Biology subjects

Frederich, B.

Publications and source records attributed to Frederich, B..

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

Hidden diversity and host specificity of Cladocopium symbionts revealed by phylotranscriptomics in giant sea anemones.

Giant sea anemones form an intricate, metabolically linked symbiosis with anemonefish (genus Amphiprion) and dinoflagellates (family Symbiodiniaceae). While the association between fish and anemone is well documented, the identity and distribution of resident Symbiodiniaceae remains poorly characterized. Here, we used RNA-sequencing of anemone tentacles and post-assembly filtering to recover Symbiodiniaceae sequences from Japanese anemones. Using transcriptome-wide phylogenetic approaches, we identified distinct Symbiodiniaceae strains in seven sea anemone species and four cryptic lineages of Entacmaea quadricolor. Phylogenies of 1300 and 214 nuclear genes resolved relationships among these symbionts with greater sensitivity than traditional molecular markers such as the Internal Transcribed Spacer 2 (ITS2) or partial 28S ribosomal DNA. Marker-based assessments indicate these Symbiodiniaceae as novel and specific to sea anemone hosts. Our transcriptome-wide phylogenies reveal previously undescribed Cladocopium (Clade C) strains associated with giant sea anemones, with symbionts clustering according to host species and lineage. Cophylogenetic analysis revealed significant phylogenetic congruence between anemone and Symbiodiniaceae, indicating a nonrandom association between host and symbiont evolutionary histories. Two sympatric cryptic lineages of E. quadricolor previously identified through host transcriptomics harbor distinct, specific Symbiodiniaceae assemblages. Analysis of genes under positive selection indicates functional divergence between these Symbiodiniaceae; three-dimensional reconstructions of symbiont cells using serial block-face scanning electron microscopy show consistent differences in cellular organization between two strains, further supporting their distinct functional identity. Together, our results uncover a hidden diversity of host-specific Symbiodiniaceae and suggest that cryptic diversification in giant sea anemones is mirrored by diversification of their algal symbionts within this tripartite symbiosis.

evolutionary biology↗

bioRxiv2026

Hyoid barbels as a key innovation triggering goatfish adaptive radiation

Key innovations can unlock ecological opportunities and redirect the evolutionary trajectory of entire lineages, yet few traits have been shown to trigger both hallmarks of a genuine adaptive radiation, rapid speciation and pronounced ecomorphological divergence, within a single lineage. This is especially true among coral reef fishes, where trophic novelties are routinely proposed as drivers of diversity but rarely tested against both criteria. Here, we show that goatfishes (Mullidae), a reef fish family having chemosensory hyoid barbels, meet this standard. First, macroevolutionary analyses of speciation dynamics reveal that goatfishes diversified at a markedly elevated rate relative to other Syngnathiformes. Using the most comprehensive phylogeny of the family to date, combining ultraconserved elements and mitochondrial data for 76 of the 103 recognized species, alongside the largest phenotypic dataset assembled for the group, we find that this elevated rate has been sustained since the family's origin roughly 25 million years ago, rather than declining as ecological opportunity became filled. Head shape, the trait most closely tied to the foraging strategy enabled by hyoid barbels, diverged rapidly among genera early in the family's history and has remained conserved ever since, while body shape and barbel microstructure evolved conservatively and pigmentation diversified later through repeated convergence. By opening access to previously untapped benthic prey resources and triggering a lasting burst of diversification, hyoid barbels emerge as a key innovation that reshaped the evolutionary trajectory of an entire reef fish lineage.

evolutionary biology↗

bioRxiv2026

Early Partitioning of Structural Paralog Diversity Shapes Immune Evolution Across Habitat Transitions in Gobiiform Fishes

Habitat transitions expose species lineages to novel pathogen regimes and are often hypothesized to drive adaptive diversification of immune gene families. However, the temporal association between gene family diversification and ecological change remains unresolved. To gain deeper insight into the relationship between the diversification of species and the evolution of their immune system, we investigated the evolutionary history of Toll-like receptors (TLRs) across Gobiiformes, a clade characterized by repeated transitions across aquatic and amphibious environments. TLRs are well-studied membrane-bound pattern recognition receptors that play crucial roles in detecting pathogens and immune activation. Phylogenomic, structural, and sequence analyses reveal that a major expansion of TLR22 predates many ecological transitions, with early paralog diversification partitioning receptor architectures into distinct structural regimes that persist across lineages. Subsequent evolution is concentrated in the extracellular ligand-binding, leucine-rich repeat (LRR) domains, where localized sequence and structural variation enables likely functional tuning without major architectural innovation. These results indicate that ecological transitions do not require repeated evolution of new immune receptor forms, but can instead be facilitated by reconfiguration of pre-existing immunogenetic diversity. These findings raise the possibility that expansions of immune gene families occurring early in a clades evolutionary history may commonly persist and subsequently act as substrates for evolutionary responses to environmental change.

evolutionary biology↗

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↗

bioRxiv2025

Rapid and repeated evolution of the pigmentation patterns in reef fishes

Pigmentation patterns are integral to animal biology1-3 and uncovering the mechanisms driving their diversification is essential for determining the evolutionary principles that shape this fundamental aspect of biodiversity4-7. Coral reef fishes are particularly notable for their extraordinary pattern diversity, ranging from simple spots and stripes to intricate, maze-like designs. Despite over a century of investigation, the evolutionary processes that govern the diversification of these pigmentation patterns remain one of the most persistent unresolved questions in evolutionary biology. Here, we investigate the relationship between pattern diversity, species richness, and geography across six iconic families of pattern-diverse coral reef fishes. Utilizing time-calibrated phylogenies, we reveal constant disparity of pigmentation patterns across globally variable reef fish communities8. We find strong evidence for a positive correlation between pattern diversity and species richness, with a high divergence of pigmentation patterns in sympatry that highlights the role of these patterns in speciation and phenotypic differentiation. Moreover, our findings support the stages model of adaptive radiation9, revealing that most pigmentation pattern diversity has emerged in evolutionary history. These results demonstrate that the evolutionary history of pigmentation patterns in reef fishes is characterized by a combination of rapid and constrained phenotypic diversification that has likely played a crucial role in their speciation dynamics.

evolutionary biology↗

bioRxiv2024

The multi-level effect of chlorpyrifos during clownfish metamorphosis

Chemical pollution in coastal waters, particularly from agricultural runoff organophosphates, poses a significant threat to marine ecosystems, including coral reefs. Pollutants such as chlorpyrifos (CPF) are widely used in agriculture and have adverse effects on marine life and humans. In this paper, we investigate the impact of CPF on the metamorphosis of a coral reef fish model, the clownfish Amphiprion ocellaris, focusing on the disruption of thyroid hormone (TH) signalling pathways. Our findings reveal that by reducing TH levels, CPF exposure impairs the formation of characteristic white bands in clownfish larvae, indicative of metamorphosis progression. Interestingly, TH treatment can rescue these effects, establishing a direct causal link between CPF effect and TH disruption. The body shape changes occurring during metamorphosis are also impacted by CPF exposure, shape changes are less advanced in CPF-treated larvae than in control conditions. Moreover, transcriptomic analysis elucidates CPFs effects on all components of the TH signalling pathway. Additionally, CPF induces systemic effects on cholesterol and vitamin D metabolism, DNA repair, and immunity, highlighting its broader TH-independent impacts. Pollutants are often overlooked in marine ecosystems, particularly in coral reefs. Developing and enhancing coral reef fish models, such as Amphiprion ocellaris, offers a more comprehensive understanding of how chemical pollution affects these ecosystems. This approach provides new insights into the complex mechanisms underlying CPF toxicity during fish metamorphosis, shedding light on the broader impact of environmental pollutants on marine organisms. HighlightsO_LIChlorpyrifos (CPF) is an insecticide widely used in agriculture for the past five decades and has adverse effects on marine life and humans C_LIO_LICPF exposure impairs the formation of characteristic white bands in clownfish larvae, indicative of metamorphosis progression C_LIO_LIDuring metamorphosis, clownfish larvae lose their elongated body shape and transform into miniature ovoid-shaped adults, these shape changes are less advanced in CPF-treated larvae C_LIO_LICPF induces systemic effects on cholesterol and vitamin D metabolism, DNA repair, and immunity, highlighting its broader TH-independent impacts C_LI

developmental 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↗

bioRxiv2022

Periodic Environmental Disturbance Drives Repeated Ecomorphological Diversification in an Adaptive Radiation of Antarctic Fishes

The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In systems with periodic disturbances, species-rich clades can contain nested adaptive radiations of subclades with their own distinct diversification histories, and how adaptive radiation theory applies in these cases is less clear. Here, we investigated patterns of ecological and phenotypic diversification within two iterative adaptive radiations of cryonotothenioid fishes in Antarcticas Southern Ocean: crocodile icefishes and notoperches. For both clades, we observe evidence of repeated diversification into disparate regions of trait space between closely related taxa and into overlapping regions of trait space between distantly related taxa. We additionally find little evidence that patterns of ecological divergence are correlated with evolution of morphological disparity, suggesting that these axes of divergence may not be tightly linked. Finally, we reveal evidence of repeated convergence in sympatry that suggests niche complementarity. These findings reflect the dynamic history of Antarctic marine habitats, and may guide hypotheses of diversification dynamics in environments characterized by periodic disturbance.

evolutionary biology↗

bioRxiv2022

Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae)

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that do not reflect the same traits as their adult forms. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. However, whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. Integrating a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, we reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.

evolutionary biology↗