Biology subjects

Gaboriau, T.

Publications and source records attributed to Gaboriau, T..

10 recordsLinked to original sources

bioRxiv2026

Genomic structural variation in clownfish adaptive radiation

Clownfishes are a complex of 28 species that rapidly diversified after acquiring mutualism with host sea anemones around 15 million years ago. The genomic mechanisms behind this radiation are only beginning to emerge, and structural variants (SVs) have received little attention. Previous phylogenomic studies suggested two large inversions on chromosome 18, but their distribution across the clownfish phylogeny and their potential effects have not been formally explored. SVs can disrupt gene function and regulation or alter gene dosage, and they have been shown to play a central role in adaptive evolution and diversification across many taxa. Here, we characterized SVs across the clownfish radiation using long-read PacBio sequencing, generating high-quality genome assemblies for sixteen species spanning the main lineages of the genus. We identified and catalogued nearly 130,000 SVs spanning close to 570 Mb. Short insertions and deletions were the most numerous, but large inversions accounted for most of the affected sequence. No SV was consistently associated with host specialization. We nevertheless confirmed a single inversion of approximately 17 Mb on chromosome 18, clarifying earlier reports of two separate rearrangements at this locus, and identified an additional inversion on chromosome 9 whose distribution suggests a history of hybridization. This study provides the first genome-wide characterization of structural variation in clownfishes, revealing extensive SVs despite the group's rapid and recent radiation. It also delivers new, high-quality genomic resources that will support future research into this iconic group of coral reef fishes and their adaptation to sea anemones.

genomics↗

bioRxiv2026

Discovery and genomic characterization of a novel wild clownfish hybrid from the Philippines

Hybridization is widespread among marine fishes and can contribute to adaptation, diversification, and the generation of novel phenotypes. In clownfishes, only two wild hybrids Amphiprion leucokranos and A. thiellei have been described, yet those naturally occurring clownfish hybrids remain rarely documented. Both hybrids involve crosses with A. sandaracinos. During field surveys in the Philippines, we identified a previously undocumented clownfish individual with an unusual phenotype resembling both A. sandaracinos and A. perideraion. To characterize its origin, we combined genomic, mitochondrial, and phenotypic comparisons to previously described clownfish hybrid systems. Genome-wide PCA and admixture analyses supported mixed ancestry between A. sandaracinos and A. perideraion. Reconstruction of the mitochondrial genome placed the individual within the A. sandaracinos mitochondrial lineage. Together, these results support a hybrid origin and suggest predominant A. sandaracinos ancestry, consistent with a backcrossed descendant rather than a first-generation hybrid. Comparisons with the previously characterized hybrid A. leucokranos further revealed similarities in genomic composition and phenotype across independently derived clownfish hybrid systems. Our findings identify a previously undocumented natural clownfish hybrid and suggest that integrating genomic and field-based approaches may reveal additional cryptic hybrid systems and improve understanding of hybridization in clownfishes.

genomics↗

bioRxiv2026

Color polymorphism in the saddleback clownfish, Amphiprion polymnus: species or complex?

Color polymorphism can facilitate local adaptation, maintain intraspecific diversity, or reflect early stages of speciation. Clownfishes (Amphiprion spp.) typically display a simple black, orange, and white pattern, but the saddleback clownfish (Amphiprion polymnus) shows striking variation in melanism and the number of vertical bars, which are thought to play a role in species recognition. In 2024, a revision on iNaturalist split A. polymnus into multiple species based solely on color pattern and geographic range. This raises the question of whether these morphs represent true species or intraspecific polymorphism, which we tested using genomic and image-based data. We sampled 97 individuals from seven populations across the species range and quantified color patterns from standardized photographs. Phenotypic and genomic analyses reveal a complex pattern of divergence. Image analysis identified three distinct phenotypic clusters, with A. polymnus, A. annamensis, and A. laticlavius each showing consistent differences in saddle shape and vertical bar extent. ADMIXTURE resolved three distinct genetic groups corresponding to the morphs. Pairwise FST (0.54-0.71) and dxy indicate extremely high differentiation between A. polymnus and A. annamensis, consistent with species-level divergence, whereas A. laticlavius shows much lower differentiation from A. polymnus (FST 0.09-0.18) and higher differentiation from A. annamensis (FST 0.64-0.66). Overall, phenotypic and genomic data show structured variation, but the status of A. laticlavius remains ambiguous. Our study reveals clear and structured divergence across the full range, yet the taxonomic interpretation of this variation remains inherently challenging. The key question remains: do these patterns reflect a single polymorphic species or a complex of closely related species?

ecology↗

bioRxiv2025

Colour and shape evolution reflect ecological specialisation in Pomacentridae

Damselfishes (Pomacentridae) display remarkable diversity in colouration and body form, yet the processes shaping this phenotypic variation remain poorly resolved. Our study aimed to characterise the evolution of these traits, evaluate their associations with ecological factors, and identify convergent patterns linked to ecological specialisation. Using image-based quantification of colour patterns, geometric morphometrics, and phylogenetic comparative methods across 343 species, we show that pomacentrid phenotypes are organised around a small number of dominant axes describing brightness, hue, contrast, body elongation, and cranial morphology. Both colour and morphology exhibit early bursts of evolutionary disparity, followed by recurrent lineage-specific radiations and widespread convergence toward similar adaptive optima across the phylogeny. Dietary ecotypes emerged as the strongest predictor of morphological diversification, whereas symbiotic and social regimes exerted the strongest effects on colour evolution. Despite these distinct ecological correlates, several colour and shape axes form partially integrated trait syndromes that evolve in concert. The pervasive convergence of colour-shape syndromes underscores deterministic components of reef-fish evolution and positions Pomacentridae as a model for understanding integrated phenotypic evolution.

evolutionary biology↗

bioRxiv2025

Phylogram instead of chronogram when assessing the neutral evolution of a trait

Comparative analyses of trait evolution aim to uncover the different evolutionary forces shaping phenotypic diversity among species. This is typically done by fitting various evolutionary models to observed trait changes along a species tree. For instance, under neutral evolution, trait values are modelled as changing randomly along the branches of the tree. In contrast, for a trait under selection, species are typically assumed to track an optimal trait value, which itself may shift along the tree. Here, rather than relying on alternative models to discriminate among evolutionary scenarios, we focus on the underlying species tree, and specifically the units in which its branch lengths are measured. Species trees are usually represented as chronograms, with branch lengths proportional to time. The rationale is that time correlates with trait changes through its connection to the number of generations. However, since the generation time of species can also vary along the phylogenetic tree, we argue that chronograms introduces biases. In contrast, phylograms with branch lengths in units of sequence divergence will account for the effect of changing generation time. In this study, we develop a method to test whether a phylogram provides a better fit than a chronogram for modelling trait evolution. We show using simulations that, for a trait evolving neutrally, the fit of a random evolution model has more support on a phylogram than on a chronogram. However, comparing models and testing different scenarios of selection using a phylogram leads to incorrect predictions. Given these results, we argue that we should use phylograms instead of chronograms when assessing the neutral evolution of a trait. Nevertheless, we support the fact that we should generally continue to use chronograms to model selection acting on a quantitative trait. Lay summaryWhen we look at different species, we can see that some traits are different between them. For example, the brain size of different primate and human lineages varies. The question we ask is: does the time that passed explain the differences in their traits? Or are genetic differences between species better at explaining the differences? The standard in evolutionary biology is to use time to explain differences in traits. However, if the trait is not under natural selection and instead is changing due to accumulating mutations, the genetic differences between species instead of time should best explain the differences in traits. As a result, we argue that using both genetic differences and species divergence time simultaneously provides a better understanding of how traits evolve across species.

evolutionary biology↗

bioRxiv2025

Genetic basis of the evolution of vertical bars in clownfishes

Clownfish exhibit striking color patterns, characterized primarily by the presence of zero to three vertical white bars, along with three main colors: orange, white, and black. The common ancestor of clownfish likely possessed three vertical bars, with several instances of gains and losses occurring throughout clownfish evolutionary history over the past 10 million years. However, the evolutionary genomic mechanisms underlying the gain or loss of vertical bars remain unknown. In this study, we tested whether vertical bar transitions across the clownfish phylogeny were associated with changes in non-synonymous to synonymous substitution rates (dN/dS values). Our analyses identified pigmentation-related genes that underwent changes in selective pressure, including gch2, oca2, and vps11, which are linked to melanophores, iridophores, and visual function. Additionally, pmel, a key melanogenesis gene, was found under positive selection, suggesting its role in shaping bar patterning. These results provide new insights into the genomic basis of coloration in clownfish, highlighting how selection and genetic variation influence phenotypic evolution.

evolutionary biology↗

bioRxiv2024

Specialization into Host Sea Anemones Impacted Clownfish Demographic Responses to Pleistocene Sea Level Changes

Fluctuating sea levels during the Pleistocene led to habitat loss and fragmentation, impacting the evolutionary trajectories of reef fishes. Species with specialized ecological requirements or habitat preferences, like clownfishes (Amphiprioninae), may have been particularly vulnerable due to their intricate dependence on sea anemones. The diverse host specializations within this group likely contributed distinct responses to sea-level fluctuations, differentially shaping their recent evolutionary histories. Leveraging a comprehensive genomic dataset, we reveal demographic patterns and connectivity dynamics across multiple populations of ten clownfish species under different host specializations. Host-generalist species demonstrated strong resilience to habitat perturbations, while those specialized on single hosts suffered dramatic bottlenecks linked to sea-level fluctuations. Spatial analyses revealed the significant role of oceanic currents in shaping clownfish genetic diversity landscapes. Dispersal barriers were driven by environmental variables, with the Coral Triangle emerging as a hub of genetic diversity. Our results reveal how clownfish associative behavior influences their population dynamics, holding major implications for their conservation such as the need to consider their mutualism with sea anemones, particularly on host-specialists, to ensure their survival in the face of climate threats. These findings extend broader principles of conservation, improving our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

genomics↗

bioRxiv2023

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macro-evolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining within- and between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it.

evolutionary biology↗

bioRxiv2023

Implementation of biotic interactions in niche analyses unravels the patterns underneath community composition in clownfishes

Biotic interactions shape the ecology of species and communities, yet their integration into ecological niche modeling methods remains challenging. Despite being a central topic of research for the past decade, the impact of biotic interactions on species distributions and community composition is often overlooked. Mutualistic systems offer ideal case studies for examining the effects of biotic I nteractions on species niches and community dynamics. This study presents a novel approach to incorporating mutualistic interactions into niche modeling, using the clownfish-sea anemone system. By adapting existing niche quantification frameworks, we developed a method to estimate the partial effects of known interactions and refine ecological niche estimates. This approach allows for a more comprehensive understanding of how mutualistic relationships influence species distributions and community assembly patterns. We also used mutualistic information to investigate the resource-use overlap, identitying patterns of competition within clownfish communities. Our results reveal significant deviations in niche estimates when biotic interactions are considered, particularly for specialist species. Host partitioning among clownfish species reduces resource-use overlap, facilitating coexistence in species-rich habitats and highlighting mutualisms role in promoting and maintaining diversity. We uncover complex dynamics in resource-use overlap among clownfish species, influenced by factors such as species richness, ecological niche overlap, and host specialization. Specialist-generalist interactions strike an optimal balance, supporting high species richness while minimizing competition. These insights enhance our understanding of clownfish biodiversity patterns, demonstrating how diverse mutualistic strategies contribute to diversity build-up and mitigate competitive exclusion in saturated communities. The analytical framework presented has broad applications beyond the clownfish-sea anemone system, potentially extending to a broader range of interactions. It enables a more comprehensive understanding of biodiversity maintenance in complex ecosystems and constitutes a valuable tool for conservation planning and ecosystem management.

ecology↗

bioRxiv2021

Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

Intraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the , {beta} and{gamma} components of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that the and{gamma} components of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to genetic {beta} diversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.

genetics↗