Catches of Japanese eels have been decreasing at an alarming rate and extinction of wild stocks is of concern. Therefore, conservation of eel habitats has become increasingly important. Here, we analyzed the habitat preferences of Japanese eels using generalized linear models from the relationships between presence/absence or population density with physical environmental factors. The models suggested the characteristics of preferred habitats that should be conserved. In the tidal reaches, the densities of small eels (< 255 mm total length) at the reach scale (generally channel width × 101 in flow direction) were only correlated with riverbed gradient, with densities decreasing with increasing gradients. Within the low-gradient reaches, small eels appeared at shallow depths (about 15–30 cm) and slow-flow runs at the channel-unit scale (generally channel width × 100 in flow direction) and their preferred substrate type was gravel (< 100 mm). The densities of large eels (≥ 255 mm total length) at the reach scale were only correlated with the percentage of concrete revetment along shoreline, with their densities decreasing with increasing revetment shoreline. At the channel-unit scale, the densities of large eels were correlated only by predominant substrate type, and they appeared to prefer rock (≥ 100 mm). Few small eels were found in the non-tidal reaches; therefore, their habitat preferences were not analyzed there. By contrast, large eels were frequently distributed at the lower riverbed gradient reaches. At the channel-unit scale, the densities of large eels increased with water depth and their preferred substrate type was rock. These habitat preferences suggest diversification of habitat with growth and difference in the preferred substrate type depending on body size at the channel-unit scale. These results indicated that various environments in rivers should be preserved. In addition, we suggest the necessity to restore habitats affected by revetment. Eel habitat preferences, especially in the non-tidal reaches, also will contribute to determining what kind of cross-river structures affect eel distribution in rivers.
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