Genetic diversity and lineage divergence of Palaemon modestus in the Three Gorges Reservoir area.

To assess the genetic diversity and population structure of Palaemon modestus in the Three Gorges Reservoir (TGR), we analyzed mitochondrial COI sequences from five populations and further evaluated the two mitochondrial clades revealed by COI using Cyt b, D-loop, and nuclear 28S rDNA markers. The TGR populations showed high genetic diversity, with a haplotype diversity of 0.920 and a nucleotide diversity of 1.400%. Bayesian phylogenetic analysis and the COI haplotype network separated 54 haplotypes into TGR Clade A and TGR Clade B, with 11 mutational steps between them; Cyt b and D-loop phylogenies also supported the two-clade pattern. However, 28S rDNA sequences were identical between the clades, and ABGD assigned all COI haplotypes to a single molecular operational taxonomic unit. The overall FST among populations was 0.067; when analysis was restricted to Clade A individuals, the overall FST remained 0.064, indicating that population differentiation was not solely attributable to the uneven distribution of Clade B. Overall, P. modestus in the TGR maintains high genetic diversity and shows detectable population differentiation. The available evidence supports interpreting TGR Clades A and B as deeply divergent mitochondrial lineages within P. modestus.