Abstract
Indo-West Pacific coral reef fishes form speciose ecological communities. A biogeographicallymeaningful interpretation of diversity patterns in this region requires accurate inventories of species. Previousstudies have suggested that biogeographic scenarios for Indo-West Pacific coral reef fishes are compromisedby an unacknowledged yet substantial amount of cryptic diversity. DNA barcoding, the use of amitochondrial gene as an internal species tag for species identification, has opened new perspectives on globalbiodiversity. The present study, based on the largest DNA barcode reference library produced to date forIndo-West Pacific coral reef fishes, sheds new light on the extent of cryptic diversity and its evolutionary origin. We analyzed 3174 DNA barcodes for 805 species of coral reef fishes sampled at three different locations across the Indo-West Pacific (including 538 new DNA barcodes for 270 species sampled from New Caledonia). Among the 183 species with Indo-West Pacific distribution and multiple specimens analyzed, 78 (42.6%) were represented by two or more monophyletic lineages alternatively sorted between the sampling sites in the Indian and Pacific oceans and another 73 (40%) showed evidence of phylogeographic structure. Spatial analyses pointed to a detectable impact of geographic isolation on the emergence of cryptic diversity. The significant correlation of several life history traits to the maximum intraspecific genetic distances suggests that genetic divergence among geographically isolated cryptic lineages accumulated though mutation and genetic drift.