Evolutionary change through genomic admixture in a hybrid fish

不同谱系之间的混合可能会促进进化过程的证据正在积累，但它究竟如何影响进化变化仍然存在高度争议。一个非常相关的效应被概括为“基因组冲击”或“基因组不稳定”。例如，转座因子（te）的激活或非同源重组率的增加可能引入新的拷贝。然而，尽管事实上早在基因组时代之前就已经知道了转位，但在很大程度上仍然不清楚所提出的机制中，哪一种解释了自然杂交谱系中TE拷贝的积累。在此，我建议通过利用技术进步、杂交起源的年轻谱系（入侵棉）和广泛的经验和资源来研究混合基因组的进化动力学问题。在我最近对欧洲棉的基因复制和转座的全基因组分析中，我发现入侵棉的重复和转座元件的拷贝数显着增加。这可以用转位爆发来解释，但也可以用重复元素和te丰富的着丝点区域的扩展来解释。当两个亲本物种杂交时，着丝粒扩展可能是一种补偿着丝粒长度不等的机制（着丝粒驱动）。因此，TE在杂交种中的积累可以用转位突变或基因组稳定的间接效应来解释。我建议将长读测序与不同的实验方法相结合，旨在区分TE活性和重复区域的扩展，作为TE积累的可能原因。基因组稳定性的进化变化将通过整个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，可以使用ChIP-seq实验测试杂交体的大小扩展，使用CENP-A抗体获得单个着丝粒序列读取。甲基化模式的变化可能影响转座子沉默也将使用纳米孔测序数据进行研究。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Cottus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.