Abstract
Endemism is thought to be relatively rare in marine systems due to the lack of allopatric barriers and the potential for long‐distance colonization via pelagic larval dispersal. Although many species of coral reef fishes exhibit regionally restricted color variants that are suggestive of regional endemism, such variation is typically ascribed to intraspecific variation. We examined the genetic structure in 5 putatively monospecific fishes from the Indo‐West Pacific ( Amphiprion melanopus , Chrysiptera talboti , and Pomacentrus moluccensis [Pomacentridae] and Cirrhilabrus punctatus , and Labroides dimidiatus [Labridae]) that express regional color variation unique to this area. Mitochondrial‐control‐region sequence analysis showed shallow to deep genetic divergence in all 5 species (sequence divergence 2–17%), with clades concordant with regional color variation. These results were partially supported by nuclear RAG2 data. An analysis of molecular variation (AMOVA) mirrored the phylogenetic results; Φ ST values ranged from 0.91 to 0.7, indicating high levels of geographic partitioning of genetic variation. Concordance of genetics and phenotype demonstrate the genetic uniqueness of southwestern Pacific color variants, indicating that these populations are at a minimum distinct evolutionarily significant units and perhaps distinct regionally endemic species. Our results indicate that the alpha biodiversity of the southwestern Pacific is likely underestimated even in well‐studied groups, such as reef fishes, and that regional endemism may be more common in tropical marine systems than previously thought.