Divergence, diversity, distance, and disequilibrium: Comparative phylogeography of six Philippine fruit bats (Chiroptera; Pteropodidae)

The Philippines is an important center of biodiversity and endemism and an ideal study sytem for evolution, diversification, and island biogeography. I used partial DNA sequences of the mitochondrial genes ND2 (∼700 bp) and cytb (∼750 bp) to investigate phylogenetic and phylogeographic patterns in six Philippine fruit bat species. Two (Cynopterus brachyotis and Macroglossus minimus) are widespread in southeast Asia, two (Ptenochirus jagori and Haplonycteris fischeri ) are endemic to but widespread within the Philippines, and two ( P. minor and Otopteropus cartilagonodus) are narrowly endemic to an island or island group. These species vary in ecology and habitat preference, making it possible to test the contribution of these factors to phylogeographic structure.; Several major patterns emerge from my analyses. In both C. brachyotis and M. minimus, a single mitochondrial lineage is present in the oceanic Philippines and is reciprocally monophyletic with respect to all lineages from other parts of Southeast Asia. Within the oceanic Philippines, substantial structure in these two species and P. jagori is associated with geographic distance between localities and between islands. In H. fascheri, O. cartilagonodus, and P. minor, multiple reciprocally monophyletic clades are associated with islands, island groups, or geologic regions within islands. Divergence times between clades are correlated with geologic history, suggesting that many islands were colonized soon after their formation; most lineages appear to be old and to have persisted with very little large-scale turnover for millions of years. Genetic diversity is high overall but is lower on small, continuously isolated islands than on islands that were part of large Pleistocene landbridge groups; diversity is weakly related to island size and degree of isolation. Ecology and habitat preference are good predictors of the degree of geographic structure in these species, but endemism, species range size, and tolerance of disturbance are not. Population sizes have probably been large throughout evolutionary history, although some populations experienced sudden population expansions during the Pleistocene. However, recent Pleistocene and Holocene climate and geographic change have been less important in structuring phylogeographic patterns in these species than deeper Pliocene and Miocene tectonic processes.