Data from: Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

In dispersive species with continuous distributions, genetic
differentiation between local populations is often absent or subtle and
thus difficult to detect. To incorporate such subtle differentiation into
management plans, it may be essential to analyse many samples from many
localities using adequate numbers of high-resolution genetic markers.
Here, we evaluated the usefulness of dense locality sampling in resolving
genetic population structure in the ayu (Plecoglossus altivelis), a
dispersive fish important in Japanese inland fisheries. Genetic
variability in, and differentiation between, ayu populations around the
Japan–Ryukyu Archipelago were investigated in 4746 individuals collected
from 120 localities by genotyping 12 microsatellite markers. These
individuals represented the two subspecies of ayu, namely the Ryukyuan
subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and
landlocked forms of the nominotypical subspecies (P. a. altivelis) along
the archipelago. We successfully detected an absence of genetic
differentiation within the landlocked form and subtle but significant
differentiation and clear geographic patterns of genetic variation among
populations of the amphidromous form, which had been considered
genetically homogeneous. This suggests that dense locality sampling
effectively resolves subtle differences in genetic population structure,
reducing stochastic deviation in the detection of genetic differentiation
and geographic patterns in local populations of this dispersive species.
Resampling analyses based on empirical data sets clearly demonstrate the
effectiveness of increasing the number of locality samples for stable and
reliable estimations of genetic fixation indices. The genetic population
structure observed within the amphidromous form provides useful
information for identifying management or conservation units in ayu.