Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades were detected: the “EA clade” comprised two species (T. standishii and T. sutchuenensis) from EA, and the “disjunct clade” comprising T. koraiensis, T. occidentalis, and T. plicata, with the first two comprising an EA–ENA disjunct pattern and T. plicata in western North America. The disjunct clade experienced a rapid radiation in the Mid–Miocene, and furthermore multispecies coalescent analysis revealed that ancient lineages of Thuja had large population sizes. These two factors m...