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发现的，其中基因组的大区域经历基因沉默和丢失。这样的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退化，以及全基因组复制后重复基因的丢失。退化性进化的驱动力仍然不清楚;一种可能性是，它可能是由一个“被动”的基因失活和损失的过程，通过减少自然选择的功效。虽然减少选择可能很重要，但适应过程也可能有所贡献：衍生基因拷贝之间的适应性差异可能导致适应性基因失活和丢失，加速退化。* 在这个提案中，我的实验室将研究几个最近经历转变的系统，这些系统能够测试驱动退化进化的力量。首先，我们将研究基因组进化在最近衍生的物种，经历了全基因组复制（多倍体），荠菜囊巴斯德。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会经历更高的适应性进化。我们还将测试亲本物种过去的进化史是否会影响最近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测序来识别植物属酸模中的性连锁基因，酸模具有“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加速了Y染色体上的基因沉默和丢失。这种比较的方法应该使独特的见解的因素驱动不同物种的退化进化率。最后，在月见草属（Oenothera）的月见报春花中多次发生有性生殖的有效丧失。我们将在这个系统中进行比较基因组学研究，以调查这些无性系经历基因退化和丢失的程度。我们还将调查是否在无性系的基因退化是停止在单倍体花粉阶段，有害和有益的突变成为暴露于选择的基因的表达。总的来说，这些退化进化的研究将有助于提供新的见解，了解倍性（基因拷贝数）和重组损失在驱动自然选择效力方面的联合和独特影响，以及适应性进化在基因沉默和损失中的作用。

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.**