Baobabs (Adansonia) are a cohesive group of tropical trees with a disjunct distribution in Australia, Madagascar, and continental Africa, and diverse flowers associated with two pollination modes. We used custom targeted sequence capture in conjunction with new and existing phylogenetic comparative methods to explore the evolution of floral traits and pollination systems while allowing for reticulate evolution. Our analyses suggest that relationships in Adansonia are confounded by reticulation, with network inference methods supporting at least one reticulation event. The best supported hypothesis involves introgression between A. rubrostipa and core Longitubae, both of which are hawkmoth pollinated with yellow/red flowers, but there is also some support for introgression between the African lineage and Malagasy Brevitubae, which are both mammal-pollinated with white flowers. New comparative methods for phylogenetic networks were developed that allow maximum-likelihood inference of ancestral states and applied to study the apparent homoplasy in floral biology and pollination mode seen in Adansonia. This analysis supports a role for introgressive hybridization in morphological evolution even in a clade with highly divergent and geographically widespread species. Our new comparative methods for discrete traits on species networks are implemented in the software PhyloNetworks.

Supplementary Tables and Figures: FigureS1.AssemblyPipeline.pdf FigureS2.HaplotypeHeatmap.png FigureS3.SVDQ.pdf FigureS4.HH_Networks.pdf FigureS5.TaxonSelectionNetworks.pdf FigureS6.PlastidTrees.pdf FigureS7.ase.pdf TableS1.Accessions.xlsx TableS2.PlastomeAssembly.xlsx TableS3.ModelSummary.xlsx Data Files: Data_S1.TargetedSequenceCaptureBaits.Adansonia.fasta primary_dataset_372.nexus.tar - Nexus alignments for the primary dataset of 372 genes 372_MLtrees.tar - RAxML gene trees from primary dataset used for the phylogenetic comparative methods. Branch lengths in substitutions/site were used calculate pair-wise genetic distances between taxa to calibrate the primary networks HapHunt_subsets.nexus.tar - Nexus alignments for the haplotype datasets