Shell DNA as an archive of phylogenetics, population genetics, and symbiosis in deep-sea clams

The low temperature deep-sea environment is assumed to be ideal for preservation of DNA, but this hypothesis has not been critically tested. Using deep-sea vesicomyid clams that are known to rely on their endosymbiotic bacteria for nutrition, we propose to test this hypothesis through a study of the shell DNA involving radioisotope dating to determine their age and high-throughput metagenomic analysis of the host clams and their endosymbionts. We will use current and subfossil shells to streamline a workflow of DNA extraction and data analysis including assessment of DNA yield and damage, species identification based on DNA marker genes, and phylogenetic analysis to determine their relationships with other vesicomyid clams and their symbionts. We will also assess the temporal changes in clam population genetics by comparing current and
subfossil shells. Furthermore, we aim to determine the phylogenetic position of both the clam host and endosymbiont for a species of vesicomyid known only from subfossil shells. Overall, our study is the first to explore the use of deep-sea molluscan shells as DNA archives for population genetics, phylogenetics, symbiosis, and palaeogenomics, and contributes to our understanding of deep-sea species diversity and genetic diversity –one of the key objectives of United Nations Decade of Ocean Science for Sustainable Development (2021-2030). It also allows us to test the hypothesis that deep-sea environments preserve shell DNA better than shallow-water environments.