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1. Documenting the occurrence and habitat occupancy of rare aquatic species is an ongoing challenge for conservation. Characterization of environmental DNA (eDNA) from bulk water samples has emerged as a powerful tool to infer species presence or absence without the need to observe or handle organisms.2. Previous eDNA studies have yet to develop species-specific markers that target taxa with many potentially sympatric confamilials. Forty-one freshwater pearly mussel species (Unionidae) are found in southern Ontario, Canada, with many of these listed as threatened, endangered, or of conservation concern; however, locating populations for protection can be challenging owing to morphological crypsis and species scarcity.3. Species-specific eDNA markers were developed to target four unionid species. Following in silico and in vitro validation, markers were validated in the field by comparing eDNA results from water samples to detections based on quadrat sampling. 4. Target species were detected by eDNA sampling at all sites where they had previously been located by quadrat sampling. 5. The paired sampling design showed that species-specific markers can be designed even within speciose families, and that eDNA detection of mussels is at least as sensitive as quadrat sampling. Furthermore, detection probabilities were not affected by sampling depth, and eDNA concentrations were positively correlated with mussel densities. 6. These findings confirm that eDNA assays are a valuable complement to traditional methods for locating and managing imperilled unionid populations.

Aim The successful conservation of endangered mussel communities requires, in part, a thorough understanding of the processes that shape their distribution. Therefore, we tested the prediction that (1) the distribution of host fishes explains a significant amount of variation in mussel community composition. In addition, because mussel distribution also depends on spatial processes and environmental variables, we predicted that (2) the distribution and community composition of mussels in Ontario varies across eight contiguous watersheds, flowing into three different basins of the Great Lakes (Huron, St. Clair and Erie); and (3) environmental variables also explain part of the mussel distribution.Location Watersheds in south-western Ontario, North America, Great Lakes Region.Methods Existing data on the distribution of mussels and fishes, and environmental and spatial information were compiled. Variation partitioning with redundancy analysis was used to examine what proportion of the variation in mussels' community composition was explained by watershed (as a spatial component), environmental differences and host fish presence. Redundancy analysis for mussel abundances was used to illustrate the similarities in the distributions of mussels and fishes, and the association of differences in community composition of mussels among watersheds with certain mussel species and environmental variables.Results Host fish presence explained 44%, watershed identity 28% and environmental factors 23% of the variation in mussel species composition. However, much of the explained variation was shared among these components, and all three components together explained 55% of the total variation in species composition. Even after statistically eliminating the other explanatory variables, host fish distribution was the most important group of predictor variables, although we used a subset of relevant environmental variables because of the scale of the study.Main conclusions Our results highlight the important role played by host fishes in shaping current distributions of freshwater mussels and underscore the necessity of incorporating these relationships in conservation efforts and management actions.

The reintroduction of endangered species is a potentially useful conservation strategy, which in the case of freshwater unionid mussels, must be preceded by the successful laboratory rearing of juvenile mussels on their host fishes. However, an understanding of the genetic and environmental implications of reintroductions of artificially propagated mussels is required. Unfortunately, there is a dearth of information on these issues with respect to freshwater mussels. In general, regarding the genetic effects of reintroductions, small founder populations may lead to low heterozygosity (reduced genetic variability) in the reintroduced populations, which can make them more susceptible to extinction. Captive breeding programs may also alter the genetic composition of species through artificial selection, whether intentional or unintentional. Captive breeding may also affect an individual’s interactions with conspecifics or predators by altering behaviour. Genetic problems in reintroduced populations also have the potential to affect wild populations, particularly by reducing variability among populations of the same species and eliminating local adaptation. There is also the possibility that diseases, parasites, or exotic species may be spread when populations are relocated or augmented. Recommendations related to the minimization of these impacts are presented for freshwater mussels, with the recognition that many of the issues will require additional study.