Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

Premise of the study: 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is built using unpublished and publicly available Sanger sequences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). Key results: While the taxonomic framework of Solanum remained
stable, gene tree conflicts and discordance between phylogenetic trees
generated from the target-capture and plastome datasets were observed. The
latter correspond to regions with short internodal branches, and network
analysis and polytomy tests suggest the backbone is composed of three
polytomies found at different evolutionary depths. The strongest area of
discordance, near the crown node of Solanum, could potentially represent a
hard polytomy. Conclusions: We argue that incomplete lineage sorting due
to rapid diversification is the most likely cause for these polytomies,
and that embracing the uncertainty that underlies them is crucial to
understand the evolution of large and rapidly radiating lineages.