Phylogenomics and biogeography of the calamoid palms

Tropical rainforests are the most diverse terrestrial biome, but their origins remain incompletely understood. Detailed analyses of the temporal and spatial context of the evolution of old and species-rich tropical rainforest lineages have potential to yield novel insights. However, only few such analyses are currently available. The palm subfamily Calamoideae is proposed here as an appropriate study system to address this knowledge gap. It has a rich fossil record, comprises 555 species, and has a pantropical distribution with the centre of diversity in the Asia-Pacific region. There is a general understanding of its taxonomy, phylogeny, and distribution, but species-level relationships, divergence times, and biogeographic history of the subfamily are known only in vague outlines. Here, three steps were undertaken to realise the full potential of the Calamoideae for providing new insights into the origins of tropical rainforests. First, targeted sequencing of 971 genes of 75 species was conducted, resulting in a robust phylogenomic framework of the Calamoideae. Second, sequencing was expanded to 653 calamoid specimens representing 502 species (90%) of the Calamoideae, resulting in 381 species (68%) in the final species-level phylogeny after data filtering. Divergence times were estimated based on four dating strategies, indicating an Early Cretaceous age of crown Calamoideae but an Oligocene and Miocene origin of most extant species. Finally, ancestral ranges and dispersal patterns were inferred for the Calamoideae in the Asia-Pacific region following the testing of 198 biogeographic models, showing that the subfamily reached its broad distribution during the Oligocene and Miocene convergence of Australia and Asia, and that migration pathways closely followed a stepping-stone model with dispersals out of the centre and into the periphery of the Asia-Pacific region. This work represents the largest densely sampled and dated molecular phylogeny of any major pantropical rainforest lineage to date and elucidates the biogeographic history of a characteristic component of the tropical rainforests in the Asia-Pacific region in unprecedented detail. It is hoped that it will serve as a detailed framework for future comparative analyses.