Wang Zhongxing, Yao Dongji, Zhao Benchi, Shao Yi, Li Fan, Ma Ka Yan, Cui Rongfeng
School of Ecology & State Key Laboratory of Biocontrol, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China.
Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum, Shanghai, China.
Mol Ecol. 2025 Jul 21:e70045. doi: 10.1111/mec.70045.
Inbreeding may initially lower population fitness by converting masked genetic load into realised load. As deleterious variants become increasingly homozygous, purifying selection acts more effectively to purge load. Nevertheless, not all populations can survive the initial fitness decline, and it would be interesting to examine scenarios that facilitate their survival. Herein, we assembled chromosome-level reference genomes of two paradise fishes, Macropodus hongkongensis and M. opercularis, and resequenced 109 wild individuals of 15 populations to infer the history of runs of homozygosity (ROH) formation, effectiveness of purging in ROH, and the role of balancing selection in maintaining lingering polymorphisms in independently evolved small populations. While the two species diverged in genes potentially adaptive to their local niches, there were large variations in inbreeding coefficients and the amount of genetic load within species. Three populations became highly inbred (F > 0.50) from independent origins. Simulations showed that the ROH segment size distribution can be best explained by living in a small population for hundreds, if not thousands, of generations. The genetic load negatively correlated with summed ROH length. This was driven by more effective purging in ROH. The non-ROH regions between individuals from different high-F populations were repeatable, with nearby signals of balancing selection persisting in the polymorphic genomic regions through species divergence.
近亲繁殖最初可能会通过将隐性遗传负荷转化为实际负荷来降低种群适应性。随着有害变异变得越来越纯合，净化选择更有效地清除负荷。然而，并非所有种群都能在最初的适应性下降中存活下来，研究有助于它们生存的情况将是很有趣的。在此，我们组装了两种斗鱼（香港斗鱼和盖斑斗鱼）的染色体水平参考基因组，并对15个种群的109个野生个体进行了重测序，以推断纯合片段（ROH）形成的历史、ROH中净化的有效性，以及平衡选择在维持独立进化的小种群中持续存在的多态性方面的作用。虽然这两个物种在可能适应其当地生态位的基因上存在差异，但物种内的近亲繁殖系数和遗传负荷量存在很大差异。三个种群从独立起源开始就高度近亲繁殖（F＞0.50）。模拟表明，ROH片段大小分布最好的解释是在一个小种群中生活了数百代，如果不是数千代的话。遗传负荷与ROH总长度呈负相关。这是由ROH中更有效的净化驱动的。来自不同高F值种群个体之间的非ROH区域是可重复的，通过物种分化，平衡选择的附近信号在多态基因组区域持续存在。
