News

New paper on clownfish resilience to past environmental change

Nicolas Salamin News ,

Paper by Garcia Jimenez et al entitled “Habitat specialisation impacts clownfish demographic resilience to pleistocene sea-level fluctuations” published in Molecular Ecology.

Study Overview:
Researchers analyzed whole-genome data from 382 individuals across 10 clownfish species to understand how host specialisation influenced demographic responses to Pleistocene sea-level fluctuations, which repeatedly fragmented coral reef habitats.

Key Findings:

  • Generalist species (those associating with multiple sea anemone hosts) maintained stable population sizes and connectivity during habitat fragmentation, showing resilience to environmental instability.
  • Specialist species, dependent on specific hosts, experienced severe population declines and strong genetic structuring, with little evidence of recovery after habitats reconnected.
  • Geographic patterns: The Indonesian Through-Flow acted as a major dispersal corridor, while continental shelves and open ocean regions were barriers to gene flow. The Coral Triangle emerged as a critical hub of genetic diversity.
Spatial patterns of population connectivity fro the 8 clownfish species used. Maps show the clownfish clade distribution range with colour shades indicating the posterior probability of a location having higher (blue) or lower (red) migration than expected under Isolation-by-distance (IBD). Taken from Figure 3 of Garcia Jimenez et al (2025) Mol Ecol

Implications:
This study highlights how ecological dependencies shape species’ vulnerability to environmental change. Incorporating host specialisation into conservation strategies is essential for predicting resilience under future habitat disruptions.

Citation:
García-Jiménez A., Talbi M., Fitzgerald L.M., et al. (2025). Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations. Molecular Ecology. https://doi.org/10.1111/mec.70134

New paper on the genomics of clownfish radiation

Nicolas Salamin News ,

Paper by Marcionetti and Salamin on “Insights into the Genomics of Clownfish Adaptive Radiation: the Genomic Substrate of the Diversification” in Genome Biol Evol.

Abstract: Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. Following the emergence of this mutualism, clownfishes diversified into different ecological niches and developed convergent phenotypes associated with their host use. The genetic basis of the initial acquisition of the mutualism with host anemones has been described, but the genomic architecture underlying clownfish diversification once the mutualism was established and the extent to which clownfish phenotypic convergence originated through shared genetic mechanisms are still unknown. Here, we investigated these questions by performing comparative genomic analyses on the available genomic data of five pairs of closely related but ecologically divergent clownfish species. We found that clownfish diversification was characterized by bursts of transposable elements, an overall accelerated coding evolution, incomplete lineage sorting and ancestral hybridization events. Additionally, we detected a signature of positive selection in 5.4 % of the clownfish genes. Among them, five presented functions associated with social behavior and ecology, and they represent candidate genes involved in the evolution of the size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, this work provides the first insights into the genomic substrate of clownfish adaptive radiation and integrates the growing collection of studies investigating the genomic mechanisms governing species diversification.

New paper on the metabolomic profile in clownfish and damselfish skin mucus

Nicolas Salamin News

Paper by Heim et al on “Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China” published in Frontiers in Ecology and Evolution.

Introduction: The clownfish – sea anemone mutualism was suggested to have triggered the adaptive radiation of clownfishes, but the origin of clownfish resistance to stinging tentacles of host anemones remains unclear. The presence of specific compounds in the mucus of clownfishes conferring them the unique ability to prevent nematocyst discharge from their hosts has been the most supported hypothesis. Yet the mystery regarding the types of compounds found in clownfish skin mucus remains unsolved.

Methods: We analyzed the chemical composition of clownfish and damselfish mucus using an untargeted metabolomics (HILIC-HRMS) and lipidomics (RPLC-HRMS) approach.

Results and Discussion: The polar and lipid metabolome signatures were highly specific and allowed to discriminate between the clownfish and damselfish clades. The most discriminative part of the signature was the sphingolipid profile, displaying a broader diversity of ceramides present in significantly higher levels in clownfish mucus. Importantly, the inter-specific variability of metabolic signature was significantly higher in clownfishes, although their diversification is evolutionarily more recent, thus implying the impact of symbiosis on metabolic variability and adaptation. Furthermore, specialists and generalists clownfish species displayed distinctive metabolite signature. Two strict clownfish specialists, which are phylogenetically distant but share the same host species, clustered together based on their molecular signature, suggesting a link with their mutualistic nature. Overall, comparative analyses of metabolic signatures highlight differences in chemical composition of clownfish mucus and provide insight into biochemical pathways potentially implicated in clownfish adaptation to inhabit sea anemones and consequently diversify.

Population structure of Primula fasciculata

Nicolas Salamin News ,

Paper by Ren et al on “Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China” published in Frontiers in Plant Sciences.

Abstract: Understanding the factors that drive the genetic structure of a species and its responses to past climatic changes is an important first step in modern population management. The response to the last glacial maximum (LGM) has been well studied, however, the effect of previous glaciation periods on plant demographic history is still not well studied. Here we investigated the population structure and demographic history of Primula fasciculata that widely occurs in the Hengduan Mountains and Qinghai-Tibetan Plateau. We obtained genomic data for 234 samples of the species using restriction site-associated DNA (RAD) sequencing and combined approximate Bayesian computation (ABC) and species distribution modeling (SDM) to evaluate the effects of multiple glaciation periods by testing several population divergence models and demographic scenarios. The analyses of population structure showed that P. fasciculata displays a striking population structure with six groups that could be identified genetically. Our ABC modeling suggested that the current groups diverged from ancestral populations located in the eastern Hengduan Mountains after the largest glaciation occurred in the region (~ 0.8–0.5 million years ago), which is consistent with the result of SDMs. Each current group has survived in different glacial refugia during the LGM and experienced expansions and/or bottlenecks since their divergence during or across the following Quaternary glacial cycles. Our study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes in alpine plant species with shallow population structure.