Genomics of adaptation and diversification in evolving populations of microbes

生命为何以及如何变得如此多样化一直是生物学的核心问题——或者更准确地说，是困扰。如果答案的历史不能相当准确地反映整个社会的态度和习俗，那么它就是生物学本身的历史。这也是我研究的动力所在。我的目的是为多样性的进化提供一个一般的理论。本提案探讨了生态多样化的潜在遗传原因。从本质上讲，我们正试图揭示进化的“圣杯”：负责适应的基因变化。为了做到这一点，我们将实验进化（一种利用微生物种群在实验室规定条件下进化的技术）与新技术结合起来，这些新技术可以实现快速和廉价的全基因组测序。通过比较进化和祖先基因型的基因组，我们可以确定负责适应的遗传变化。在这个建议中，我概述了一系列使用这些技术来回答以下问题的项目：多少基因负责生态多样化？适应性进化的可重复性如何？什么样的突变导致了适应性多样化？综上所述，这些问题的答案使我们向一个综合了生态学和遗传学的一般性多样性理论迈出了第一步。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以及受多样性进化出现影响的人类和生态系统健康的更多实际问题产生广泛的影响。

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.