Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
College of Life Sciences, Shaanxi Normal University, Xi'an, China.
BMC Ecol Evol. 2024 Jun 6;24(1):75. doi: 10.1186/s12862-024-02266-7.
The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear.
In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata.
Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.
相似特征或物种的平行进化为自然选择在进化中的作用提供了强有力的证据。反复进化的特征或物种可能是由单独的新突变或种间基因流驱动的。尽管在许多研究中都报道了平行进化，但与其他研究相比，有文献记录的由基因流引起的平行进化案例却很少。耧斗菜和甘肃耧斗菜都属于耧斗菜属，是最接近的姐妹种。先前的研究报告称，耧斗菜有多次起源，但它们是否是由单独的新突变或基因流驱动的尚不清楚。
在这项研究中，我们对来自两个反复进化的耧斗菜对（包括中国东部的耧斗菜和甘肃耧斗菜）的 158 个个体进行了基因组分析。所有样本根据系统发育和种群结构分为两个明显具有地理分布的不同分支。种群动态建模表明，中国东部的耧斗菜起源于基因流，东部耧斗菜是由西部耧斗菜种群的基因渗入引起的。Treemix 和 D-统计分析也表明，从西部耧斗菜到东部耧斗菜检测到强烈的基因流信号。树系分歧和选择清除分析推断出基因组分歧的平行区域，并鉴定出许多与物种对间生态适应性分歧相关的候选基因。平行分化区域和基因渗入的比较分析证实了基因流促进了耧斗菜的平行进化。
我们的研究结果进一步证实了耧斗菜的多次起源，并强调了基因流的作用。这些发现为杂交后的平行起源提供了新的证据，并深入了解了物种平行起源背后的生态适应机制。
