One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex
- 1Marine Evo-Evo-Devo Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
Abstract
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.
Related
- Temporal dynamics of incomplete lineage sorting, introgression and divergence in eucalypts distributed across an expansive and ancient landscape
- Phenotypic and genetic variation among Rhododendron arboreum species complex widely distributed throughout the Himalayas suggests an obscure geographic origin of the clade
- Beyond elevation: climate, geography, and the diversification of Himalayan Rhododendrons. A commentary on ‘Phenotypic and genetic variation among Rhododendron arboreum species complex widely distributed throughout the Himalayas suggests an obscure geographic origin of the clade’
- Genome-wide parallelism in divergence and diversity across three Hydrophis sea snake species
- Regulatory divergence and effector turnover shape species-specific bacterial clearance in Drosophilidae
BibTeX
@misc{zwahlen2026species,
title = {{One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex}},
author = {J. Zwahlen and A. Marcionetti and M. Mercader and S. Miura and C. Leiva and J. D. Reimer and N. Salamin and V. Laudet},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.17.752292},
url = {https://www.biorxiv.org/content/10.64898/2026.09.17.752292v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex
AU - J. Zwahlen
AU - A. Marcionetti
AU - M. Mercader
AU - S. Miura
AU - C. Leiva
AU - J. D. Reimer
AU - N. Salamin
AU - V. Laudet
PY - 2026
DA - 2026/09/17
PB - bioRxiv
DO - 10.64898/2026.09.17.752292
UR - https://www.biorxiv.org/content/10.64898/2026.09.17.752292v1
AB - 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.
ER -