Mutation, adaptation, and speciation in experimental populations of fungi

这项建议的总体目标是观察和测量实验种群中的突变、适应和初始物种形成，每个实验种群都有已知的祖先和历史。突变是所有遗传变异的最终来源，但对突变及其在自然种群中的比率的推断仍然是间接的。目的1是对树根上重要的机会性真菌病原菌--蜜环菌的长寿个体进行采样。银杏的每一个个体都发生在一个交配事件中，然后生长到占据一个离散的空间区域，包括许多相邻的树木根系。实际上，这留下了一个随时间增长的空间记录，并允许以一种以前在自然条件下不可能实现的直接方式估计选择性中性和有利突变的比率。为了识别突变，将对个体样本的整个基因组进行测序。目的2观察在高盐和低糖两种不同环境中繁殖500代的12个二倍体酿酒酵母种群的突变情况及其对适合度和生殖隔离的影响。大多数关于物种形成的研究，即一个物种分裂成两个物种的过程，都是基于现存的、羽翼丰满的物种。这可能是有问题的，因为物种形成的最早事件可能被自分裂以来漫长的进化历史中积累的变化所掩盖。这里提出的进化实验将把重点放在物种形成过程的早期阶段，所有潜在的突变都是在DNA水平上识别的，并以适应效应为特征。这将确定哪些适应模式和生殖隔离发生得最普遍。目标3是将所有12个酵母种群在各自的环境中再繁殖10,000代，在接下来的四年里每天进行转移，将观察适应和物种形成的时间框架延长一个数量级以上，同样充分描述潜在的分子决定因素。这将确定哪些适应和隔离机制随着时间的推移而被修改，并将确定任何有信心出现的新机制。

The overall goal of this proposal is to observe and measure mutation, adaptation, and incipient speciation in experimental populations, each with a known ancestor and history. Mutation is the ultimate source of all genetic variation and yet inferences on mutations and their rates in natural populations have remained indirect. Objective 1 is to sample long-lived individuals of Armillaria gallica, an important opportunistic fungal pathogen of tree roots. Each individual of A. gallica arises in a single mating event and then grows to occupy a discrete spatial territory including many adjacent tree root systems. In effect, this leaves a spatial record of growth over time and allows estimation of the rate of selectively neutral and advantageous mutations in a direct manner not previously possible under natural conditions. To identify the mutations, the entire genomes of samples of individuals will be sequenced. Objective 2 is observe the mutations and measure their effects on fitness and on reproductive isolation in 12 diploid populations of the yeast Saccharomyces cerevisiae, that were propagated in two different environments, high salt and low glucose for 500 generations. Most studies of speciation, the process by which one species splits into two, are based on extant, fully fledged species. This can be problematic because the earliest events of speciation may be obscured by changes accumulated during the long evolutionary history since the split. The evolution experiments proposed here will bring focus to the earliest stages of the speciation process, with all underlying mutations identified at the DNA level and characterized for fitness effects. This will establish which modes of adaptation and reproductive isolation occur most generally. Objective 3 is to propagate all 12 yeast populations for a further 10,000 generations in their respective environments with daily transfers over the next four years, extending the time frame for observation of adaptation and speciation by more than an order of magnitude, again with full characterization of the underlying molecular determinants. This will establish which mechanisms of adaptation and isolation are modified over time and will identify any new mechanisms that emerge with confidence.