Chengmin Sun¹ , Rudi Mai²

1 Center for Tropical Marine Fisheries Research, Hainan Institute of Tropical Agricultural Resouces, Sanya, 572025, Hainan, China
2 Tropical Biological Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
Author    Correspondence author
International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2   
Received: 18 Jan., 2025    Accepted: 24 Feb., 2025    Published: 06 Mar., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Siniperca or Chinese perch is a freshwater fish family indigenous to East Asia, of great economic value and ecological particularity. Though of great significance in aquaculture, the phylogenetic histories of the Siniperca genus are unclear due to morphological convergence and a dearth of molecular data. We rebuilt the genome-wide single-copy orthologous genes-based phylogenetic framework of Siniperca and inferred divergence times between species using a molecular clock model in this study. We further performed comparative genomics to identify expansions of gene families, positive selection signals, and adaptive evolutionary trajectories linked with ecological specialization. Several genetic candidates for environmental tolerance, immune response, and sensory systems were detected, suggesting lineage-specific adaptation to various freshwater environments. This study not only illuminates the phylogenetic history of Siniperca, but also reveals the genetic mechanism of its adaptive divergence, providing theoretical evidence for species conservation, utilization of resources, and molecular breeding in aquaculture.

Siniperca; Phylogenetic reconstruction; Comparative genomics; Adaptive evolution; Freshwater fish