Although many workers have investigated the ecological and evolutionary significance of cryptic organisms and short-term (seasonal to annuals) fluctuations in environments and fauna within submarine caves, no studies have examined millennia-scale variations in the organisms and environments. In this study, we analyzed the sedimentary characters and species composition of bivalves from surface and cored sediments within the Daidokutsu submarine limestone cave on the fore-reef slope of Ie Island, off the island of Okinawa, Japan. The sediments in the central and innermost area of the cave consist of carbonate mud. Their deposition indicates that a still-water environment prevailed over the past 5,000 years. Analysis of the spatial and temporal distribution of the bivalves shows that species living in the innermost area of the cave became dominant over at least the past 5,000 yrs, while species living near the entrance of the cave declined in abundance. This indicates that the environmental conditions of the innermost cave area gradually spread to the entrance of the cave. We believe that this phenomenon is explained by spreading nutritional deficiency within Daidokutsu cave.
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