Unionid mussels are a key taxon for stable isotope studies of aquatic food webs, often serving as the primary integrator of the pelagic baseline. Past isotope studies with mussels have commonly used either foot tissue or mantle tissue, but no study has yet to quantify the relation of both carbon and nitrogen isotopes between these two tissue sources. This makes it difficult to justify cross-study comparisons when different tissue compartments and different species were used as the basis of food web models. Therefore, we collected foot and mantle tissues from two common mussel species, Amblema plicata and Fusconaia flava, from lotic and lentic sites in the Upper Mississippi and St. Croix rivers (Minnesota/Wisconsin). Paired tissue samples from each individual were analyzed for stable isotopes of nitrogen and carbon. There were strong relations between tissue types for both isotopes between species (r² > 0.93). Paired t-tests indicated that there were statistically significant differences between the tissue sources in some instances, but the difference (0.04–0.21‰) was less than the analytical precision of the mass spectrometer (circa 0.2–0.3‰). We conclude that the isotopic values from these two tissue sources are biologically comparable and recommend that researchers use the tissue source and extraction technique that minimizes stress to the mussels. We also tested for significant differences between species within a site for either isotope or tissue type and found no statistically significant difference between species with the exception of carbon in foot tissue at two sites. The highly correlated isotopic response supports the interchangeable use of both tissue compartments and both species. These findings support comparisons between studies whether the results were based on either of these tissues or the two species studied. Comparability will also simplify sampling designs, save time, and save money for processing samples without diminishing the usefulness of the data.

In the 20th century, Pendleton Island (PI) in the Clinch River of southwestern Virginia was a singularly important location for conservation of freshwater mussels in North America, supporting at least 45 species. Comprising 55,500 m² of available habitat, PI is the largest contiguous patch of habitat for mussels in the unregulated reaches of the Clinch River in either Virginia or Tennessee. Mussel density at PI declined by 96% from its historical baseline of 25/m² in 1979 to ∼1/m² in 2014, indicating a collapse of the fauna. We provide a quantitative description of the PI mussel assemblage collapse and establish baseline conditions for restoration scenarios. We examined long-term monitoring data collected at 15 sites in the Tennessee and Virginia sections of the river over a 35-yr period (1979–2014). While the mussel assemblage of PI has declined precipitously, density in the Tennessee section of the river has increased at an annual rate of 2.3% (1979–2004) and 1.3% (2004–14), stabilizing at a mean density of 29/m² over the last 10-yr period, a reasonable baseline density to gauge recovery and restoration at PI and at other disturbed sites in the river. Lost mussel abundance can and should be translated to ecosystem services loss at PI, representing more than 1.38 million mussels and tens of millions of lost mussel service years. When density of the PI mussel assemblage is projected forward 30 yr (2014–44), it returns to a baseline of 25/m² in 2036 only under a high-growth-rate scenario of 15% per yr. If realistic growth rate scenarios of 1% and 5% are used, density reaches 1.4/m² (∼75,000 individuals) and 4.3/m² (∼240,000 individuals), respectively, by 2044. These scenarios assume healthy nondegraded habitat conditions, which do not reflect current water and sediment quality at PI. Recovery of the assemblage to baseline densities will take decades and require active restoration of the fauna and habitat, including mussel translocations and stocking of hatchery-propagated juveniles.

High-throughput sequencing technologies, such as RNA sequencing (RNA-Seq), have greatly enhanced our ability to sequence and characterize the transcriptome of nonmodel organisms. The ability to study expression of thousands of genes in highly threatened yet understudied organisms holds great potential for advancing the field of conservation biology. Despite rapid gains in our analytical abilities and understanding of the physiological underpinnings of the organism, genomic resources remain limited for nonmodel organisms such as freshwater mussels, one of the most imperiled groups of animals worldwide. Here we provide the first characterization of the transcriptome of the North American freshwater mussel Amblema plicata (threeridge) using an RNA-Seq approach. Gill tissue samples were collected from mussels in the Muskingum River in Washington County, Ohio, USA. RNA was extracted and sequenced on the Illumina HiSeq 2500 sequencer with output as 100-base-pair paired-end reads. De novo assembly of sequenced reads was performed using Trinity. Assembled transcripts were used as BLASTx queries against the National Center for Biotechnology nonredundant database, and functional annotation using gene ontology (GO) terms was performed using Blast2GO. Transcriptome assembly produced 264,027 transcripts. Of these transcripts, 54,331 (20.58%) received BLAST hits and 22,223 were annotated with GO terms. We provide examples of identified candidate genes that may be useful for studying physiological responses of freshwater mussels to various environmental stressors, such as temperature, hypoxia, and pollutants. The A. plicata transcriptome improves the genomic resources available for freshwater mussels, and may aid in the development of molecular tools, with the ultimate goal of increasing our understanding of freshwater mussel physiology and improving conservation techniques.