Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component‐based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence‐simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.

中文翻译：

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反复杂交的摇蚊姐妹类群中的基因组分化景观表明相互基因流和分离之间存在稳定的稳态

分歧大多被视为一个渐进的过程，通常是由针对单个基因座的选择引发的，最终导致由于连锁而不断增加的基因组分离。然而，最近的研究表明，该过程可能会停滞在中间稳定平衡状态，而无法实现完全的基因组分离。我们通过分析分歧景观，测试了两个经常杂交的非咬性蠓姐妹类群摇蚊和猪摇蚊之间的基因组分离程度。使用基于主成分的方法，我们估计只有约 28.44% 的基因组是相互分离的，而其余的仍然是交换的。分歧景观被分割成平均 30 kb 的孤立区域，分布在整个基因组中。选择和分歧时间强烈影响孤立区域的长度，而局部重组率仅具有较小的影响。从几个合并模拟的发散场景中获得的发散时间分布与在近似贝叶斯计算框架中观察到的发散时间估计的比较有利于过去短暂且结束的发散事件。大多数分歧发生在大约 450 万代之前的短时间内，随后通过大部分基因组的持续杂交实现相互基因流之间的稳定平衡，并由于基因渗入的快速纯化选择而在某些区域进行分离，并得到高效的支持。种群规模和重组率。