Extensive hybridisation throughout clownfishes evolutionary history

Schmid, Sarah; Micheli, Baptiste; Cortesi, Fabio; Donati, Giulia; Salamin, Nicolas

doi:10.1101/2022.07.08.499304

Cited by 8 publications

(41 citation statements)

References 106 publications

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“…The full details of the analyses are found in Schmid et al (2022). Ancestral nodes for both mitochondrial and nuclear phylogenetic trees are well supported, while more recent splits display lower node support, particularly in the tree inferred with the mitochondrial genome (Figure 4.2).…”

Section: Incongruence In Phylogenomic Inferencementioning

confidence: 98%

“….1 Dated phylogeny of anemonefishes based on the 20 most informative genes using BEAST v2.6.2. (Schmid et al 2022). Geographical distributions, sea anemone hosts and representative phenotypes are schematized for each species.…”

Section: A a A B Bmentioning

confidence: 99%

“…While previous analyses were based on very limited genetic data and did not include all the species , the recent increase in genomic data available for the group provides a unique opportunity to clarify the role played by hybridization in the evolution of anemonefishes and to evaluate the impacts of hybridization on the genealogical relationships across the genome of clownfishes. Here, we build on two recent studies extending the genomic analyses in anemonefishes (Marcionetti et al 2022;Schmid et al 2022) to illustrate potential genomic signatures of past introgression. Such analyses might be valuable to potentially highlight parts of the genome exhibiting patterns of adaptive introgression and thus playing a key role in the adaptive radiation process.…”

Section: A a A B Bmentioning

confidence: 99%

“…However, the main summary statistics obtained by the two studies were congruent (Marcionetti et al 2019, Chapter 2), which gave the first hint that the overall genomic architecture within the genus is conserved. This data was recently augmented with whole-genome sequencing data for all 28 species of clownfishes (Schmid et al 2022), following the same procedure as the one described in . The genomic reads of each clownfish species were mapped to the chromosomelevel assembly obtained for A. percula to obtain comparable alignments across all the species sampled (see Schmid et al 2022 for the details).…”

Section: Whole-genomic Data For All Anemonefish Species and The Detec...mentioning

confidence: 99%

“…This data was recently augmented with whole-genome sequencing data for all 28 species of clownfishes (Schmid et al 2022), following the same procedure as the one described in . The genomic reads of each clownfish species were mapped to the chromosomelevel assembly obtained for A. percula to obtain comparable alignments across all the species sampled (see Schmid et al 2022 for the details).…”

Section: Whole-genomic Data For All Anemonefish Species and The Detec...mentioning

confidence: 99%

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Evolution, Development and Ecology of Anemonefishes

Laudet¹,

Ravasi²

2022

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Anemonefishes, one of the most popular and recognizable fishes in the world, are much more than film characters; they are also emerging model organisms for studying the biology, ecology, and evolution of coral reef fishes. They are a group of 28 species often employed to study patterns and processes of social organization, intra-and inter-specific competition, sex change, mutualism, dispersal and connectivity of fish populations, habitat selection, pigment pattern formation, lifespan, and predator-prey interactions. This multi-authored book covers all these areas and provides an update on the research done with this model and the perspective it opens for the future. Key Features• Contains basic and up-to-date information on an emerging fish model • Allows non-specialist readers to grasp the relevance of a wide research area Cover photo: OIST/Kina Hayashi 林希奈 Licensed under CCBY4.0 (attribution) First edition published 2023 by CRC Press

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Section: Incongruence In Phylogenomic Inferencementioning

confidence: 98%

Section: A a A B Bmentioning

confidence: 99%

Section: A a A B Bmentioning

confidence: 99%

Section: Whole-genomic Data For All Anemonefish Species and The Detec...mentioning

confidence: 99%

Section: Whole-genomic Data For All Anemonefish Species and The Detec...mentioning

confidence: 99%

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Evolution, Development and Ecology of Anemonefishes

Laudet¹,

Ravasi²

2022

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

Schmid,

Salvy,

Jimenez

et al. 2023

Preprint

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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 onAmphiprion 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 ofA. clarkiihas been under debate. We used whole-genome resequencing data of 67A. clarkiispecimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found thatA. clarkiispread 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 ofA. 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 ofA. clarkiias a single species.

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Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation

De Jode,

Quattrini,

Chiodo

et al. 2024

Preprint

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The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes- a charismatic group of 28 described species in the genus Amphiprion. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time. Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA. The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership.

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Extensive hybridisation throughout clownfishes evolutionary history

Cited by 8 publications

References 106 publications

Evolution, Development and Ecology of Anemonefishes

Evolution, Development and Ecology of Anemonefishes

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

Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation

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