Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

clownfish mutualism; demographic resilience; genetic structure; habitat specialisation; population genomics; sea‐level fluctuations; Animals; Population Dynamics; Gene Flow; Genetic Variation; Biodiversity; Population Density; Indonesia; Ecosystem; Genetics, Population; Perciformes/genetics; Perciformes; Ecology, Evolution, Behavior and Systematics; Genetics

Abstract :

[en] Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes ( Ne ) and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severe Ne declines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Disciplines :

Aquatic sciences & oceanology
Environmental sciences & ecology
Zoology

Author, co-author :

García-Jiménez, Alberto ; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

Talbi, Marion; Department of Aquatic Ecology & Evolution, University of Bern, Bern, Switzerland

Fitzgerald, Lucy M; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

Heim, A; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

Marcionetti, Anna ; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

Schmid, Sarah; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland

Bertrand, Joris ; Laboratoire Génome et Développement des Plantes, UPVD, Perpignan, France

Shaughnessy, Abigail; Queensland Brain Institute, The University of Queensland, Brisbane, Australia

Santiago, Carl; Queensland Brain Institute, The University of Queensland, Brisbane, Australia

Rangseethampanya, Ploypallin; Marine Biodiversity Research Group, Ramkhamhaeng University, Bangkok, Thailand

More authors (11 more)

Language :

English

Title :

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

Publication date :

November 2025

Journal title :

Molecular Ecology

ISSN :

0962-1083

eISSN :

1365-294X

Publisher :

John Wiley and Sons Inc, England

Volume :

Issue :

Pages :

e70134

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.70134

Funders :

SNF - Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung
ARC - Australian Research Council

Funding text :

Funding: Financial support for this research was provided by the University of Lausanne funds and the Swiss National Science Foundation (Grant 310030_185223). We also acknowledge support from the Australian Research Council (ARC) with the Discovery Early Career Research Award DE200100620 and Discovery Project DP180102363 to FC, contributing to this study. We express our gratitude to Rosanna Pescini for the DNA extractions, to the Lausanne Genomic Technologies Facility for their assistance in sequencing the samples, and to the DCSR infrastructure of the University of Lausanne for providing computational resources essential for data analysis. Special thanks are extended to the staff at the Lizard Island Research Station for their invaluable support during fieldwork and acknowledgment to the Dingaal, Ngurrumungu and Thanhil peoples as traditional owners of the lands and waters of the Lizard Island region. We are deeply appreciative of the local authorities of Australia, Indonesia, Thailand, Kenya, Mayotte, Madagascar, Maldives and New Caledonia for granting permits to collect samples and their assistance with field logistics. In particular, we extend our gratitude to the Quesnel family and Victoria Fahey from COREsea for their invaluable help and logistical support during fieldwork in New Caledonia and Thailand, respectively. Finally, we thank Daniele Silvestro, Diego A. Hartas\u00E1nchez and Thibault Latrille for their useful comments on the manuscript. Open access publishing facilitated by Universite de Lausanne, as part of the Wiley - Universite de Lausanne agreement via the Consortium Of Swiss Academic Libraries.Financial support for this research was provided by the University of Lausanne funds and the Swiss National Science Foundation (Grant 310030_185223). We also acknowledge support from the Australian Research Council (ARC) with the Discovery Early Career Research Award DE200100620 and Discovery Project DP180102363 to FC, contributing to this study. Funding:

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