Genomics of adaptation and diversification in evolving populations of microbes

为什么以及如何使生命变得如此多样化一直是生物学中的中心问题--更准确地说，是痴迷。答案的历史就是生物学本身的历史，如果不是相当准确地反映整个社会的态度和习俗的晴雨表的话。这也是激励我进行研究的问题。我的目的是为多样性的进化提供一个普遍的理论。这项建议探讨了生态多样性的潜在遗传原因。从本质上讲，我们正试图发现已被称为进化的“圣杯”：导致适应的基因变化。为了做到这一点，我们结合了实验进化，这是一种使用在实验室特定条件下进化的微生物种群的技术，以及允许快速和廉价的全基因组测序的新技术。通过比较进化和祖先基因类型的基因组，我们可以确定导致适应的基因变化。在这份提案中，我概述了一系列使用这些技术来回答以下问题的项目：有多少基因对生态多样性负责？适应性进化的可重复性如何？哪些突变是导致适应性多样化的原因？综上所述，这些问题的答案让我们迈出了迈向多样性一般理论的第一步，一个整合了生态学和遗传学的理论。这项工作的结果将对我们关于多样性如何演变的基本知识产生广泛的影响，并为人类和生态系统健康方面受到多样性进化的影响的更多实际问题提供信息。

Why and how life became so diverse has been the central problem – one might more accurately say obsession – in biology. A history of answers would be a history of biology itself, if not a fairly accurate barometer of the attitudes and mores of society at large. It is also the problem that motivates my research. My aim is to provide a general theory for the evolution of diversity. This proposal explores the underlying genetic causes of ecological diversification. In essence, we are attempting to uncover what has become known as the ‘holy-grail’ of evolution: the genetic changes responsible for adaptation. To do this, we combine experimental evolution, a technique that uses microbial populations evolving in the defined conditions of the laboratory, with new technologies that permit rapid and inexpensive whole genome sequencing. By comparing the genomes of evolved and ancestral genotypes, we can identify the genetic changes responsible for adaptation. In this proposal I outline a series of projects that use these techniques to answer questions such as: How many genes are responsible for ecological diversification? How repeatable is adaptive evolution? What kinds of mutations are responsible for adaptive diversification? Taken together, the answers to these questions allow us to take the first steps towards a general theory of diversity, one that integrates both ecology and genetics. The results of this work will have wide implications both for our basic knowledge about how diversity evolves as well as informing more practical problems in human and ecosystem health that are impacted by the evolutionary emergence of diversity.