Focusing on the bacterial gene(s) responsible for cellular metabolism and symbiotic relationships with other marine organisms, we are conducting phylogenetic analyses of the Vibrionaceae, a group of highly divergent marine bacteria, and other closely related bacterial species. Our research has revealed the number of luminous species in Vibrionaceae to be greater than previously thought. Our findings also show that luciferase genes in bacterial symbionts, from fish light organs, form host-dependent phylogenetic clades, which highlights the significance of symbiosis as one of the major driving forces for molecular evolution of marine luminescent Vibrios.

In Palau Archipelago, about 80 marine lakes are located and they possess marine flora and fauna. Algae and other organisms in the marine lakes are isolated geologically and genetically from those of open oceans for longer than 10,000 years. It is the center to elucidate the mechanisms of speciation and peculiar evolution of algae and phytoplankton as well as invertebrates and fishes in these closed ocean environments.

In order to reveal the evolutionary mechanism of marine invertebrates on the basis of the comparison between various deep-sea and shallow-water species, we carried out molecular phylogenetic and phylogeographic studies for some groups endemic to deep-sea reducing environments, namely, provannid gastropods, vestimentiferan tube worms, bivalves of the genera Calyotogena and Bathymodiolus, and neoverrucid barnacles as well as many shallow-water species such as tideland snails of the genera Batillaria and Cerithidea, netitiliid gastropods endemic to anchialine-caves, ostracods, and brachiopods. We also succeeded rearing of larval of a hydrothermal vent-endemic barnacle for the first time in the world. In addition, we reconstructed the phylogenetic relationships within Bilateria on the basis of the mitochondrial genome structure.

Organisms occupying higher trophic positions in marine ecosystems are mostly vertebrates, in particular fishes. Therefore, for understanding the marine biosystem, it is indispensable to elucidate the phylogenetic relationships and evolutionary history of fishes. To reconstruct the evolutionary history of the fishes, the vertebrate evolution team of this project has aimed to establish a comprehensive fish phylogeny on the basis of whole mitochondrial genome data. More than 500 complete (or nearly complete) mitochondrial genomes from purposefully chosen fish species have been sequenced so far in this project. This huge data set has been elucidating the outline of fish phylogeny, which includes many new aspects that are unexpected from the previous studies based on morphological characters. By calibrating genetic distance for the comprehensive phylogenetic tree, this team is also trying to reconstruct the fish evolutionary history along the absolute time axis. In addition to these large-scale phylogenetic studies, we are conducting some small-scale bio- and phylogeographical studies, too. Our studies of an antitropical labrid genus Pseudolabrus and island populations of some Pacific gobies have revealed ancient global migration and resultant speciation of these coastal fishes.

To understand biodiversity of marine organisms comprehensively, it is necessary to reveal the present status of biodiversity as well as to find the mechanism of creating and maintaining the diversity. Taxonomic studies on Kinorhyncha, Annelida and Nematoda have been carried out mainly for the faunae in Tanabe Bay, Central Japan have been carried out to realize the biodiversity of coastal meiobenthic organisms. So far, only one kinorhynch species has been reported from Japanese water, but 7 species inclusive of 3 new species have identified in the course of the present study. To evaluate the geographic separation for speciation of marine nematodes, existence of gene flow between two populations separated for 1 mile was studied. As a result, though it seems very difficult considering their body size, there does be a genetic exchange between these two populations. We also confirmed that biodiversity of bathyal harpacticoid copepods is very high. As a mechanism to create and maintain such a high biodiversity in the deep sea, mesoscale disturbance hypothesis is the most well appreciated. To evaluate this hypothesis, analyses of deep-sea benthic meiofauna in an experimentally disturbed area are being carried out.