Evolutionary change through genomic admixture in a hybrid fish

越来越多的证据表明，不同血统之间的混合可能会促进进化过程，但它究竟如何影响进化变化仍存在很大争议。一种重要的影响被概括为“基因组休克”或“基因组不稳定”。例如，可转座元件(TES)的激活或非同源重组速率的增加可能会引入新的拷贝。然而，尽管在基因组时代之前就已经知道转座的事实，但在很大程度上仍然不清楚所提出的哪种机制可以解释天然杂交谱系中TE拷贝的积累。在这里，我建议通过利用技术进步、杂交起源的年轻谱系(入侵棉花)以及可用于研究它的广泛经验和资源来解决关于混合基因组进化动力学的问题。在我最近对欧洲棉花基因复制和转座的全基因组分析中，我发现入侵棉花的重复和转座元件的拷贝数明显增加。这可以用转座爆发来解释，也可以用着丝粒区域的扩张来解释，那里有丰富的重复元件和TES。着丝粒扩张可能代表着丝粒长度不相等的补偿机制，当两个亲本物种杂交时(着丝粒驱动)。因此，杂交种中TE的积累可以用转座猝发来解释，也可以用基因组稳定的间接效应来解释。我建议将长阅读测序与不同的实验方法相结合，旨在区分TE活动和重复区域的扩展作为TE积累的可能原因。基因组稳定性的进化变化将通过全种群的结构重排数据进行评估。这些数据将使用纳米孔测序从杂交种群和亲本种群中收集。超长序列的产生将允许组装着丝粒区域，这可以通过使用CENP-A抗体获得单个着丝粒序列读数的CHIP-SEQ实验来测试杂交后代的大小扩展。可能影响转座子沉默的甲基化模式的变化也将使用纳米孔测序数据进行调查。最后，我将使用小RNA测序来测试小RNA介导的TE沉默在侵袭性棉花中的快速进化。

Evidence that admixture between divergent lineages may enhance evolutionary processes is accumulating, but how exactly it affects evolutionary change is still highly contentious. One effect of great relevance is broadly summarized under the terms “genomic shock” or “genomic instability”. For example, activation of transposable elements (TEs) or increased rates of non- homologous recombination may introduce new copies. However, despite the fact that transposition has been known since before the genomic era, it remains largely unknown which of the proposed mechanisms explain the accumulation of TE copies in natural hybrid lineages. Herein, I propose to address questions regarding evolutionary dynamics of admixed genomes by taking advantage of technological advances, a young lineage of hybrid origin (Invasive Cottus) and the extensive experience and resources available to study it. In my recent genome wide analysis of gene duplications and transposition in European Cottus I have found a conspicuous increase of copy numbers of repetitive and transposable elements invasive Cottus. This could be explained by a transposition burst, but also by an expansion of centromeric regions where repetitive elements and TEs are abundant. Centromere expansion could represent a mechanism that compensates for unequal centromere lengths when two parental species hybridize (centromere drive). Hence, TE accumulation in hybrids could be explained by a transposition burst or alternatively, as an indirect effect of genomic stabilization. I propose to combine long-read sequencing with different experimental approaches designed to distinguish between TE activity and expansions of repetitive regions as possible causes of TE accumulation. Evolutionary change of genomic stability will be assessed through population-wide data of structural re-arrangements. This data will be collected from both hybrid and parental populations using nanopore sequencing. The generation of ultra-long sequences will allow to assemble centromeric regions, which can be tested for size expansions in hybrids with ChIP-seq experiments that use a CENP-A antibody to obtain individual centromeric sequence reads. Changes in methylation patterns that may affect transposon silencing will also be investigated using the nanopore sequencing data. Finally, I will use small-RNA sequencing to test for rapid evolution of small-RNA-mediated TE silencing in invasive Cottus.