Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep‐Sea Molluscs

ABSTRACT Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon‐dated to 1671–1135 years old before present) deep‐sea vesicomyid clam shells, including species Archivesica marissinica , A. nanshaensis and A. okutanii , using whole‐genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on‐target read recovery of UCEs from fresh soft tissue, but A. marissinica and A. okutanii , based on reads mapped with bwa‐mem2 and bbmap, exhibited characteristic post‐mortem DNA damage signals, with average 5′‐end C‐to‐T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh A. marissinica shells (maximum 1.24%). UCE‐based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target‐capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells—one of the most abundant invertebrate remains—for evolutionary, biogeographic and conservation studies.