School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom.
Tanzanian Fisheries Research Institute, Kyela Research Centre, P.O. Box 98, Kyela, Mbeya, Tanzania.
Mol Biol Evol. 2022 Nov 3;39(11). doi: 10.1093/molbev/msac251.
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
在淡水鱼类中，深度梯度的快速生态物种形成反复发生，然而促进这种多样化的分子机制通常尚不清楚。在非洲火山口湖马索科湖中，慈鲷 Astatotilapia calliptera 在过去 1000 年中分化为浅岸和深底栖生态型，其颚结构明显不同。利用全基因组转录组数据，我们探索了两种主要的调控转录机制，表达和剪接-QTL 变体，并研究了它们对功能表型基础上的差异基因表达的贡献。我们在生态型之间鉴定出了 7550 个具有显著差异表达的基因，其中 5.4%受顺式调控表达 QTL 调控，9.2%受顺式调控剪接 QTL 调控。我们还发现与颅面发育相关的差异表达基因存在强烈的分歧选择信号。这些结果表明，大规模转录组修饰在早期物种形成过程中发挥了重要作用。我们得出的结论是，调节变体是选择的重要目标，可在适应性多样化过程中驱动与生态相关的基因表达差异。
