High-throughput degraded DNA sequencing of subfossil shells of a critically endangered stenoendemic land snail in the Aegean

Abstract

High-throughput sequencing has enabled the comprehensive genetic exploration of biological diversity, especially by using natural history collections to study hard-to-find, threatened or even extinct-in-the-wild taxa. Mollusk shells are under-exploited as a source for DNA-based approaches, despite their apparent advantages in the field of conservation genetics. More particularly, degraded DNA techniques combined with high-throughput sequencing have never been used to gain insights about the DNA preservation in land snail subfossil or historical shells. Here, we applied degraded DNA analysis on two historical shells of Levantina rechingeri, a stenoendemic Critically Endangered species that has never been found alive, in order to explore the patterns of DNA preservation on land snail shells originating from the eastern Mediterranean, as well as to infer its molecular phylogenetic placement. Our results showed that centuries to decades-old DNA from an empty shell collected in an Aegean island exhibits characteristic post-mortem damage patterns similar to those observed in ancient DNA from eastern Mediterranean terrestrial animals, setting a precedent for future museomics studies on taxa distributed in areas with similar climate. Finally, genome skimming of the empty shell allowed high coverage of multiple nuclear and mitochondrial loci, enabling the phylogenetic placement of the focal taxon, the re-evaluation of its taxonomic classification, and the revealing of a new Aegean land snail lineage, Aristena genus novum. This approach is a non-invasive way to sample DNA from threatened land snail species and suitable to study the evolutionary history of taxa with cryptic ecology, stenoendemics, or extinct-in-the-wild, as well as old museum specimens.

Keywords: Aristena genus novum; DNA preservation; Genome skimming; Helicini; Levantina rechingeri; Museomics.