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 Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.)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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Three new species of Markea from Colombia are described and their morphological affinities and conservation status are discussed. Markea hunzikeri is different from other species of Markea because it presents a 3-lobed calyx and 3-lobed stigma. Markea huilensis shows affinity with Markea lopezii and Markea epifita, from which it differs by its exerted anthers, tubular-campanulate corolla and fruit with leathery, black, non-translucent exocarp when dry. Markea purpurea is clearly differentiated from other species in this genus by its very reduced, extra-axillary, short-pedunculate inflorescence, generally bearing one short-pedicellate or sessile flower with corolla dark purple or black inside. For new species illustrations, photographs of live plants and distribution maps are presented. As a tool for species identification of Markea, this paper is accompanied by a key to all species currently recognized in the genus. Additionally, photographs of live plants for most of the species of the genus are included.Key words: Colombia, Hawkesiophyton, Juanulloeae, Markea, Solanaceae, taxonomy ResumenSe describen tres especies nuevas de Markea para Colombia y se discuten sus afinidades morfológicas y estado de conservación. Markea hunzikeri se distingue fácilmente de otras especies de Markea por su cáliz y estigma 3-lobulados. Markea huilensis es semejante a Markea lopezii y Markea epifita, de las que se diferencia por sus anteras exertas, corola tubular-campanulada y fruto con exocarpo coriáceo, negro y no translúcido en material de herbario. Markea purpurea se diferencia fácilmente de otras especies del género por su inflorescencia muy reducida, corto pedunculada, de posición extra-axilar, generalmente con una flor cortamente pedicelada o sésil, de corola púrpura en su interior. Para las nuevas especies se presentan ilustraciones, fotografías en vivo y mapas de distribución. Como herramienta para la identificación de las especies de Markea, este artículo va acompañado de una clave para todas las especies reconocidas actualmente en el género. Adicionalmente, se incluyen fotos en vivo para muchas de las especies del género.

Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well‐sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >100 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50–100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits in Solanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades of Solanum can be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species.

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Solanum L. is one of the worlds largest and economically most important plant genera, including 1,245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >150 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50-100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits in Solanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades of Solanum can be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species.