Biotic exchange leaves detectable genomic patterns in the Australian rain forest flora

The movement (or invasion) of plant lineages from Sunda (the Malay Archipelago) into Sahul (mainland Australia) has resulted in a present‐day Australian rain forest flora of mixed ancestries. Floristic integration increased during the Quaternary when continental vegetation was subjected to recurrent expansion/contraction cycles. To date, this expansion history has yet to be investigated through multi‐species, landscape‐level genetic analyses within tropical Northern Australia, presumably the main point of contact for Sunda lineages. Here, we characterize and compare the dynamics of 53 species of Sunda and Sahul ancestry co‐distributed across the Australian Tropics and Subtropics. We use whole chloroplast genomic datasets to obtain comparable measures of species‐level diversity and estimate community dynamics through time across multiple rain forest sites. Unlike Sahul‐derived species, Sunda‐derived species show consistently low genomic diversities, with recent accumulation rates for Sunda species being detected across all sites, confirming recent arrival and expansion across eastern Australia. A subset of Sunda‐derived species with continental distributions consistently exhibited highest diversity at the most northerly site sampled, suggesting north to south colonization processes. The same species, however, differed in the levels of genomic differentiation between the Tropics and Subtropics, suggesting that continental expansion occurs at different temporal scales, with some species experiencing a northern time lag before a southern expansion along the east coast of Australia.