Genomic Architecture of the Clownfish Hybrid Amphiprion leucokranos
Schmid, Sarah, Hartasánchez, Diego A., Huang, Wan Ting, Gainsford, Ashton, Jones, Geoffrey P., and Salamin, Nicolas (2025) Genomic Architecture of the Clownfish Hybrid Amphiprion leucokranos. Genome Biology and Evolution, 17 (3). evaf031.
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Abstract
Natural hybridization is increasingly recognized as playing a significant role in species diversification and adaptive evolution. Amphiprion leucokranos, the naturally occurring clownfish hybrid between Amphiprion chrysopterus and Amphiprion sandaracinos, is found within the hybrid zone of the two parental species. Based on whole-genome sequencing of parental and hybrid individuals sampled in Kimbe Bay, Papua New Guinea, we found that most of the hybrids collected were first-generation hybrids, a few were first- and second-generation backcrosses with A. sandaracinos, and the first evidence, to our knowledge, of both an early backcross with A. chrysopterus and a second-generation hybrid in the wild, highlighting the richness and diversity of genomic architectures in this hybrid zone. The frequent backcrossing with A. sandaracinos has led to higher levels of introgression from A. chrysopterus into the A. sandaracinos genomic background, potentially allowing for adaptive introgression. We have additionally identified morphological features which could potentially allow differentiating between first-generation hybrids and backcrosses. By comparing population genetic statistics of first-generation hybrids, backcrosses, parental populations within the hybrid zone, and parental allopatric populations, we provide the context to evaluate population differentiation and the consequences of ongoing hybridization. This study is the first whole-genome analysis of a clownfish hybrid population and builds upon the growing body of literature relative to the evolutionary outcomes of hybridization in the wild and its importance in evolution.
| Item ID: | 88260 |
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| Item Type: | Article (Research - C1) |
| ISSN: | 1759-6653 |
| Keywords: | admixture, hybrid zone, hybridization, introgression, whole-genome |
| Copyright Information: | © The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com. |
| Date Deposited: | 07 Apr 2026 04:52 |
| FoR Codes: | 31 BIOLOGICAL SCIENCES > 3103 Ecology > 310305 Marine and estuarine ecology (incl. marine ichthyology) @ 100% |
| SEO Codes: | 18 ENVIRONMENTAL MANAGEMENT > 1805 Marine systems and management > 180504 Marine biodiversity @ 100% |
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