Mutation, adaptation, and speciation in experimental populations of fungi

这项提议的总体目标是观察和测量实验种群中的突变、适应和早期物种形成，每个种群都有一个已知的祖先和历史。突变是所有遗传变异的最终来源，但对自然种群中突变及其发生率的推断仍然是间接的。目的1对一种重要的树根条件致病菌高卢蜜环菌（Armillaria gallica）的长寿个体进行取样。高卢花的每一个个体都是在一次交配中产生的，然后成长为一个离散的空间领土，包括许多相邻的树根系统。实际上，这留下了一个随时间增长的空间记录，并允许以一种直接的方式估计选择性中性和有利突变的速率，这在以前的自然条件下是不可能的。为了确定突变，将对个体样本的整个基因组进行测序。目的2观察12个二倍体酵母群体在高盐和低糖环境下繁殖500代后的突变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，因为最早的物种形成事件可能会被分裂后漫长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，所有潜在的突变都在DNA水平上被识别出来，并以适应性效应为特征。这将确定哪种适应模式和生殖隔离最普遍发生。目标3是在接下来的四年里，通过每天的转移，在各自的环境中繁殖所有12个酵母种群，再繁殖10000代，将观察适应和物种形成的时间框架延长一个数量级以上，再次充分表征潜在的分子决定因素。这将确定哪些适应和隔离机制会随着时间的推移而改变，并将确定有信心出现的任何新机制。

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.