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Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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