LAUSR

Evaluating the spatial genetic structure of rare species is important because it could provide information on the degree of habitat fragmentation and effective population size that are necessary for conservation planning. We examined the genetic structure of the grassland butterfly Plebejus argyrognomon that has severely declined in recent decades using single nucleotide polymorphisms obtained by the MIG‐seq method. The study region was in the southern Ina Basin located in central Japan, where P. argyrognomon inhabits grasslands in agricultural field margin as well as in riverbank. We found a positive association between genetic and geographic distances, but the pattern was nonlinear, with little change in genetic distance above 12 km. The genetic differentiation was considerable, as demonstrated by FST and Structure. Moreover, genetic diversity was positively associated with habitat connectivity index, suggesting severe genetic drift in isolated populations. Comparing two habitat types, the genetic structure tended to be similar among agricultural field margin populations while dissimilar among riverbank populations, suggesting frequent gene flow in the former. Coupled with the presence of many habitat patches in agricultural field margin, we consider that agricultural field margin populations in the northern part of the study sites appear valuable to ensure long‐term persistence of the regional P. argyrognomon population.