Biology subjects

Mercader, M.

Publications and source records attributed to Mercader, M..

6 recordsLinked to original sources

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

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↗

bioRxiv2023

Anemonefish are better taxonomists than humans.

The symbiosis between giant sea anemones, photosynthetic algae of the family Symbiodiniaceae, and anemonefish is an iconic example of a mutualistic "menage a 3"1. Patterns of associations among 28 species of anemonefish and 10 species of giant sea anemone hosts are complex: Some anemonefish species are highly specialized to inhabit only one species of sea anemone (e.g., Amphiprion frenatus with Entacmaea quadricolor), whereas others are more generalist and can live in almost any host species (e.g., Amphiprion clarkii)1,2,3. Reasons for host preferences and the mechanisms involved are obscured, among other things, by the lack of resolution of giant sea anemone phylogeny. Recent molecular analyses have shown that giant sea anemones hosting anemonefish belong to three distinct clades: Entacmaea, Stichodactyla, and Heteractis4,5,6. Inside these clades, however, species delimitation has been impeded by morphological variability of the giant sea anemones and is poorly resolved with classical markers4,5. Here, we employed an extensive transcriptomic dataset from 55 sea anemones collected from southern Japan to build a robust phylogeny. With this dataset, we observed that the bubble-tip sea anemone E. quadricolor, currently considered to be a single species, can in fact be separated into at least four distinct cryptic lineages (A-D). Moreover, these lineages can be precisely distinguished by their association with anemonefish: A. frenatus is only found associated with lineage D, whereas A. clarkii lives in the other three lineages.

evolutionary biology↗

bioRxiv2022

Megacolonies: an alternative social organization in anemonefishes?

Anemonefish are iconic examples of marine fishes living in mutualistic symbiosis with sea anemones. In a given sea anemone, the anemonefishes have a stereotyped social organization with a dominant female, a semi-dominant male, and several juveniles. A strict size-based hierarchy governs the social interactions within these colonies, with each individual differing from the previous or next fish in the order by +/- 20% size. This social organization is conserved across the Indo-Pacific in all 28 species of anemonefish found on any of ten giant sea anemone species. We report the existence of huge "megacolonies" of up to 100 fish living in large carpets of sea anemones. This alternative organization was observed for different fish and anemone species in different coral reef locations (French Polynesia, Japan, Taiwan, and Vietnam). In these colonies, the strict size-based hierarchy is no longer recognizable, and the level of aggressivity of the different members appears lower than in "normal" colonies. These megacolonies may correspond to a previously overlooked type of social organization that could be linked to host availability and offer a unique opportunity to understand anemonefishs behavioral, social, and hormonal plasticity.

ecology↗

bioRxiv2022

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanophore development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkiis many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

genomics↗

bioRxiv2020

Marine reserve benefits and recreational fishing yields: the winners and the losers

Marine reserves constitute effective tools for preserving fish stocks and associated human benefits. However, not all reserves perform equally, and predicting the response of marine communities to management actions in the long run is challenging. Our decadal-scale survey of recreational fishing yields at Frances 45-year old Cerbere-Banyuls marine reserve indicated significant protection benefits, with 40-50% higher fishing yields per unit effort in the partial-protection zone of the reserve (where fishing is permitted but at a lower level) than in surrounding non-reserve areas. Over the period 2005-2014, catch per unit effort (CPUE) showed a similar pattern of decline inside and outside the reserve while weight per unit effort (WPUE) increased by 131% inside and decreased by 60% outside. Different CPUE and WPUE trajectories among fish families indicated changing catch assemblages, with yields increasing for the family most valued by fisheries, Sparidae (the ecological winners). However, reserve benefits were restricted to off-shore fishermen (the social winners), as on-shore yields were [~]4 times lower and declining, even inside the reserve. Our study illustrates how surveys of recreational fishing yields can help evaluate the effectiveness of marine protected areas for key social and ecological protagonists. We show that, more than four decades after its establishment, fishing efficiencies at the historical Cerbere-Banyuls marine reserve are still changing, but benefits in terms of catch abundance, weight, and composition remain predominantly restricted to off-shore fishermen. Further regulations appear necessary to guarantee that conservation strategies equitably benefit societal groups.

ecology↗