Phylogeny and topological incongruence in the Rubioideae (Rubiaceae)

Abstract: The work with this thesis has focused on evolutionary relationships in the Rubioideae, the most species-rich subfamily of the large and diverse coffee family (Rubiaceae). Despite considerable efforts during the last decades, uncertainty regarding several relationships in this group has remained, either as a result of unconvincing statistic support, incongruent results, or insufficient taxon sampling. Here, sequence data were obtained using both traditional and recently developed molecular methods, substantially expanding the amount of sequence data available for phylogenetic analysis within Rubioideae. Leveraging considerable amounts of data from a comprehensive sample of taxa showed to be highly effective in resolving phylogenetic relationships in the group, including its most recalcitrant parts. The results indicated that nuclear gene tree discordance at short internodes were frequently consistent with high levels of incomplete lineage sorting (ILS) owing to rapid diversification in the group. This finding may explain why some relationships have been notoriously difficult to resolve. Furthermore, while the results from coalescent simulations indicated that ILS alone can explain most of the observed cytonuclear incongruence, plastome introgression may be the more likely explanation in at least one case. Within Rubioideae the tribe Anthospermeae was studied in more detail. The phylogenetic analyses of this tribe revealed several cases and types of topological incongruence. Nevertheless, the deepest splits of the Anthospermeae phylogeny were congruent among analyses, but partly inconsistent with the traditional subtribal delimitation of the tribe. The infratribal classification of Anthospermeae was therefore partly updated. Unusual plastome features were also found within Anthospermeae, comprising large inversions and (putative) mitochondrial-to-plastome DNA transfer. With few other exceptions, plastomes across the Rubioideae tend to be highly conserved and typically conform to the canonical structure, gene content, and gene order of the majority of flowering plants.