Biology subjects

Zwahlen, J.

Publications and source records attributed to Zwahlen, J..

5 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↗

bioRxiv2025

Decoding the constraints acting on a coastal fish using landscape transcriptomics

Understanding how wild organisms respond to complex mixtures of environmental stressors remains a major challenge in ecology1,2. To move beyond laboratory-based studies of the effect of individual stressors on model species, landscape transcriptomics - the study of how genome-wide expression patterns reveal environmental conditions - has been suggested3. Here, we apply landscape transcriptomics to the damselfish Chrysiptera cyanea, a sentinel species from Okinawas coastal ecosystems, by sampling juveniles and adults across 18 sites from natural to urbanized habitats. We uncover a striking molecular signature of urbanization: fish from human-impacted sites exhibit elevated expression of genes involved in inflammation and immune responses. Remarkably, their transcriptomes resemble those of overfed individuals from laboratory feeding experiments - suggesting that urban reefs act as "fast food" environments, offering energy-rich diets while imposing chronic stress. This pattern is illustrated by the altered expression of key genes in metabolic and stress pathways (e.g., downregulation of ppargc1a and insrb, indicative of dietary intake surplus and insulin resistance; upregulation of interleukins, chemokines, toll-like receptors and caspase linked to the immune response and inflammation). Our results demonstrate that wild transcriptomes capture the invisible biological costs of environmental degradation, positioning fish as living biosensors for coastal ecosystem health.

bioinformatics↗

bioRxiv2025

Socially regulated developmental plasticity in the color pattern of an anemonefish

Understanding the developmental basis of phenotypic plasticity is key to unraveling the origins of biodiversity. In coral reef fishes, color pattern changes during ontogeny can serve adaptive functions, yet the mechanisms and ecological contexts shaping these transitions remain largely unknown. Here, we investigated color pattern development in the tomato anemonefish (Amphiprion frenatus), which exhibits transient posterior white barring during early juvenile stages. We demonstrated that the timing of bar loss is plastic and modulated by the social environment, where juveniles cohabiting with adult conspecifics exhibited bar loss [~]24 days earlier than those isolated from adults. Through transcriptomic profiling, we identified gene expression changes implicating apoptosis- and autophagy-related pathways, as well as alterations in chromatophore development. Moreover, shifts in the expression of multiple thyroid hormone marker genes highlighted the potential neuroendocrinal integration of social cues that promoted bar loss. Ultrastructural analyses via transmission electron microscopy and in-situ assays indicated massive apoptosis of iridophores and associated dermal remodeling during the white-to-orange transition. The pharmacological inhibition of caspases delayed bar loss, confirming the functional role of programmed cell death. Behavioral trials revealed that adults responded differently to juveniles with/without the posterior bar, suggesting a role of transient barring in conflict avoidance during recruitment. Lastly, our evolutionary reconstruction of this plastic trait suggests that colony size is an important factor promoting this ontogenetic switch throughout anemonefishes. Our results provide compelling evidence for socially mediated plasticity in color pattern ontogeny with ecological and evolutionary implications for communication and species diversification in reef fishes.

developmental biology↗

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↗