Genomics of adaptation and diversification in evolving populations of microbes

生物为什么以及如何变得如此多样化一直是生物学的中心问题--更准确地说是困扰。答案的历史将是生物学本身的历史，如果不是一个相当准确的晴雨表的态度和道德的社会。这也是促使我进行研究的问题。我的目的是为多样性的进化提供一个一般理论。这一提议探讨了生态多样化的潜在遗传原因。从本质上讲，我们试图揭示被称为进化的“圣杯”：负责适应的遗传变化。为了做到这一点，我们将联合收割机实验进化（一种使用在实验室特定条件下进化的微生物种群的技术）与允许快速和廉价的全基因组测序的新技术相结合。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，我概述了一系列项目，使用这些技术来回答问题，如：有多少基因负责生态多样化？适应性进化的可重复性如何？什么样的突变是适应性多样化的原因？总的来说，这些问题的答案使我们能够迈出第一步，走向一个通用的多样性理论，一个整合生态学和遗传学。这项工作的结果将有广泛的影响，我们的基本知识，多样性如何演变，以及通知更多的实际问题，在人类和生态系统健康的多样性的进化出现的影响。

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.