Genetics of diapause termination timing in the water flea Daphnia - identifying genes and evolutionary processes of relevance in nature

在季节性环境中，许多生物的生命周期以休眠期为特征。这允许在不利的条件下存活，直到下一个生长季节开始时休眠结束。水蚤是一种甲壳类浮游动物，是静止水域中关键的食草动物，它通过产生滞育卵来实现这一点。滞育终止的确切时间是一种与适应度相关的生活史表型，在不同的生境之间有自适应的区别。经验证据表明，自然种群适应当前的气候变化是通过改变这种时间，而不是改变他们的热最佳值或耐受性。有必要揭示控制这种时间的遗传结构，以便了解这种特征如何在自然种群中进化。在此，我们提出了一种研究策略来揭示控制水蚤滞育释放时间的遗传结构。这将通过基因定位，随后进一步表征和验证所产生的候选基因座来实现。将在纬度梯度和微地理尺度上评估自然界中基于遗传的时间分化的流行程度。为了测试该性状在自然界中的适应性分化是否由相同基因和途径的重复招募引起，将使用候选基因座进行关联研究。此外，适应性等位基因的来源和适应性进化的机制将使用古基因组学方法进行追踪。在水蚤中，通过分析沉积物中保存的滞育休息阶段，这是可行的。我们将对候选基因座进行测序，并通过祖先创始群体和衍生群体的中性标记评估遗传背景。利用这些数据，我们将确定滞育释放时间的差异是通过(a)从创始群体中存在的遗传变异中选择(b)优势等位基因的混合和渗入到常驻群体的遗传背景中，还是(c)在高度可变的基因组区域中重新突变而进化的。

In seasonal environments, the life cycle of many organisms is characterized by a period of dormancy. This allows surviving unfavourable conditions until dormancy is terminated upon the onset of the next growth season. In the water flea Daphnia, a crustacean zooplankter that is a pivotal herbivore in standing waters, this is realised through the production of diapausing eggs.The exact timing of diapause termination is a fitness relevant life history phenotype which is adaptively differentiated between habitats. Empirical evidence suggests that natural populations adapt to current climate change by the modification of such timing rather than shifting their thermal optima or tolerance. There is a need to reveal the genetic architecture in control of this timing in order to understand how this trait can evolve in natural populations. Here, we present a research strategy to reveal the genetic architecture controlling the timing of release from diapause in Daphnia. This will be achieved through gene mapping followed by further characterization and validation of the resulting candidate loci. The prevalence of genetically based timing differentiation in nature will be assessed for populations over a latitudinal gradient and on a micro-geographic scale. In order to test whether adaptive differentiation of this trait in nature is caused by the repeated recruitment of the same genes and pathways, association studies using the candidate loci will be performed. Additionally, the source of adaptive alleles and mechanisms of adaptive evolution will be traced using a paleogenomics approach. In Daphnia, this is feasible through the analysis of diapause resting stages which are preserved in sediments. We will sequence candidate loci and assess the genetic background through neutral markers in ancestral founding populations and derived populations. Using these data, we will determine if divergence in diapause release timing evolves via (a) selection from standing genetic variation in the founding populations (b) admixture and introgression of advantageous alleles into a resident population's genetic background or (c) de novo mutation in highly variable genomic regions.