Abstract The loss of lateral hydrological connectivity (LLHC) in freshwater ecosystems is increasingly threatening biodiversity; however, studies reporting this situation are limited, especially those assessing multi‐measure biodiversity features at large spatial scales. Here, and using one the most threatened taxonomic groups in freshwater ecosystems, we examined the possible influence of LLHC on the species diversity, density, and biomass of mussel assemblages and the genetic diversity and structure of Nodularia douglasiae (a common and widespread native species) in the Yangtze River floodplain. Results showed that the species diversity of freshwater mussels (α and β diversity) significantly differed between the connected and the disconnected areas, with higher α diversity and lower β diversity in the connected areas. At the same time, relative abundance, density, biomass, and genetic diversity of freshwater mussels were higher in the connected areas. High genetic differentiation and low gene flow were found among the 18 analysed N. douglasiae populations, indicating that LLHC is affecting genetic structure of this particular freshwater mussel species. Overall, results indicated that river–lake connectivity is affecting freshwater mussel biodiversity. In addition, this study highlights that multi‐measure biodiversity features provide distinct information about biodiversity dynamics, and are essential to evaluate the effects of floodplain disconnection. We advocate that an integrative approach to floodplain management embracing species and genetic diversity is needed for effective biodiversity conservation in large river ecosystems.
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