Evolutionary change through genomic admixture in a hybrid fish

不同谱系之间的混合可能会增强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很大争议。一个非常相关的效应被概括为“基因组休克”或“基因组不稳定性”。例如，转座因子（TE）的激活或非同源重组速率的增加可以引入新的拷贝。然而，尽管事实上，转座已经知道，因为之前的基因组时代，它仍然在很大程度上是未知的，所提出的机制，解释TE拷贝在自然杂交谱系的积累。在这里，我建议解决有关混合基因组的进化动力学的问题，利用技术进步，一个年轻的血统的混合起源（入侵Cottus）和广泛的经验和资源，可用于研究it. In我最近的基因组范围内的基因复制和转座分析在欧洲Cottus我发现了一个显着增加的重复和转座因子入侵Cottus的拷贝数。这可以通过转座爆发来解释，但也可以通过重复元件和TE丰富的着丝粒区域的扩展来解释。着丝粒扩展可能代表了一种机制，补偿不平等的着丝粒长度时，两个亲本物种杂交（着丝粒驱动）。因此，TE在杂种中的积累可以通过转座爆发来解释，或者作为基因组稳定的间接影响。我建议将联合收割机长读测序与不同的实验方法相结合，这些实验方法旨在区分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。将使用纳米孔测序从杂交群体和亲本群体收集该数据。超长序列的产生将允许组装着丝粒区域，其可以使用使用CENP-A抗体以获得单个着丝粒序列读数的ChIP-seq实验来测试杂交体中的大小扩展。也将使用纳米孔测序数据研究可能影响转座子沉默的甲基化模式的变化。最后，我将使用小RNA测序来测试入侵杜父鱼中小RNA介导的TE沉默的快速进化。

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.