Systematics of Andean Lupinus L. and the origin of L. mutabilis Sweet

This thesis contributes to the central goals of systematics - the inventory of species, building the tree of life and understanding evolutionary processes - through a descriptive taxonomic study, molecular phylogenetic analysis and morphological survey of the genus Lupinus L. Lupinus comprises ca. 290 annual and perennial species placed in the Genistoid clade of the Papilionoid legumes. In this study three new DNA sequence datasets are used to reconstruct species relationships. The new phylogeny is used to investigate character evolution, species diversification, domestication and as the basis for a new infrageneric classification. Approaches to plant species-level phylogeny reconstruction and criteria for selecting DNA sequence loci are evaluated from a theoretical standpoint, and experimental work to develop hypervariable nuclear DNA sequence loci is presented. The comparative morphology of Lupinus species is investigated and presented. This includesstudies of seed coats, cotyledons, leaves, and chromosomes. Optimisation of these data onto the 3-locus phylogeny reveals congruence between chromosome number and geographyand shows that non-digitate leaves have evolved twice independently within Lupinus. Evolutionary rates analysis is used to estimate divergence times for clades and to investigate the tempo of species diversification. Notably, a strongly supported clade representing ca. 81 Andean species is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants providing the most spectacular example of explosive plant species diversification documented to date. Lupin species have been independently domesticated as grain legume crops in the Old and New Worlds. The origins of the Andean domesticate, L. mutabilis, are investigated. Lack of resolution amongst the Andean species, attributable to exceptionally rapid species diversification, meant that the progenitor(s) of L. mutabilis could not be firmly established. However, four Andean species are tentatively identified as closely related to L. mutabilis based on morphology. A taxonomic account of these species is presented. Finally, a new infrageneric classification based on morphological diagnosability monophyly is proposed.