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Abstract Freshwater mussels provide important functions and services for aquatic ecosystems, but populations of many species have been extirpated. Information on biodiversity plays an important role in the conservation and management of freshwater mussels. The Xin River Basin is a biodiversity hotspot for freshwater mussels in China, with more than 43 species known, but populations of which are decreasing. Here, we quantify the diversity of freshwater mussels in the middle and lower reaches of the Xin River Basin and study the correlation of habitat characteristics and freshwater mussel diversity. Compared to the historical period, the number of species, density, and biomass of freshwater mussels decreased 33%, 83%, and 82% in the current period, respectively. Fifty two percent of recorded species were empty shells, and 14 native freshwater mussels were not found in the study area. Four species are currently listed as vulnerable species using IUCN criteria and their global status. The assemblage structure of freshwater mussels exhibits significant spatial differences, and there was a correlation with substrate and physicochemical parameters. The main tributary of the Xin River with higher freshwater mussel diversity should be established as one large protected area because the nestedness component was the main pattern of beta diversity. These results indicated freshwater mussel diversity was declining rapidly, which can help focus conservation effort for freshwater mussel biodiversity.

The Yangtze River Basin (Changjiang Basin) hosts one of the most diverse freshwater mussel assemblages on Earth. However, due to human activities this fauna is dramatically imperiled in this region, highlighting the need for urgent conservation measures. To better protect and conserve these taxa, it is crucial to understand the main drivers that control the diversity patterns, as well as the anthropogenic influence on these patterns. Here, we estimated distinct diversity metrics (i.e. species richness and alpha, gamma, and beta diversity) to analyze the spatial freshwater mussel diversity changes across 16 tributaries and lakes from the middle and lower Yangtze River Basin, in two periods: past 1962–2012 and present. For the past, mussel records were compiled from previous studies, for the present, we surveyed 565 sites for freshwater mussel presence and abundance within the 16 selected areas. We also assessed several climatic and geographical parameters to try to identify the main factors that modulate species composition across the study area. We show that from the historical to the present periods, species diversity experienced a significant decrease, registering, per river/lake, an average of 5.4 extirpations of species native to China and 3.9 of the Yangtze River Basin endemics. The gamma diversity of the whole study area and the alpha diversity of each of the studied rivers and lakes have also decreased during this period. The beta diversity values indicated a significant trend towards taxonomic homogenization over the last decades. Poyang and Dongting Lakes should be considered for protection given due to their high diversity and species loss given that nestedness in these lakes represented the main component of beta diversity.