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It is known that environmental parameters, such as water depth, size of substrate material, and current velocity influence the organization of stream fish communities. However, few studies have investigated the effects of these parameters on sympatric freshwater eels. Here, the habitat use of two anguillid eels, Anguilla marmorata Quoy and Gaimard, 1824 and A. japonica Temminck and Schlegel, 1846, coexisting in the same river systems in Japan was investigated. It was found that the tropical species A. marmorata exclusively utilized habitats with larger substrate materials, fewer fallen leaves and less leaf detritus, higher current velocity, and lower turbidity than the temperate species A. japonica, and the distributions of the two anguillid eels were clearly segregated. Thus, when both species co-occur in the same river systems, clear flowing mainstems and tributaries are preferred habitats for A. marmorata, while stagnant muddy estuaries, backwater areas, irrigation channels, and reservoirs are preferred habitats for A. japonica. These habitat segregations were consistent through body-size increases and life-stage developments from elver to yellow eel and did not show ontogenetic shifts. The findings indicated that both species had strong habitat preferences, and these environmental parameters must be considered in the conservation of anguillid eels in sympatric zones.

Water-choice trial experiments revealed that Anguilla japonica glass eels collected in southern Japan possess strong preferences for fresh water and agricultural water.Their locomotor activity and preference for fresh water were higher and stronger, respectively, in this study when compared to previous studies conducted at lower temperatures. These results suggest that their locomotor activity and preference for fresh water is influenced by water temperature. The attraction to agricultural water indicates their upstream migration and habitat selection could be influenced by agricultural water.

Selection acting across environmental gradients, such as latitudes, can cause spatial structuring of genomic variants even within panmictic populations. In this study, we focused on the within‐generation latitudinal selection between northernmost and southernmost individuals of the North Pacific population of a tropical eel Anguilla marmorata, which shares its northernmost distribution with a temperate eel Anguilla japonica. Whole‐genome sequencing data indicated that the northernmost and southernmost individuals of A. marmorata belong to a single panmictic population, as suggested by previous studies. On the contrary, parts of genomic regions across multiple chromosomes exhibited significant genetic differentiation between the northernmost and southernmost individuals, and in these genomic regions, the genotypes of the northernmost individuals were similar to those of A. japonica. These findings suggested within‐generation latitudinal selection of A. marmorata, which might have led to genetic closeness between northernmost A. marmorata and A. japonica.

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