Deep phylogeny, a candidate ancestral whole-genome duplication, and gene-family evolution in Delphinieae

Delphinieae is a species-rich group in the buttercup family (Ranunculaceae) and its only lineage with complex, bilaterally symmetrical flowers, yet its early evolutionary relationships remain unresolved. To address this, we analyzed nuclear gene sequences from 54 transcriptomes, representing 40 species and two infraspecific taxa that cover all four genera of Delphinieae. Coalescent analyses consistently recovered Staphisagria as the earliest-diverging genus, followed by Gymnaconitum, with Delphinium and Aconitum as sister genera. These main intergeneric divergences occurred rapidly between 29.6 and 27.5 million years ago. Deep gene-tree conflict was concentrated around these early divergences and was best explained by incomplete lineage sorting; no clear signal of ancient hybridization was detected. Furthermore, analyses of duplicated genes and their chromosomal positions jointly supported a candidate whole-genome duplication on the Delphinieae stem lineage, with duplication ages concentrated near 52 million years ago. Two gene families involved in floral development also duplicated near this interval. For one family, corresponding copies occur in duplicated chromosome segments, and two related copies are adjacent, a pattern consistent with a large-scale duplication followed by a later local duplication. For the second family, one copy is incompletely represented in the chromosome-scale assembly, preventing a conclusive structural comparison. The candidate whole-genome duplication predates crown diversification of the living genera by more than 20 million years, indicating a prolonged interval between genome duplication and subsequent radiation.