Population genomics of degenerative genome evolution

基因组进化最显著的特征之一是在退化进化的情况下，基因组的大片区域经历基因沉默和丢失。这种基因组退化令人惊讶，因为它与自然选择应该继续推动基因改善功能的普遍预测背道而驰。尽管如此，大规模的基因退化还是反复发生，包括非重组性染色体上的基因反复退化，以及全基因组复制后重复基因的丢失。推动退化进化的进化力量尚不清楚；一种可能性是，它可能是由通过自然选择效率降低而导致的基因失活和丧失的“被动”过程驱动的。虽然减少选择可能很重要，但适应过程也可能起到作用：衍生基因拷贝之间的适合度差异可能会导致适应性基因失活和丢失，从而加速退化。 在这项提案中，我的实验室将研究几个最近经历转变的系统，这些系统能够测试推动退化进化的力量。首先，我们将研究最近衍生的经历了全基因组复制(多倍体)的物种的基因组进化，法氏囊野菜。我们将研究全基因组复制后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具有更高的适应性进化速度。我们还将测试亲本物种过去的进化史是否影响最近的多倍体中的基因沉默和丢失。其次，我们将使用比较基因组和RNA测序来识别Rumex属植物中与性别相关的基因，Rumex属植物具有年轻的性染色体；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使我们对驱动不同物种退化进化的不同速度的因素有独特的见解。最后，在月见草属植物中，有性生殖的有效丧失已多次发生。我们将在这个系统中进行比较基因组学，以调查这些无性世系经历基因退化和丢失的程度。我们还将调查无性世系中的基因退化是否会因为单倍体花粉阶段的基因表达而停止，在单倍体花粉阶段，有害和有益的突变会暴露在选择之下。总体而言，这些关于退化进化的研究将有助于对倍性(基因拷贝数)和重组丢失在驱动自然选择效率方面的联合和独特影响，以及适应性进化在基因沉默和丢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.