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A genomic perspective on the conservation status of the endangered Nashville crayfish (Faxonius shoupi)

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Abstract

The Nashville crayfish (Faxonius shoupi, Hobbs 1948) was federally listed as an endangered species in 1986 due to its limited distribution in the Mill Creek watershed; this waterway lies in the rapidly developing Nashville basin and has experienced habitat degradation due to agricultural run-off, contamination, and urban development. Recovery efforts, including dam removal and restoration of riparian zones, have improved conditions in Mill Creek and F. shoupi has increased in numbers and recolonized extirpated stream segments. However, a history of demographic bottlenecks and restricted gene flow may have negatively impacted the long-term recovery of this species. A recently discovered population of F. shoupi in a disjunct segment of the Lower Tennessee River at the Pickwick Tailwater may provide an additional source of genetic variation. Uncertainty surrounding the origins of the Pickwick population and its taxonomic relationship to F. shoupi in Mill Creek raises questions about the conservation and management implications of this population. We used mitochondrial sequencing and SNP genotyping to assess genetic variation and connectivity of F. shoupi in the Mill Creek drainage and to investigate the taxonomy and demographic history of the newly discovered population at Pickwick. We found substantial genetic variation and evidence of connectivity for samples throughout Mill Creek for both mitochondrial and genome-wide SNPs. Our results also suggest a recently severed connection between crayfish in Pickwick and Mill Creek. Unique mitochondrial haplotypes and SNP variation in the Pickwick population highlight the need for prioritizing this population in future conservation and management plans for this species.

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Data Availability

Raw sequence reads obtained from GBS sequencing are available at NIH Sequence Read Archive: BioProject PRJNA817058. Mitochondrial sequences from Sanger sequencing are deposited on Genbank: Accession Numbers ON025677-ON025783.

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Acknowledgements

We thank Philip Hedrick, Jeff Simmons, David Withers and Gerry Dinkins for comments and suggestions on earlier versions of the manuscript. We would also like to thank the USFWS, Edward Lisic and the URECA Team grant program for providing partial funding for this work.

Funding

Funding for this project was provided by the USFWS and through the Undergraduate Research and Creative Activities Program (URECA) at Tennessee Tech University.

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  1. Department of Biology, Tennessee Tech University, Cookeville, TN, USA

    Carla Hurt & Parker Hildreth

  2. Tennessee Wildlife Resources Agency, Nashville, TN, USA

    Carl Williams

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Correspondence to Carla Hurt.

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Hurt, C., Hildreth, P. & Williams, C. A genomic perspective on the conservation status of the endangered Nashville crayfish (Faxonius shoupi). Conserv Genet 23, 589–604 (2022). https://doi.org/10.1007/s10592-022-01438-6

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