Biology subjects

Marcionetti, A.

Publications and source records attributed to Marcionetti, A..

12 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

One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex

Defining what a species is remains one of the biggest questions in biology and directly challenges species delimitation in species complexes. The wide-spread Clarks' anemonefish Amphiprion clarkii has the widest range of all anemonefishes, from the Indian Ocean to the Central Pacific. However, the taxonomy of this species has been confused since its initial description due to its great variation in morphology and pigmentation even within the same locality. Here, we combined whole genome re-sequencing data from 166 individuals spanning most of the distribution of A. clarkii, including remote islands such as Ogasawara and Guam in the northwestern Pacific, and also including three individuals of the closely related A. tricinctus from the Marshall Islands. Our population genomic analyses reveal an unexpected level of divergence, with five deeply separated lineages corresponding to the Indian Ocean, Central Indo-Pacific, Melanesia, and the isolated population of Ogasawara. The fifth lineage comprises A. clarkii from Guam and A. tricinctus, revealing that A. tricinctus is phylogenetically nested within A. clarkii, challenging its current taxonomic status. The most divergent lineage, Melanesia, is genetically more distant from other A. clarkii lineages than several recognised species pairs within the Amphiprion genus, yet demographic modelling shows ongoing gene flow between all lineages. Together, our results highlight a hidden diversity and stress the necessity of an integrative taxonomic revision of the A. clarkii species complex.

evolutionary biology↗

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

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↗

bioRxiv2024

Host-use Drives Convergent Evolution in Clownfish and Disentangles the Mystery of an Iconic Adaptive Radiation

Clownfishes (Amphiprioninae) are a fascinating example of marine radiation. From a central Pacific ancestor, they quickly colonized the coral reefs of the Indo-Pacific and diversified independently on each side of the Indo-Australian Archipelago. Their association with venomous sea anemones is often thought to be the key innovation that enabled the clownfish radiation. However, this intuition has little empirical or theoretical support given our current knowledge of the clade. To date, no ecological variable has been identified that can explain clownfish niche partitioning, phenotypic evolution, species co-occurrence, and thus, the adaptive radiation of the group. Our synthetic work solves this long-standing mystery by testing the influence of sea anemone host use on phenotypic divergence. We provide the first major revision to the known clownfish-sea anemone host associations in over 30 years, accounting for host associations in a biologically relevant way. We gathered whole-genome data for all 28 clownfish species and reconstructed a fully supported species tree for the Amphiprioninae. Integrating this new data into comparative phylogenomic approaches, we demonstrate for the first time, that the host sea anemones are the drivers of convergent evolution in clownfish color pattern and morphology. During the adaptive radiation of this group, clownfishes in different regions that associate with the same hosts have evolved the same phenotypes. Comparative genomics also reveals several genes under convergent positive selection linked to host specialisation events. Our results identify the sea anemone host as the key ecological variable that disentangles the entire adaptive radiation. As one of the most recognizable animals on the planet and an emerging model organism in the biological sciences, our findings bear on the interpretation of dozens of prior studies on clownfishes and will radically reshape research agendas for these iconic organisms.

evolutionary biology↗

bioRxiv2023

Recurrent gene flow events shaped the diversification of the clownfish skunk complex

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which was shown to have triggered the adaptive radiation of the group. Within clownfishes, the skunk complex is particularly interesting as, besides ecological speciation, gene flow between species and hybrid speciation are suggested to have shaped the diversification of the group. We investigated, for the first time, the mechanisms underlying 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 the population structure, genomic divergence patterns and introgression signals, and performed demographic modeling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation, of hybrid origin of A. sandaracinos, and ruled out the presence of extensive gene flow in sympatry. 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 process of the group. We identified introgressed regions in A. sandaracinos and detected two large regions of high divergence in A. perideraion, likely maintained by the disruption of recombination. Altogether, our results show that ancestral hybridization events shaped the groups diversification. However, more recent gene flow is less pervasive than initially thought and suggests a role of host repartition or behavioral barriers in maintaining the genetic identity of the species in sympatry.

evolutionary biology↗

bioRxiv2023

Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterise the species population structure, demographic history, and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Moreover, edge populations exhibited more similar colouration patterns compared to central populations. However, we demonstrate that colour polymorphism is not associated with population structure, thus, colour phenotype is unreliable in assessing the taxonomic status of A. clarkii. Our study further highlights the power of whole-genome comparative studies to determine the taxonomy of geographically wide-ranging and phenotypically diverse species, supporting the status of A. clarkii as a single species.

evolutionary biology↗

bioRxiv2022

Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification

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. We investigated the genomic architecture underlying this process to determine the genomic characteristics associated with the adaptive radiation of the group and assess the mechanisms of parallel evolution in clownfishes. We took advantage of the available genomic data of five pairs of closely related but ecologically divergent clownfish species to perform comparative genomic analyses. We found that clownfish genomes show two bursts of transposable elements, overall accelerated coding evolution, and topology inconsistencies potentially resulting from hybridization events. These characteristics possibly facilitated the rapid diversification of the group. We also detected a signature of positive selection throughout the radiation in 5.4 % of the clownfish genes. Among them, five presented functions associated with social behavior and ecology. They could have potentially played a role in the evolution of 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, these results provide the first insights into the genomic substrate of clownfish adaptive radiation. This work integrates the growing collection of studies investigating the genomic mechanisms governing species diversification, which brings us a step closer to understanding how biodiversity on Earth is created

evolutionary biology↗

bioRxiv2019

Convergent changes in gene expression associated with repeated transitions between hummingbird and bee pollinated flowers

The repeated evolution of convergent floral shapes and colors in angiosperms has been largely interpreted as the response to pollinator-mediated selection to maximize attraction and efficiency of specific groups of pollinators. The genetic mechanisms contributing to certain flower traits have been studied in detail for model system species, but the extent by which flowers are free to vary and how predictable are the genetic changes underlying flower adaptation to pollinator shifts still remain largely unknown.\n\nHere, we aimed at detecting the genetic basis of the repeated evolution of flower phenotypes associated with pollinator shifts. We assembled and compared de novo transcriptomes of three phylogenetic independent pairs of Gesneriaceae species, each with contrasting flower phenotype adapted to either bee or hummingbird pollination. We assembled and analyzed a total of 14,059 genes and we showed that changes in expression in 550 of them was associated with the pollination syndromes. Among those, we observed genes with function linked to floral color, scent, shape and symmetry, as well as nectar composition. These genes represent candidates genes involved in the build-up of the convergent floral phenotypes.\n\nThis study provides the first insights into the molecular mechanisms underlying the repeated evolution of pollination syndromes. Although the presence of additional lineage-specific responses cannot be excluded, these results suggest that the convergent evolution of genes expression is involved in the convergent build-up of the pollination syndromes. Future studies aiming to directly manipulate certain genes will integrate our knowledge on the key genes for floral transitions and the pace of floral evolution.\n\nData availabilityRaw Illumina reads will be available in the Sequence Read Archive (SRA) in NCBI database. The assembled transcriptomes and their annotation will by available in DRYAD repository. Details and accession ID will be provided at the time of the manuscript acceptance.

evolutionary biology↗

bioRxiv2017

First draft genome assembly of an iconic clownfish species (Amphiprion frenatus)

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, particularly known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment.\n\nHere, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (Benchmarking Universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies.\n\nThis resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.

genomics↗