Using Molecular Tools to Recalibrate Freshwater Mussel Taxonomy with a Focus on Imperiled Species

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Freshwater mussels of the family Unionidae, also known as naiads, pearly mussels, freshwater clams, or unionids, are a diverse group of bivalve mollusks that are distributed on every continent except Antarctica. Approximately 300 species are known from the United States, with most of this diversity residing in rivers of the Southeast where many endemic taxa have evolved.

Figure 1. Phylogenetic tree of select freshwater mussels from North America

Figure 1. Phylogenetic tree of select freshwater mussels from North America

The Science Issue and Relevance: Accurate and precise species identification and classification provide the foundation for understanding evolution relationships, are key to identifying biogeographic processes, and facilitate the targeting of conservation programs. The ability to identify distinct evolutionary lineages objectively in some groups remains an important challenge for modern systematics research. Urgency increases for assessments involving imperiled species, particularly those fraught with taxonomic instability, because conservation efforts are typically based on species-level designations.

Freshwater mussels of the family Unionidae, also known as naiads, pearly mussels, freshwater clams, or unionids, are a diverse group of bivalve mollusks that are distributed on every continent except Antarctica. Approximately 300 species are known from the United States, with most of this diversity residing in rivers of the Southeast where many endemic taxa have evolved. This fauna is highly imperiled, with about 78% of currently recognized species considered either extinct, endangered, threatened, or of special concern. At least 10% of North American mussel taxa became extinct in the past 100 years, which is comparable to extinction rates observed in the rainforest and for other freshwater organisms. Despite the realization that native unionid populations are in peril, taxonomic uncertainties remain for many species and limit the development of effective conservation management strategies. Furthermore, the identification of many unionid species is complicated by the lack of discrete morphological characters that are useful for diagnosing species accurately, delimiting species boundaries, or determining evolutionary relationships. The conservation of remaining North American mussel populations would benefit greatly from improved methods for identification and delineation of species boundaries, which would also enable a better understanding of the biogeographic processes responsible for creating this biodiversity.

Figure 2. Photo illustrating difficulties distinguishing between federally endangered and common freshwater mussel species

Figure 2. Photo illustrating difficulties distinguishing between federally endangered and common freshwater mussel species using only external shell morphology.

Methodology for Addressing the Issue: A variety of molecular-based tools are used to test current taxonomic hypotheses at both the generic and species level. We rely primarily on mitochondrial genes to test species-level relationships and more conserved, nuclear genes for supraspecific relationships. Most recently, we’ve began employing next generation sequencing technologies. Specifically, we are using restriction site-associated DNA sequencing (RADseq) and exon capture via anchored hybrid enrichment for massively high-throughput phylogenomics. These molecular data are then analyzed within an integrative taxonomic framework, in which we consider information from multiple independent lines of evidence to resolve taxonomy and better inform conservation decisions.

Future Steps: Information produced by this research is being used to guide U.S. Fish and Wildlife Service (FWS) listing decisions and actions. In addition, the findings will help FWS understand how to adaptively manage for freshwater mussels, along with other aquatic organisms, including potential changes that may occur as a result of climate change.