Conclusions
Unlike reduced-representation approaches (Andrews, Good, Miller, Luikart, & Hohenlohe, 2016), low depth whole-genome resequencing allows for sequencing in smaller batches, which can be very cost-effective, besides having a much lower turnover time, allowing for a flexible project design. In this study, we took advantage of state-of-the-art bioinformatic tools to extract information from low depth sequencing data, which enabled us to assess patterns of genetic variation across the genome of the European sardine. We were able to show how different parts of the nuclear genome yield population structure and diversity patterns congruent with those observed in previous studies that were seemingly contradictory. This approach also recovers full mitochondrial genomes for comparison with genetic sequences with different modes of inheritance, also previously highlighted as being essential for a complementary insight on sardine population history (Gonzalez & Zardoya, 2007).
Our main results provide evidence for three main genetic clusters of sardine populations across the analyzed specimens, suggesting at least two important barriers to gene flow. Although these do not seem complete, with gene flow possibly occurring between the three main phylogeographic regions identified, they are strong enough to maintain populations genetically differentiated following their own evolutionary trajectory. Our results thus offer an important baseline for further studies trying to identify the nature of these and other possible barriers between sardine populations, which can be compared with the phylogeographic patterns of other organisms with a similar distribution. Finally, the differentiation patterns reported here together with the genetic resources generated for this commercially important taxon, offers precious information for transnational stock management of this highly exploited species towards sustainable fisheries.
Acknowledgments
All figures were edited in Inkscape (http://www.inkscape.org/). Thanks to Alessandro Laio, Amélia Fonseca, Ludovic Dickel, Patrícia Campos, Sara Rocha, Yorgos Athanasidis, for supplying tissue samples. We would also like to thank Anders Albrechtsen, Katherine Richardson, Lounes Chikhi, Jonas Meisner, Jørgen Bendtsen, Rasmus Heller, Ricardo Pereira, and Stephen Sabatino for advice. The authors gratefully acknowledge the following for funding their research: Villum Fonden Young Investigator Grant VKR023446 (R.D.F.); Fundação para a Ciência e a Tecnologia (FCT), Portugal, Scientific Employment Stimulus Initiative, grants CEECIND/00627/2017 to E.F and CEECIND/01799/2017 to P.F.C.. R.D.F. thanks the VILLUM FONDEN for the Center for Global Mountain Biodiversity (grant no 25925). M.P. and I.R. thank the Axencia Galega de Innovación (GAIN), Xunta de Galicia, Spain, for its funding of the AQUACOV and MERVEX Research Groups (grants IN607B 2018/14 and IN607-A 2018/4) and IMPRESS project supported by Spanish MICINN through grant RTI2018-099868-B-I00. R. F. is currently funded by FEDER through the Operational Competitiveness Factors Program (COMPETE) and by FCT (project “Hybrabbid”, grants PTDC/BIA-EVL/30628/2017 and POCI-01-0145-FEDER-030628). E.F. research was funded by the project The Sea and the Shore, Architecture and Marine Biology: The Impact of Sea Life on the Built Environment Project No. POCI-01-0145-FEDER-029537, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the European Regional Development Fund (ERDF). L.F.C.C research was funded by: project VALORMAR (reference nr. 24517), supported by COMPETE2020, LISBOA2020, ALGARVE2020, PORTUGAL2020, through ERDF; strategic funding UIDB/04423/2020 through FCT and ERDF, in the framework of the programme PT2020. We thank the scientific and technical staff and the crew of the PELACUS0315 and SARLINK oceanographic surveys conducted by the Instituto Español de Oceanografía. Alboran Sea samples were collected during the SARLINK oceanographic survey. Samples from Galicia, Cantabrian Sea and Bay of Biscay were collected during the PELACUS 0315 Oceanographic survey, funded by the EU through the European Maritime and Fisheries Fund (EMFF) within the National Program of collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy.
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Author contributions
R.D.F. and L.F.C. designed the study; F.T., M.N., S.A., M.P., I.R., P.C., A.J-R., M.T.G.S. organized and executed the sample collection; P.F.C., A.R-I. and E.F. performed the laboratory work; R.D.F. analyzed the data with contributions from G.B., L.B., R.F., A.M.M.; R.D.F., P.F.C., E.F. and L.F.C. wrote the manuscript with contributions from all authors. All authors have read and approved the manuscript.