Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

Genome, Mitochondrial* ; Gene Flow* ; Selection, Genetic* ; Phylogeny* ; Fishes*/genetics ; Fishes*/classification; Animals ; Genetic Variation ; Europe ; Evolution, Molecular

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.
Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics statement: Sampling for the present study focused on the European sardine from almost the entire species distribution range. Ethical or government approval, specific permissions or licenses for sample collection were not required for this study, as all specimens were collected as part of routine fishing procedures by fishermen of commercial fleets or scientific research campaigns. Fish are killed during the hauling of fishing gears due to differences in atmospheric pressure and fishing procedures. The experiments were conducted on dead animals, hence, no animal welfare or animal use permits were required for this study. Sardina pilchardus is not an endangered or protected species.
(© 2024. The Author(s).)

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CEECIND/01528/2017 Fundação para a Ciência e a Tecnologia; UIDB/00329/2020 Fundação para a Ciência e a Tecnologia; UIDB/00329/2020 Fundação para a Ciência e a Tecnologia; UIDB/00329/2020 Fundação para a Ciência e a Tecnologia; UIDB/04292/2020 Fundação para a Ciência e a Tecnologia; UIDB/00329/2020 Fundação para a Ciência e a Tecnologia

Keywords: Geographic structure; Late Miocene cooling; Mid-Pliocene warm period; Mitogenome; Positive selection; Small pelagic fish

Date Created: 20241227 Date Completed: 20241227 Latest Revision: 20250104

20250104

PMC11681243

10.1038/s41598-024-82054-x

39730618