Nemeczek Cait M, Delgado M Lisette, Smith Meg E, MacMillan John, Van Wyngaarden Mallory, Ruzzante Daniel E
Department of Biology Dalhousie University Halifax Nova Scotia Canada.
Inland Fisheries Division Nova Scotia Department of Fisheries and Aquaculture Halifax Nova Scotia Canada.
Ecol Evol. 2025 Sep 15;15(9):e72075. doi: 10.1002/ece3.72075. eCollection 2025 Sep.
Understanding the role of structural variants such as chromosomal inversions in local adaptation among small, isolated populations is an important addition to robust conservation strategies, as most studies investigating inversions to date have been conducted on high gene flow systems. Brook Trout (), an economically important top sportfish, is extremely vulnerable to thermal stress. Local adaptation with respect to this trait warrants investigation as climate change accelerates the loss of cold-stream ecosystems. We performed low-coverage whole-genome sequencing on 192 Brook Trout from 9 small, isolated streams in Nova Scotia, Canada, to assess genetic diversity within and among stream populations. We detected four structural variants in the three westernmost populations, which differ from all other streams in water temperature, streamflow, and surficial geology. The structural variants appear to be chromosomal inversions. These genomic regions exhibit high linkage disequilibrium, and PCA revealed the presence of three karyotypes. Redundancy analysis provides support for potential local adaptation, with temperature, pH, and streamflow being important predictors of genomic variance and statistically significant SNPs falling within potential inverted regions. Mitogenome analyses suggest that a single glacial lineage recolonized the region. Individuals carrying the potential chromosomal inversions exhibited one of five related mitochondrial DNA haplotypes, but these haplotypes were found also in individuals without the potential inversions, suggesting they arose post-recolonization. The genetic differentiation among the nine surveyed Brook Trout populations persists even after exclusion of the potentially inverted regions, suggesting these regions do not control the population structure of these Brook Trout populations.
了解诸如染色体倒位等结构变异在小型孤立种群局部适应中的作用，是对稳健保护策略的重要补充，因为迄今为止，大多数研究染色体倒位的工作都是在高基因流系统中进行的。溪红点鲑（）是一种具有重要经济价值的顶级游钓鱼类，极易受到热应激的影响。随着气候变化加速冷溪生态系统的丧失，针对这一特征的局部适应性值得研究。我们对来自加拿大新斯科舍省9条小型孤立溪流的192条溪红点鲑进行了低覆盖度全基因组测序，以评估溪流种群内部和种群之间的遗传多样性。我们在最西部的三个种群中检测到四个结构变异，这三个种群在水温、水流和表层地质方面与所有其他溪流不同。这些结构变异似乎是染色体倒位。这些基因组区域表现出高度连锁不平衡，主成分分析揭示了三种核型的存在。冗余分析为潜在的局部适应性提供了支持，温度、pH值和水流是基因组变异的重要预测因子，且潜在倒位区域内存在具有统计学意义的单核苷酸多态性。线粒体基因组分析表明，一个单一的冰川谱系重新定殖了该地区。携带潜在染色体倒位的个体表现出五种相关线粒体DNA单倍型之一，但在没有潜在倒位的个体中也发现了这些单倍型，这表明它们是在重新定殖后出现的。即使排除了潜在的倒位区域，九个被调查的溪红点鲑种群之间的遗传分化仍然存在，这表明这些区域并不控制这些溪红点鲑种群的种群结构。
