Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

► Topological heterogeneity is found among nDNA gene trees for annual sunflowers. ► There is a general lack of reciprocal monophyly of species among gene trees. ► Partitioned Bayesian analyses support monophyly of most annual sunflower species. ► nDNA gene trees provide an effective means for detecting recent hybridization. ► These do not effectively detect ancient hybridization even with linkage considered.