斑鳠(Hemibagrus guttatus)被誉为“珠江四大名鱼”之首, 然而在梯级开发、水体污染、过度捕捞等多种因素的影响下, 其野外资源量严重衰退, 并于2021年2月被列为国家二级重点保护野生动物。为了能够有效支撑斑鳠种群的科学管理与保护工作, 本研究在珠江水系和韩江水系19个站位收集了111尾斑鳠样本, 基于线粒体全基因组数据, 综合系统发育、分化时间估算、种群遗传学等多种研究方法开展了遗传多样性、遗传结构与种群历史动态的研究。种群遗传学分析结果显示, 珠江和韩江水系的斑鳠种群均呈现较低水平的核苷酸多样性, 表明斑鳠种群的保护刻不容缓。系统发育分析和单倍型网络图发现, 珠江水系和韩江水系的斑鳠种群分别形成独立的进化谱系, 其中珠江水系的斑鳠种群形成了两个共域分布的亚谱系。分化时间估算发现珠江和韩江两个水系斑鳠种群的分化时间介于0.284-0.401百万年前(Ma), 珠江水系两个亚谱系的分化时间介于0.092-0.132 Ma, 暗示华南地区更新世气候变化可能是斑鳠种群谱系分化的重要驱动因素。种群动态历史分析发现, 斑鳠种群分别在0.072-0.101 Ma和0.024-0.033 Ma期间经历了明显的种群收缩和种群扩张事件, 并支持珠江水系斑鳠种群在0.024-0.032 Ma之间经历了显著的种群扩张, 表明后更新世期间的冰期与间冰期循环引起的海平面波动及末次盛冰期可能对斑鳠种群的分布与有效种群大小造成了显著影响。基于上述研究结果, 建议加强渔政监管力度或者划立保护区, 提升韩江水系斑鳠种群的关注度, 并指出放流前需明晰放流样本的(亚)谱系来源, 避免非本地谱系亲本或者苗种的盲目投放。

Aim: Hemibagrus guttatus has historically been known as one of the “four famously economic fish in the Pearl River”. However, due to cascade development, water pollution, and overfishing, wild populations of H. guttatus have drastically declined. In February 2021, H. guttatus was listed as a national category II key protected wild animal species. The study is to investigate the population genetic structure and evolutionary history of H. guttatus to identify actions that can improve scientific management and protection of wild H. guttatus populations.

Methods: A total of H. guttatus samples were collected from 19 locations in the Pearl River and the Hanjiang River. We used multiple approaches, including phylogeny, divergence time estimation, and population genetics, to explore genetic diversity, genetic structure and population historical demography based on mitochondrial genomes.

Results: Genetic diversity analyses revealed nucleotide diversity in the H. guttatus populations of the Pearl River and Hanjiang River exhibit extremely low nucleotide diversity, indicating an urgent protection of H. guttatus populations is necessary. Phylogenetic trees and haplotype network indicated that H. guttatus populations in the Pearl River and the Hanjiang River formed independent lineages, with two sub-lineages present in the Pearl River. Divergence time estimation analysis suggests that the Pearl River populations and the Hanjiang River populations split between 0.284 and 0.401 million years ago (Ma), while the two sub-lineages in the Pearl River diverged between 0.092 to 0.132 Ma. Bayesian skyline plots suggested that overall H. guttatus populations experienced significant population contraction and expansion between 0.072 and 0.101 Ma and 0.024 and 0.033 Ma, respectively. This analysis also suggested that the Pearl River populations underwent significant population expansion between 0.024 and 0.032 Ma.

Conclusions: Results from this study suggest Pleistocene climate change in South China may be an important driving factor that triggered H. guttatuslineage divergence. Further, sea level fluctuations induced by the late Pleistocene glacial cycles and the Last Glacial Maximum may have influenced the distribution and effective population size of H. guttatus populations. Based on the results of this study, we recommend the following: (1) strengthen supervision of fisheries administration, (2) establish protected areas to maintain H. guttatushabitat, and (3) increase monitoring of Hanjiang River populations. Moreover, the maternal lineage of sampled fish should be determined (by mitochondrial sequencing) before reintroduction to avoid blind release of non-local parents or offsprings into local rivers. Implementation of these practices will help preserve, and even improve, the genetic diversity of H. guttatus, which will allow them to remain an important economic fish for years to come.