Phylotranscriptomic analysis reveals the phylogeny and evolutionary history of Epinephelidae
5 affiliations
- 1School of Life Sciences, State Key Laboratory of Biocontrol / Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) / Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
- 2Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR 999077, China
- 3Molecular Population Genetics Group, Temasek Life Sciences Laboratory, Singapore City 117604, Singapore
- 4China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, Guangdong 510275, China
- 5Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture and Rural Affairs, Hainan Engineering Research Center for Germplasm Innovation and Utilization, Hainan Chenhai Aquatic Co., Ltd, Sanya, Hainan 570000, China
Abstract
Coral reef fishes, distinguished by remarkable species diversity and unique speciation mechanisms, offer an exceptional framework for understanding evolutionary diversification. As ecologically dominant predators, groupers (family Epinephelidae) exemplify high diversity in coral reef ecosystems, yet their phylogenetic relationships remain partially unresolved in previous studies based on mitochondrial and nuclear markers. Here, we performed a comprehensive phylotranscriptomic analysis of 92 specimens representing 32 species across seven genera of Epinephelidae. Leveraging concatenated nucleotide data analyzed with maximum likelihood and Bayesian inference, we first reconstructed a robust transcriptomic phylogeny with markedly enhanced resolution and nodal support compared to traditional marker-based frameworks. Our results revealed Plectropomus as the earliest diverging lineage, resolving a longstanding debate regarding the basal divergence within this family, and robustly supported the non-monophyly of Epinephelus and Cephalopholis. The origin and early diversification of Epinephelidae, currently distributed across the Indian and Pacific Oceans, may have occurred in the West Pacific during the Paleocene, followed by subsequent dispersal mediated by prevailing ocean currents. Furthermore, we found that the vicariance and speciation of major clades were likely driven by repeated episodes of sea level regression associated with glacial cycles. Enhanced upwelling and elevated primary productivity in recent periods may have further promoted the rapid radiation of groupers. To our knowledge, this represents the first application of phylotranscriptomics in the phylogenetic study of Epinephelidae, providing new insights into its phylogeny and evolutionary history.
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BibTeX
@article{wang2026phylotranscriptomic,
title = {{Phylotranscriptomic analysis reveals the phylogeny and evolutionary history of Epinephelidae}},
author = {Qing-Hua Wang and Wei-Wei Zhang and Zhuo-Ying Weng and Yang-Fan Chen and Xi Wang and Le Wang and Xiao-Chun Liu and Yang Yang and Zi-Ning Meng},
journal = {Zoological Research},
year = {2026},
month = sep,
doi = {10.24272/j.issn.2095-8137.2025.486},
url = {https://doi.org/10.24272/j.issn.2095-8137.2025.486},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Phylotranscriptomic analysis reveals the phylogeny and evolutionary history of Epinephelidae
AU - Qing-Hua Wang
AU - Wei-Wei Zhang
AU - Zhuo-Ying Weng
AU - Yang-Fan Chen
AU - Xi Wang
AU - Le Wang
AU - Xiao-Chun Liu
AU - Yang Yang
AU - Zi-Ning Meng
PY - 2026
DA - 2026/09/18
JO - Zoological Research
DO - 10.24272/j.issn.2095-8137.2025.486
UR - https://doi.org/10.24272/j.issn.2095-8137.2025.486
AB - Coral reef fishes, distinguished by remarkable species diversity and unique speciation mechanisms, offer an exceptional framework for understanding evolutionary diversification. As ecologically dominant predators, groupers (family Epinephelidae) exemplify high diversity in coral reef ecosystems, yet their phylogenetic relationships remain partially unresolved in previous studies based on mitochondrial and nuclear markers. Here, we performed a comprehensive phylotranscriptomic analysis of 92 specimens representing 32 species across seven genera of Epinephelidae. Leveraging concatenated nucleotide data analyzed with maximum likelihood and Bayesian inference, we first reconstructed a robust transcriptomic phylogeny with markedly enhanced resolution and nodal support compared to traditional marker-based frameworks. Our results revealed Plectropomus as the earliest diverging lineage, resolving a longstanding debate regarding the basal divergence within this family, and robustly supported the non-monophyly of Epinephelus and Cephalopholis. The origin and early diversification of Epinephelidae, currently distributed across the Indian and Pacific Oceans, may have occurred in the West Pacific during the Paleocene, followed by subsequent dispersal mediated by prevailing ocean currents. Furthermore, we found that the vicariance and speciation of major clades were likely driven by repeated episodes of sea level regression associated with glacial cycles. Enhanced upwelling and elevated primary productivity in recent periods may have further promoted the rapid radiation of groupers. To our knowledge, this represents the first application of phylotranscriptomics in the phylogenetic study of Epinephelidae, providing new insights into its phylogeny and evolutionary history.
SN - 2095-8137
ER -