. E. Stromberg Date:_________________________________ Contents CHAPTER I: Investigating the evolution of Lantaneae using multiple loci .................. 1 SUMMARY .............................................................................................................. 1 INTRODUCTION ..................................................................................................... 2 Background information ....................................................................................... 3 Phylogeny reconstruction using multiple, independent loci ................................. 6 MATERIALS AND METHODS ................................................................................ 8 Sampling .............................................................................................................. 8 DNA extraction, amplification and sequencing .................................................... 8 Phylogenetic analyses ....................................................................................... 10 Fruit evolution and biogeography ...................................................................... 11 RESULTS .............................................................................................................. 12 Data collection ................................................................................................... 12 Phylogenetic analyses ....................................................................................... 13 Fruit evolution and biogeography ...................................................................... 14 DISCUSSION ........................................................................................................ 15 Analyses of individual data sets ........................................................................ 16 Incongruence between loci ................................................................................ 17 Taxonomic implications ..................................................................................... 20 Fruit evolution .................................................................................................... 21 Biogeographic patterns ...................................................................................... 23 Future prospects ................................................................................................ 26 LITERATURE CITED ............................................................................................ 34 CHAPTER II: Resolving the genera Aloysia and Acantholippia within Lantaneae ... 48 SUMMARY ............................................................................................................ 48 INTRODUCTION ................................................................................................... 48 Background Information .................................................................................... 50 Objectives .......................................................................................................... 53 MATERIALS AND METHODS .............................................................................. 54 Sampling ............................................................................................................ 54 DNA Extraction, Amplification and Sequencing ................................................. 55 Alignment and Phylogenetic Inference .............................................................. 55 i RESULTS .............................................................................................................. 58 DISCUSSION ........................................................................................................ 59 Major Lineages of Aloysia and Acantholippia species ....................................... 60 Gene Tree Incongruence and Species Tree Inference ..................................... 64 Patterns of trait evolution ................................................................................... 66 Taxonomic Recommendations .......................................................................... 68 LITERATURE CITED ............................................................................................ 77 CHAPTER III: Phylogeny, fruit evolution, and diversification rates in Lantana and Lippia ........................................................................................................................ 84 SUMMARY ............................................................................................................ 84 INTRODUCTION ................................................................................................... 85 MATERIALS AND METHODS .............................................................................. 90 Data collection ................................................................................................... 90 Phylogenetic analyses ....................................................................................... 91 Diversification rates ........................................................................................... 93 RESULTS .............................................................................................................. 94 DISCUSSION ........................................................................................................ 97 Diversification rates: fleshy fruit and biogeography ........................................... 99 Taxonomic implications ................................................................................... 102 Conclusions ..................................................................................................... 104 LITERATURE CITED .......................................................................................... 110 Concluding remarks ...............................................................................................