Population Genomics and Historical Demography of the Vulnerable American Elephantfish Callorhinchus callorynchus (Chimaeriformes)

ABSTRACT Holocephalans, together with sharks and rays, form the oldest lineage of jawed vertebrates, yet they remain severely understudied and basic biological knowledge is lacking for most species. The American elephantfish ( Callorhinchus callorynchus ) is a coastal holocephalan species distributed along the South American continental shelf. It is classified as Vulnerable by the IUCN Red List of Threatened Species due to a combination of extensive fishing pressure from both industrial and local artisanal fisheries, and limited regulatory oversight. To inform stock assessment and aid transnational management and conservation, we investigated population structure and genetic diversity of this species across most of its distribution using genome‐wide single nucleotide polymorphisms generated through double‐digest restriction‐site associated DNA (ddRAD) sequencing. In addition, we reconstructed the species' recent demographic history to infer potential glacial refugia during the last glacial maximum (LGM). We detected three weakly differentiated population units in Peru, Chile and Argentina. These results point to the need for country‐specific conservation, as local population depletion may lead to the loss of region‐specific genetic variation and the reduction of the species' evolutionary potential to respond to future environmental change. Demographic modelling indicated that present‐day populations possibly originated from a single Pacific refugium in northern South America, when coastal habitats were strongly reduced along the southern Pacific and Atlantic margins, followed by postglacial expansion after the LGM. Current spatial sampling did not allow robust inference of the processes shaping genetic differentiation (e.g., isolation‐by‐distance vs. isolation‐by‐environment), and future studies including denser sampling could improve our understanding of these processes across the species' range.