Systematics of Buddleja (Scrophulariaceae): phylogenetic relationships, historical biogeography, and phylogenomics

Thesis (Ph.D.)--University of Washington, 2017-06Plants display incredible diversity, in morphology and spatial distribution, which can best be understood in an evolutionary context. The reconstruction of how this diversity has evolved can illuminate patterns and trends in the evolution of functionally and ecologically important traits and on how modern plant communities have formed around the globe. Case studies of individual taxa that encompass such diversity allow for thorough taxonomic sampling and detailed analysis of traits and distribution. The tribe Buddlejeae in Scrophulariaceae comprises 108 species of trees and shrubs in five genera: Buddleja, Chilianthus, Emorya, Gomphostigma, and Nicodemia. They are variable in flower color and shape, inflorescence architecture, fruit type, leaf shape and texture, and habitat preference, among other traits. They also have a wide distribution in tropical montane and subtropical regions of Africa, Madagascar, Asia, North America, and South America. Prior phylogenetic studies including the group have had limited taxonomic sampling, and evolutionary relationships between species and genera remained unknown. In Chapter 1, I infer a phylogeny for tribe Buddlejeae with extensive taxonomic sampling from all five genera and all major areas of distribution, using multiple nuclear and plastid markers. Buddleja and Chilianthus were resolved to be non-monophyletic, with Buddleja paraphyletic with respect to the other four genera. A new classification is proposed in which the other four genera are combined with Buddleja and seven sections in Buddleja are erected. Ancestral character state reconstructions show that some traits, including stamen exsertion, corolla shape, and inflorescence type, converged on similar states multiple times. The plesiomorphic trait states in Buddlejeae include capsular fruits, included stamens, white and tube-shaped corollas, and paniculate inflorescences. In Chapter 2, I infer a time-calibrated phylogeny for Buddleja, reconstruct ancestral distributions, and test for shifts in diversification rate dynamics. We found that from an ancestral distribution on continental Africa, Buddleja expanded its range to the New World, Asia, and Madagascar, one time each, in the mid to late Miocene. Long-distance dispersal or migration through northern high-latitude corridors may have allowed for these range expansions. An increase in speciation rate early in the diversification of the New World clade suggests conditions conducive to speciation in the American cordilleras. In Chapter 3, I use phylogenomic methods to infer a better-supported phylogeny for Buddleja, with particular focus on the Asian clade. Four locus sets were identified as targets for sequence capture and high-throughput sequencing. A “taxon-specific” locus set was developed using genomic and transcriptome data from two species of Buddleja. Three “general” locus sets were chosen from previous studies that used genomic data from several distantly related angiosperms. A greater number of loci were developed for the “taxon-specific” set. All sets had a very high proportion of target loci with assembled sequences for Buddleja species, but “general” sets had greater assembly for outgroup taxa. The “taxon-specific” and PPR loci had the highest average percentage of variable sites. A fully resolved and highly supported phylogeny for the Asian Buddleja clade can serve as a framework for future evolutionary studies