Contextualizing enigmatic extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders

• Published in: Conservation genetics 2022-04, Vol.23 (2), p.375-386
• Main Authors: Pyron, R. Alexander, Beamer, David A., Holzheuser, Chace R., Lemmon, Emily Moriarty, Lemmon, Alan R., Wynn, Addison H., O’Connell, Kyle A.
• Format: Article
• Language: English
• Subjects: Amphibians; Animal Genetics and Genomics; Biodiversity; Biomedical and Life Sciences; Conservation Biology/Ecology; Deoxyribonucleic acid; Desmognathus; DNA; DNA damage; DNA sequencing; Ecology; Ethanol; Evolutionary Biology; Extinct species; Extraction procedures; Genomics; Laboratory methods; Life Sciences; Mitochondria; Museums; Phylogeny; Plant Genetics and Genomics; Population decline; Populations; Research Article; Species extinction; Swamps
• ISSN: 1566-0621; 1572-9737
• DOI: 10.1007/s10592-021-01424-4

Species that went extinct prior to the genomic era are often considered out-of-reach for modern phylogenetic studies. This is particularly limiting for conservation studies, as genetic data from such taxa may be key to understanding extinction risks and causes of decline that can inform the management of related, extant populations. Fortunately, continual advances in biochemistry and DNA sequencing offer increasing ability to recover DNA from historical fluid-preserved museum specimens. Here, we report on success in recovering nuclear and mitochondrial data from the putative subspecies Desmognathus fuscus carri Neill 1951, a plethodontid salamander from spring runs in central Florida that is apparently extinct. The two ethanol-preserved topotypic specimens we studied are 50 years old and were likely fixed in unbuffered formalin, but application of a recently derived extraction procedure yielded usable DNA and partially successful Anchored Hybrid Enrichment sequencing. These data suggest that D. f. carri from peninsular Florida is conspecific with the D. auriculatus A lineage as suggested by previous authors, but may have represented an ecogeographically distinct population segment that has now been lost. Genetic data from this enigmatic disappearance thus confirm the geographic extent of population declines and extirpations as well as their ecological context, suggesting a possibly disproportionate loss from sandy-bottom clearwater streams compared to blackwater swamps. Success of these laboratory methods bodes well for large-scale application to fluid-preserved natural history specimens from relevant historical populations, but the possibility of significant DNA damage and related sequencing errors remains a hurdle to overcome.