Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

An increasing use of genomic data has forced molecular phylogeneticists to confront gene tree discordance. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss, and the influence of incomplete sampling through assembly errors and filtering criteria. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history including interspecific gene flow. Here, we used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance.