Phylotranscriptomic analysis reveals the phylogeny and evolutionary history of Epinephelidae

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.