Refining phylogenetic hypotheses using chloroplast genomics and incomplete data sets in Lasthenia (Madieae, Asteraceae)

The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are largely endemic to the California Floristic Province of western North America and occupy a large range of habitat types. With high levels of morphological and ecological diversity, Lasthenia is a robust tool, capable of providing a natural non-model organism for answering a diverse array of ecological and evolutionary questions. Future studies would benefit greatly from a strong phylogenetic hypothesis and more molecular resources, such as the whole plastome sequence for a representative species in the genus. Over a decade ago there was a study that laid a strong foundation for a molecular phylogenetic hypothesis, however, many critical nodes still remained ambiguous. Since that study was conducted, there have emerged new statistical and biological methods to maximize the information obtained from the sequence data. With the advent of next-generation sequencing, it is now simpler than ever to obtain molecular resources for a genus, and it is possible to apply some of those molecular resources to resolving the phylogenetic relationships in Lasthenia. My research has two specific outcomes: 1) I have provided the first whole plastome in the tribe Madieae of the Asteraceae and used the plastome to analyze rates of evolution across the regions of other sequenced plastomes in the Asteraceae, and 2) Through the use of modern phylogenetic methods and incomplete data sets consisting of freely available and newly obtained sequence data, I have for the first time resolved all seven sections of the Lasthenia genus with moderate to high bootstrap support