Plastid phylogenomics clarifies broad-level relationships in (Orchidaceae) and provides insights into range evolution of Australasian section .

The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only section with a center of diversity in Australasia is sect. . However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within , and interspecific relationships within sect. , a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (K and 1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in , including phylogenetic evidence for the non-monophyly of sections , , , , , , , , , and . Section and sect. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of in the Early Oligocene (ca. 33.2 Ma) and sect. in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. facilitating allopatric speciation.