Der Sarkissian C., Pichereau V., Dupont C., Schiøtte T., Ilsøe P.C., Butler P., Chauvaud L., Eiríksson J., Scourse J., Paillard C., Orlando L.., 2017 - Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Molecular Ecology Resources.DOI: 10.1111/1755-0998.12679, 1-19.

Marine mollusc shells enclose a wealth of information on coastal organisms and
their environment. Their life history traits as well as (palaeo-) environmental conditions,
including temperature, food availability, salinity and pollution, can be traced
through the analysis of their shell (micro-) structure and biogeochemical composition.
Adding to this list, the DNA entrapped in shell carbonate biominerals potentially
offers a novel and complementary proxy both for reconstructing
palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess
this potential by applying DNA extraction, high-throughput shotgun DNA sequencing
and metagenomic analyses to marine mollusc shells spanning the last
~7,000 years. We report successful DNA extraction from shells, including a variety
of ancient specimens, and find that DNA recovery is highly dependent on their
biomineral structure, carbonate layer preservation and disease state. We demonstrate
positive taxonomic identification of mollusc species using a combination of
mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic
approaches. We also find shell biominerals to contain a diversity of microbial DNA
from the marine environment. Finally, we reconstruct genomic sequences of organisms
closely related to the Vibrio tapetis bacteria from Manila clam shells previously
diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as
novel genetic archives of the past, which opens new perspectives in ancient DNA
research, with the potential to reconstruct the evolutionary history of molluscs,
microbial communities and pathogens in the face of environmental changes. Other
future applications include conservation of endangered mollusc species and aquaculture