This study examined the genetic diversity and composition of 15 populations of Zostera japonica in the Hii River system, Japan. Genetic and genotypic diversity were consistently higher in populations in the Ohashi River than those in Lake Nakaumi, and the local tidal movements may explain the observed patterns of genetic diversity. Pairwise fixation index values among the populations in Lake Nakaumi were higher than among those in the Ohashi River, even though the ranges of the distances among the populations in the two locations were almost the same. The gene flow from the Ohashi River populations was important for some populations in Lake Nakaumi. The low genotypic diversity and gene flow in Lake Nakaumi seemed similar to those of marginal populations. If this low genotypic diversity and genetic differentiation were partly caused by human activities, the promotion of gene flow should be taken into account in conserving the populations in Lake Nakaumi.
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