Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae)

•A well-resolved species tree of Chamaecyparis was constructed using target enrichment sequencing of multiple individuals per species for the first time.•Cytonuclear discordance and conflicting topologies between nuclear gene trees were detected.•Incomplete lineage sorting is the major contributor to the observed phylogenetic discrepancies.•Chamaecyparis is a Paleogene relict genus of the “boreotropical” flora.