One major and long-standing controversy in conifer evolution concerns the phylogenetic relationships in the subfamily Cupressoideae (Cupressaceae) between Juniperus, Cupressus and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) clade. Mao et al. reconstruct their phylogenetic relationships using transcriptome data.
All tree-building methods lend strong support for the relationship (HCX, (Juniperus, Cupressus)), despite strongly supported conflicts among individual gene trees. Rapid evolutionary divergence and incomplete lineage sorting likely acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Subsequent analyses yield a clearer picture of biogeographic history yet small changes to previous molecular dating efforts.