Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan

Demographic events can shape genetic diversity through genetic drift,
often leaving a persistent signal in the genetic characteristics of
species. Rhodeus atremius suigensis is an endangered bitterling
fish endemic to the Okayama Plain, Japan. In this study, we inferred its
demographic history and genetic structure using a comprehensive analysis
of the mtDNA ND1 gene, microsatellite
markers (MS) and MHC class IIB gene. Based on
mtDNA, R. a. suigensis included two sublineages; A and
B. While the former was widely distributed, the latter was
restricted to eastern populations that were monomorphic in MHC.
Phylogenetic analysis revealed that R. a. suigensis, together
with R. a. atremius, experienced a substantial bottleneck in the
middle Pleistocene. In MS and MHC, genetic diversity was low in all
populations; ranked as the lowest among bitterling species. Bayesian
clustering suggested that two clusters of MS had been widely introgressed
in the centre of its distribution. These clusters seem to have been formed
by the disruption of the distribution in the last Pleistocene, and later
admixed by a large-scale reclamation in the Okayama Plain since the 16th
century, which triggered a decline in effective population size (Ne) in
many populations. Based on coalescence analysis, all populations reached
their lowest Ne around the middle of the 20th century.
Accordingly, R. a. suigensis seems to
have experienced two large bottlenecks in the past. While the first
bottleneck was probably due to climatic changes in the middle Pleistocene,
the second is due to anthropogenic degradation and fragmentation of
habitats in recent years.