Population genomics of degenerative genome evolution

基因组进化最显著的特征之一是在退行性进化的情况下发现的，即基因组的大片区域经历基因沉默和丢失。这种基因组退化是令人惊讶的，因为它与自然选择应该不断推动基因改善功能的一般预测背道而驰。尽管如此，大规模的基因退化已经反复发生，包括非重组性染色体上基因的复发性变性，以及全基因组复制后重复基因的丢失。驱动退化进化的进化力量仍不清楚；一种可能性是，它可能是由基因失活和损失的“被动”过程驱动的，因为自然选择的效力降低了。虽然减少选择可能很重要，但适应过程也可能起作用：衍生基因拷贝之间的适应度差异可能导致适应性基因失活和丢失，加速退化。***在本提案中，我的实验室将研究几个正在经历最近转变的系统，这些系统可以测试驱动退化进化的力量。首先，我们将研究一个最近衍生的物种的基因组进化，该物种经历了全基因组复制（多倍体），荠菜。我们将研究全基因组复制后的适应和基因组进化的早期动态，以测试经历退化和沉默的基因是否受到更高的适应进化率的影响。我们还将测试亲本物种过去的进化史是否会影响新近多倍体的基因沉默和丢失。其次，我们将使用比较基因组和RNA测序来鉴定具有“年轻”性染色体的Rumex植物属的性别连锁基因；这将使我们能够量化基因退化和重组抑制的程度，并询问X染色体上的适应性进化是否会加速y染色体上的基因沉默和丢失。这种比较方法应该能够对驱动物种间退化进化差异率的因素有独特的见解。最后，在月见草属（Oenothera）中多次发生有性繁殖的有效丧失。我们将在这个系统中进行比较基因组学，以调查这些无性谱系经历基因退化和丧失的程度。我们还将研究在一个无性谱系中，基因退化是否会被单倍体花粉期的基因表达所阻止，在这个阶段，有害和有益的突变会暴露在选择中。总之，这些退化性进化的研究将有助于对倍性（基因拷贝数）和重组缺失在驱动自然选择效能中的联合和独特作用，以及适应性进化在基因沉默和缺失中的作用提供新的见解

One of the most striking features of genome evolution is found in cases of degenerative evolution, whereby large regions of the genome experience gene silencing and loss. Such genome degeneration is surprising, as it runs counter to the general prediction that natural selection should continually be driving genes towards improved function. Despite this, large-scale gene degeneration has occurred repeatedly, including recurrent degeneration of genes on non-recombining sex chromosomes, and loss of duplicate genes following whole genome duplication. The evolutionary forces driving degenerative evolution remain unclear; one possibility is that it may be driven by a 'passive' process of gene inactivation and loss through a reduction in the efficacy of natural selection. While reduced selection is likely important, the process of adaptation may also contribute: differences in fitness between derived gene copies may lead to adaptive gene inactivation and loss, accelerating degeneration. ***In this proposal, my lab will examine several systems experiencing recent transitions that enable tests of the forces driving degenerative evolution. First, we will examine genome evolution in a recently derived species that experienced whole genome duplication (polyploidy), Capsella bursa-pastoris. We will investigate the early dynamics of adaptation and genome evolution following whole genome duplication, to test whether genes experiencing degeneration and silencing are subject to higher rates of adaptive evolution. We will also test whether the past evolutionary history of parental species influences gene silencing and loss in a recent polyploid. Second, we will use comparative genome and RNA sequencing to identify sex-linked genes across the plant genus Rumex, which has 'young' sex chromosomes; this will allow us to quantify the extent of gene degeneration and recombination suppression, and ask whether adaptive evolution on the X chromosome accelerates gene silencing and loss on the Y. This comparative approach should enable unique insights into the factors driving differential rates of degenerative evolution across species. Finally, effective loss of sexual reproduction has occurred numerous times in the evening primrose genus Oenothera. We will conduct comparative genomics in this system to investigate the extent to which these asexual lineages experience gene degeneration and loss. We will also investigate whether gene degeneration in an asexual lineage is halted by the expression of genes in the haploid pollen phase, where deleterious and beneficial mutations become exposed to selection. Overall, these studies of degenerative evolution will help provide new insights into the joint and unique effects of ploidy (gene copy number) and loss of recombination in driving the efficacy of natural selection, and the role of adaptive evolution in gene silencing and loss.**