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 Adansonia 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 were 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. [Comparative methods; Hyb-Seq; introgression; network inference; population trees; reticulate evolution; species tree inference; targeted sequence capture.]

Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

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We assessed the validity of a recently described baobab species Adansonia kilima that was suggested to be a diploid occurring in both eastern and southern Africa at high elevations within the range of the well‐known tetraploid species A. digitata. We used a combination of phylogenetic analyses and statistical comparisons of various traits (e.g., flowers, stomata, pollen, chromosome counts) to test for the presence of two continental African baobab species. Ordination of the floral features of 133 herbarium specimens from across the natural range of A. digitata, including the putative type of A. kilima and other Tanzanian accessions as previously assigned A. kilima, revealed no distinct clusters of specimens. Likewise, stomatal size and density varied greatly across the specimens examined, with no clear bimodal pattern and no obvious association with altitude. The type specimen of A. kilima was found to have a chromosome number of 2n ≈ 166, showing it to be a tetraploid, like A. digitata. Phylogenetic analysis of the ITS region showed little resolution within the African baobab clade and a lack of distinction between the A. kilima type and A. digitata regional accessions. Among the 13 haplotypes detected, no distinct haplotype representing A. kilima was identified. Based on the data at hand we conclude that A. kilima is neither cytologically nor morphologically distinct and is here reduced to synonymy with A. digitata.