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Dispersal ability and environmental adaptability are profoundly associated with colonization and habitat segregation of deep-sea animals in chemosynthesis-based communities, because deep-sea seeps and vents are patchily distributed and ephemeral. Since these environments are seemingly highly different, it is likely that vent and seep populations must be genetically differentiated by adapting to their respective environments. In order to elucidate dispersal ability and environmental adaptability of deep-sea mussels, we determined mitochondrial ND4 sequences of Bathymodiolus platifrons and B. japonicus obtained from seeps in the SagamiBayand vents in the Okinawa Trough. Among more than 20 species of deep-sea mussels, only three species in the Japanese waters including the above species can inhabit both vents and seeps. We examined phylogenetic relationships, genetic divergences (Fst), gene flow (Nm), and genetic population structures to compare the seep and vent populations. Our results showed no genetic differentiation and extensive gene flow between the seep and vent populations, indicating high dispersal ability of the two species, which favors colonization in patchy and ephemeral habitats. Our results also indicate that the environmental type (vent or seep) is not the primary factor responsible for habitat segregation in the two species.