Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the tropical Andes

The subtribe Espeletiinae (Asteraceae) is endemic to the high-elevations in the Northern Andes. It exhibits an exceptional diversity of species, growth-forms and reproductive strategies, including large trees, dichotomous trees, shrubs and the extraordinary giant monocarpic or polycarpic caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has long been recognised as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution. Here we produce the first fully resolved phylogeny of all morphological groups of Espeletiinae, using whole plastomes and about a million nuclear nucleotides obtained with an original de novo assembly procedure without reference genome, and analysed with traditional and coalescent-based approaches that consider the possible impact of incomplete lineage sorting and hybridisation on phylogenetic inference. We show that the diver...