Premise: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set).
The tribe Juanulloeae is composed of seven to nine Neotropical genera of lianas and epiphytic or terrestrial shrubs that exhibit a wide variety of floral morphologies and pollination syndromes. Their commonly epiphytic habit in the forest canopy and relatively infrequent flowering has resulted in few and fragmentary specimens and has complicated taxonomic study of the tribe so that many of its genera remain poorly understood. Solandra, currently included in the monotypic tribe Solandreae, is morphologically very similar to the Juanulloeae but its phylogenetic affinities are unclear. In this study, a phylogeny of the Juanulloeae and Solandra was inferred from maximum parsimony and Bayesian analyses of nuclear and plastid DNA sequences (ITS, waxy, trnT‐trnF, rps16‐trnK). Solandra was strongly supported as sister to the Juanulloeae and the two tribes are combined here under the older name Solandreae. Many genera within the group, notably Juanulloa, Markea, and Trianaea, are not monophyletic as currently circumscribed. We review the morphological characteristics of the genera and clades in light of the phylogenetic evidence presented here and highlight the need to re‐evaluate the morphological characters used to delimit genera of the tribe. On the basis of our results, we propose to (1) broaden the circumscription of tribe Solandreae to include tribe Juanulloeae, (2) recognize nine genera in the Solandreae, including the reinstatement of Poortmannia and Hawkesiophyton, and (3) make two new species‐level combinations, propose one new species‐level synonym, and designate a lectotype for Trianaea neovisae.
Increased volumes of phylogenomic data have revealed incongruent topologies in gene trees, both between and within genomes across many organisms. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here, widespread gene-tree discordance is uncovered along the backbone of Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. First, a densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of the Sanger-based topology is tested by examining a plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum. Clear incongruences between species trees generated from the supermatrix, plastome, and nuclear target-capture datasets are revealed. Discordance within the plastome and target-capture dataset are found at different evolutionary depths in three different areas along the backbone of these phylogenetic trees, with polytomy tests suggesting that most of these nodes have short branches and should be collapsed. We argue that incomplete lineage sorting due to rapid diversification is the most likely cause behind these polytomies, and that embracing the uncertainty that underlies them is crucial to depict the evolution of large and rapidly radiating lineages.
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