Phylogenomic discordance suggests polytomies along the backbone of the large genusSolanum

Abstract

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 First, a densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.)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.

Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

“…11 A single genus – the Solanum – accounts for nearly half of these species. 12 Nightshades grow in environments ranging from deserts to rainforests, with growth habits that vary from epiphytes to trees. The family includes four major food crops (potato, tomato, pepper, and eggplant), a host of minor food crops (including tomatillo, naranjilla, tamarillo, and groundcherry) as well as the several ornamental crops (including petunia, salpiglossis, schizanthus, and brugmansia) and weed species (Jimson weed and bittersweet).…”

Genome sequence for the blue‐flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae

“…Comparative genomic analyses of I. cyaneum and related taxa have the potential to provide new insights into the evolutionary history of Solanaceae broadly as well as the changes unique to this hummingbird-pollinated lineage. For example, phylogenomic analyses may reveal discordant gene histories, even in parts of the tree that were well supported in previous phylogenetic analyses with fewer markers (Gagnon et al, 2021). Moreover, the expansion of sequenced genomes will allow us to isolate major genomic events, such as the amplification of repetitive content, rearrangements, and the gain and loss of coding genes, which may be tied to particular morphological or ecological transitions.…”

Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae

“…Comparative genomic analyses of Iochroma and related taxa have the potential to provide new insights into the evolutionary history of Solanacaee broadly as well as the changes unique to this hummingbird-pollinated lineage. For example, phylogenomic analyses may reveal discordant gene histories, even in parts of the tree that were well-supported in previous phylogenetic analyses with fewer markers (Gagnon et al, 2021). Moreover, the expansion of sequenced genomes will allow us to isolate major genomic events, such as the amplification of repetitive content, rearrangements, and the gain and loss of coding genes, which may be tied to particular morphological or ecological transitions.…”