Finding the Elusive Salamander Mussel Alive in Illinois After a Century in Obscurity

The salamander mussel (Simpsonaias ambigua) is a diminutive, thin-shelled freshwater mussel and one of the rarest mussels encountered. Unseen in Illinois for over a century, researchers used both cutting-edge genetics and tried and true searching by hand the muck under rocks in the Sangamon river to rediscover this rare species.

About the Salamander Mussel

Historically, salamander mussels were found throughout the Midwest in medium to large rivers, usually occupying mud, sand, and gravel substrates under flat or slab rocks and bedrock ledges.

Like all native freshwater mussels, salamander mussel larvae, called glochidia, require a host to attach to before metamorphosing and completing their life cycle. Larval attachment and metamorphosing on their host often occur over a matter of weeks for numerous mussel species. Once that cycle is complete, juvenile mussels slough off their host and settle into the streambed.

What makes the salamander mussel truly unique is that while other freshwater mussels have fish hosts (attaching to gills or fins), the salamander mussel only utilizes the fully aquatic salamander, mudpuppy (Necturus maculosus). Hence, the accepted common name: salamander mussel.

Mudpuppies, an Illinois-threatened species, inhabit areas with shelter like slab rock, bedrock shelves, large woody debris, and tree roots. In turn, salamander mussels also inhabit these same areas to remain in close proximity their host. Over the past several decades, salamander mussels have become increasingly rare across their range, raising concern for their future.

Presently, the salamander mussel is state-endangered and has not been collected alive in Illinois in more than a century. Frank C. Baker, a naturalist in the early 1900s and once curator of the Chicago Academy of Science, listed presumably live specimens from a handful of records collected statewide during the late 1800s and early 1900s. Salamander mussels were recorded primarily in northern and east central Illinois watersheds. Since Baker, a tremendous amount of effort has been expended trying to find this elusive species, but without success. Quite simply, salamander mussels are remarkably difficult to detect during conventional surveys given their small size (maximum 2 inches), rarity, and rather unique habitat association with large slab or flat rocks, which their salamander hosts also inhabit.

Typically, during timed-search conventional mussel surveys, we visually and tactilely (e.g., with our hands, also called “grubbing”) search the best available habitat most mussels may inhabit. Many mussel species inhabit stable sandy gravel and cobble substrates, and occasionally mud or slightly silty areas along the riverbed or banks. However, searching for salamander mussels requires a targeted sampling approach due to their propensity to inhabit beneath rock and slab materials. One concerted effort occurred in the early 2000s to survey specifically for salamander mussels with historical shell collection records, and more recently in 2024 to survey locations in Vermilion County. Mudpuppies are also an elusive species, often nocturnal, thus making detections, status assessments and updating distributions difficult (Matson, 2013, Collins et al., 2019).

Finding Rare Organisms Using eDNA

Both historically and contemporarily, the mussel and their salamander host both remain difficult to detect via conventional means. As such, emerging technologies and methodologies such as environmental DNA (eDNA) as a survey tool to detect rare freshwater species have shown promise. Environmental DNA is trace amounts of DNA that all organisms leave behind in the environment. Using forensic techniques and modern genetic technologies, we can harness that DNA to detect species sight unseen. Finding threatened or endangered freshwater mussels with eDNA has resulted in successful live captures of mussel species with more unique habitat requirements, like the spectaclecase (Cumberlandia monodonta) that shelters under rocks, and helped assess other rare species’ distributions. Buoyed by these mussel eDNA studies, and particularly one with the salamander mussel conducted by a team at Fisheries and Oceans Canada, partially led to interest in utilizing eDNA methodologies for this species in Illinois. Similarly, mudpuppy eDNA research has been successfully conducted in nearby states, but not yet in Illinois. Thus, we were interested in employing eDNA methodologies for both species to help assess distributions in tandem.

Our programs at the Illinois Natural History Survey, the Collaborative Conservation Genomics Laboratory (CCGL; Mark Davis) and the Freshwater Mollusk Ecology and Conservation Lab (Sarah Douglass), have engaged in various eDNA projects and recently joined forces on an environmental DNA (eDNA) project focused on the salamander mussel and mudpuppy occurring in east central Illinois. A summer undergraduate research fellow, Savanna Palmer, had sampled and completed an analysis of eDNA for salamander mussel and mudpuppy at several sites in the upper Sangamon River for her project in the University of Illinois 2024 Summer Research Opportunity Program. Her results revealed one positive detection of the salamander mussel and several positive detections of mudpuppy. These results offered a most excellent opportunity for a collaborative mussel sampling effort.

Sampling the Sangamon

On a crisp autumn morning, we donned waders and wetsuit gear (and sock hats!) before slipping into the still waters of the Sangamon River. Cement slabs placed for bank stabilization lined the streambank, and we knew to target that area.

Slab habitat, whether artificial or natural, like bedrock or shale, is challenging to sample regardless. Often, two to three people are necessary to help lift and hold the slab upright while one or two samplers search the area underneath the slab when sampling specifically for salamander mussels. Sometimes, the areas under the rocks are large enough to stick your hand or arm in but often are limited in maneuverability. It’s almost guaranteed you’ll run into some type of unexpected creature, but usually not the one you’re hoping for. Little catfishes, such as stonecats or bullheads, and crayfish all use these spaces for shelter. One will hear the occasional shriek from these encounters. I (Sarah) have been pinched by crayfish, stabbed by the barb of a stonecat and nibbled on by other fish. However, when you suspect you encountered a mudpuppy (which feels like a wet lasagna noodle) and when you finally find the mussel species you’re looking for, it is so worth it.

We found 12 individuals after searching for approximately 7 person hours. The mussels were in groupings of one to five individuals under several large slab-type cement material. Each individual was marked with unique shellfish ID tags, swabbed for genetic analysis, and aged. After processing, mussels were returned to their respective habitats. Two specimens were kept as vouchers, the first in more than a century, for the Illinois Natural History Survey Mollusk Collection.

The Value of eDNA

This remarkable finding has already sparked additional research, including a more extensive eDNA survey of the Sangamon River, in hopes of finding additional populations. We are also sampling this site every two weeks, to learn more about the activity patterns of both the salamander mussel and the mudpuppy. But the bigger picture is that our observation illustrates the immense value of eDNA to concentrate efforts and taxonomic expertise for our rarest segments of biodiversity. In this case, eDNA prompted a targeted search that yielded live salamander mussel individuals for the first time in more than a century, despite persisting in a state with perhaps the most detailed and comprehensive biodiversity inventory in all the world.

And perhaps above all, this finding reminds us that species that are thought to have been lost can be found again.

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Sarah Douglass is a malacologist who specializes in freshwater mussels for the Illinois Natural History Survey (INHS) in the Prairie Research Institute (PRI) at the University of Illinois Urbana-Champaign. Her primary work in the Urban Biotic Assessment Program involves conducting biological assessments of rare and threatened freshwater mollusks in areas slated for construction activities within Tollway corridors in northern Illinois. Her broad research interests include the conservation of freshwater mussels and riverine ecosystems, environmental DNA, and community science. Sarah pursues additional research projects with native and non-native mollusks as time and funding allows. Originally a Hoosier, Sarah completed her undergraduate degree in Biology at Hanover College, Hanover, Indiana and a masters in Environmental Science at Taylor University, Upland, Indiana.

Mark Davis is a Conservation Biologist and Director of the Collaborative Conservation Genomics Laboratory at the Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, since 2012. He has a B.S. and a M.S. in Zoology from North Dakota State University (Fargo), a M.S. in Ecology from Colorado State University (Fort Collins), and Ph.D. in Natural Resources and Environmental Sciences from the University of Illinois Urbana-Champaign. His research over the past decade leverages cutting-edge genetic and genomic tools in a highly collaborative and interdisciplinary way to measure and monitor biodiversity, understand the extinction process and inform management interventions with the goal of extending the evolutionary trajectories of imperiled species into the future. Though he works on a broad array of taxa, spanning microbes, plants, invertebrates, and vertebrates, Davis has an inordinate fondness for those often maligned, overlooked, and underappreciated species, including snakes, bats, salamanders, and, yes, freshwater mussels.