Rapid urbanization is one of the major pressures on amphibian species. Elucidating changes in genetic structure will be useful in evaluating the effects of urbanization on amphibian populations. Our study focused on Rana japonica, which is common in complex agricultural landscapes known as satoyama, which are also under intense development pressure. We conducted landscape genetic analyses based on mitochondrial DNA haplotype frequencies of 13 breeding sites in a rapidly urbanizing area of Japan. We found several breeding sites had significantly higher F(st) values, and we also identified the barriers to gene flow between these sites. Observation of past aerial photographs revealed that these barriers coincided with the construction of man-made structures in the last few decades, suggesting that urbanization has restricted gene flow in R. japonica. Our results show that landscape genetic approaches are useful in conservation planning where rapid habitat degradation has taken place.

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Invasive carnivores often cause heavy damage to native species on small islands. Endangered Amami rabbit (Pentalagus furnessi) populations have been fragmented into a north‐isolated population (NI) and a south‐large population (SL) caused by predation pressure from the invasive small Indian mongoose (Herpestes auropunctatus) on Amami Oshima Island in southern Japan. We investigated the genetic structure of these rabbit populations to determine the effects of fragmentation. We collected rabbit feces from most of the Amami Oshima Island habitat and sequenced the mitochondrial DNA (mtDNA) control region along with its 5′‐flanking region (312 bp) and genotyped eight microsatellite DNA loci. Genetic diversity was lower in the NI than that in the SL population, and FST values between the two populations were significantly higher than zero in both the mtDNA and microsatellite DNA. Bayesian clustering analyses suggested four ancestral clusters of Amami rabbit, but clear genetic structure was not observed. A partial Mantel test supported isolation‐by‐distance but not habitat fragmentation. These results suggest that the low genetic diversity in the NI population was caused by the small population size after fragmentation; however, the difference in genetic structure between the two populations was caused by isolation‐by‐distance and the structure has been maintained.

We report on the isolation and characterization of eight polymorphic and five monomorphic microsatellites in the Amami rabbit (Pentalagus furnessi). Microsatellite polymorphism was determined using 25 individuals. There were 2-11 alleles for each polymorphic locus with heterozygosity ranging between 0.08 and 0.76. Linkage disequilibrium was not suggested between any pairs among the eight polymorphic loci. We suggest that these primers be used in future studies to monitor population size, determine dispersal patterns, and genetic diversity within and between populations of this and related species.