Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean

Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009-2012) specimens with archival (1911-1926) and archaeological (2nd century BCE-15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.We thank two anonymous reviewers whose comments improved the quality of the manuscript. This work was carried out under the provision of the FARB Project (University of Bologna), the ICCAT Atlantic Wide Research Programme for Bluefin Tuna (GBYP) Data Recovery Plan, the International Governance Strategy of Fisheries and Oceans Canada (F5211-180183 and F5211-160166), and the MARES Joint Doctorate programme selected under Erasmus Mundus and coordinated by Ghent University (Grant Number: FPA 2011-0016). This work is also a contribution to the MSCA SeaChanges ITN and was part-funded by EU Horizon 2020 (Grant Number: 813383)