The Indo-Burma biodiversity hotspot for ferns: Updated phylogeny, hidden diversity, and biogeography of the java fern genus (Polypodiaceae).

The Indo-Burma Biodiversity Hotspot is renowned for its rich biodiversity, including that of vascular plants. However, the fern diversity and its endemism in this hotspot have not been well understood and so far, the diversity of very few groups of ferns in this region has been explored using combined molecular and morphological approaches. Here, we updated the plastid phylogeny of the Java fern genus with 226 (115% increase of the latest sampling) samples across the distribution range, specifically those of three phylogenetically significant species, , . , and . . We also reconstructed the first nuclear phylogeny of the genus based on gene data. Based on molecular and morphological evidence, we identified three new major clades and six new subclades, redefined three existing species, discovered a number of cryptic species of the genus, and elucidated the evolution of the three most variable characters. Our divergence time analyses and ancestral area reconstruction showed that originated in the Oligocene and diversified from early Miocene and 15 dispersal events from lower to higher latitudes are identified. The evolution of three most important morphological characters is analyzed in a context of the new phylogeny. Our analysis showed that 30 (59% of total 51) species of occur in Indo-Burma hotspot, 24 (80% of the 30 species) of which are endemic to this hotspot. We argue that the Indo-Burma hotspot should be recognized as a diversity hotspot for ferns.