Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)

The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9–11 deeply divergent lineages both within and between islands, with the largest islands each containing parapatrically-distributed non-sister lineages. Population clustering and demographic analyses confirmed these genetic boundaries and suggest the occurrence of 9–10 cryptic and non-cryptic species rather than the two species currently recognized. These analyses indicate initial entry of Draco into the archipelago at 5.5–7.5 Ma, with most inter-i...