Genetic Diversity and Population Differentiation of Yangtze Finless Porpoise in Poyang Lake

The Yangtze finless porpoise (<i>Neophocaena asiaeorientalis asiaeorientalis</i>; YFP) is the only freshwater cetacean species that remains in the Yangtze River, China. Poyang Lake is connected to the main stream of the Yangtze River, and the number of YFPs in Poyang Lake constitutes approximately half of the total species population. To implement effective conservation measures and formulate scientific genetic management strategies for the YFPs in Poyang Lake, we conducted population genetic analyses on 125 blood samples from the Poyang population and 46 tissue samples from the Anqing population, utilizing mitochondrial DNA D-<i>loop</i> and microsatellite loci. The genetic diversity analysis revealed two haplotypes in the Poyang population, with mitochondrial genetic diversity indices of Hd = 0.481 ± 0.020 and Pi = 0.00078 ± 0.00030. Microsatellite markers further demonstrated indices of Ho = 0.610 and He = 0.655. The genetic differentiation analysis indicated that the two populations exhibited moderate genetic differentiation (0.05 < Fst < 0.15). Upon excluding the dead samples from the Anqing population, the genetic differentiation between the two populations increased and the gene flow diminished. This indicated that certain dead samples from the Anqing population might have originated from Poyang Lake or had a background of Poyang Lake-Yangtze River migration and gene exchange. This finding was further corroborated by STRUCTURE analysis, which revealed genetic admixture between the two populations. We assessed the current genetic diversity of the Poyang population and its genetic differentiation from the Anqing population. This study provides fundamental data for formulating a conservation program for YFPs in Poyang Lake.