Genomic responses to rapid environmental change: selection, plasticity and adaptation.

地球环境正在以前所未有的速度变化，其生物有机体将不得不适应或灭绝。对于许多生物体来说，任何适应的至少一部分都可能涉及生命的遗传密码--DNA的变化。进化生物学家长期以来一直对这种进化适应过程感兴趣，尽管我们所知的绝大多数是基于数千年或数百万年发展起来的适应过程。这种进化是通过自然选择的过程进行的，在自然选择的过程中，个体之间的DNA变异使一些个体更成功，而负责的DNA变异在很长一段时间内频率缓慢增加。为了适应人为的环境变化，生物需要更快地进化。这曾被认为是不可能的，但近年来越来越多的证据表明，这是可能发生的。导致这种快速适应的一个机制可能是“表型可塑性”：由环境变化带来的生物体形式或生理(“表型”)的变化。表型可塑性源于DNA表达的变化：细胞读取密码的方式。传统上，表型可塑性并没有被认为在适应过程中有任何特殊的地位，但关于这一点，特别是它对快速适应环境变化的贡献，一直存在着长期的争论。表型可塑性可能会让有机体在快速变化的环境中坚持下去，让DNA的变化有时间积累，并产生与新环境更好的进化匹配。或者，表型可塑性可能表明有机体正在努力应对，这实际上可能会在DNA上产生更强的自然选择。到目前为止，这些不同的适应模型很难测试，但现代技术的进步意味着可以非常准确地测量DNA代码及其表达的变化。在这个项目中，我们将利用这项新技术来研究快速适应短期环境变化的过程。我们将通过将海洋三刺鱼重复引入淡水池塘，并记录在适应的最早阶段DNA密码及其表达的变化来做到这一点。刺鱼是一种小鱼，常见于北半球的海洋中。它们无数次地殖民和适应淡水，在上一个冰河时代结束后，在湖泊和河流中建立了种群。在对淡水的长期适应过程中，刺鱼DNA的变化得到了特别好的记录。众所周知，刺鱼可以非常迅速地适应淡水，表型甚至一些基因会在一到十年内发生显著变化。然而，人们对DNA及其表达的短期变化模式知之甚少。我们将记录在引入淡水后基因的表达是如何改变的，以及在潜在的DNA中发生了什么样的变化。通过量化鱼类在被放入海水中时控制体内盐分的能力与其潜在DNA变异之间的相关性，我们将识别控制这种能力的基因组部分。我们将比较池塘之间的变化模式，以确定这些变化平行发生的程度，或者是独特的，从而揭示进化在多大程度上是可预测的，这是生物学、古生物学和哲学中另一个长期存在的争议。我们的工作将为理解生物体如何适应快速的环境变化提供一个模型。

The Earth's environments are changing at an unprecedented rate, and its living organisms will have to adapt or go extinct. For many organisms at least part of any adaptation will likely involve changes in the genetic code of life, the DNA. Evolutionary biologists have long been interested in this process of evolutionary adaptation, although the overwhelming majority of what we know is based on adaptations which developed over thousands or millions of years. This evolution occurs through the process of natural selection, in which some variations between individuals in their DNA make some individuals more successful, and the DNA variations responsible increase slowly in frequency over long time periods. To allow adaptation to anthropogenic environmental change, organisms will need to evolve much more rapidly. This was once thought impossible, but in recent years there has been increasing evidence that it can happen. One mechanism that might contribute to such rapid adaptation is 'phenotypic plasticity': alterations in the form or physiology ('phenotype') of organisms brought about by changes in the environment. Phenotypic plasticity results from changes in the expression of DNA: the way in which the code is read by cells. Traditionally, phenotypic plasticity has not been acknowledged as having any special place in the process of adaptation, but there has been a long-lasting debate about this, especially its contribution to rapid adaptation to environmental change. Phenotypic plasticity might allow organisms to persist in rapidly changing environments, allowing time for changes in the DNA to accrue and produce a better evolutionary match to the new environment. Alternatively, phenotypic plasticity might indicate that organisms are struggling to cope, which might actually engender stronger natural selection on the DNA. Hitherto, these different models for adaptation have been difficult to test, but advances in modern technology mean that changes in both the DNA code and its expression can be measured with great accuracy.In this project we will take advantage of this new technology to examine the process of rapid adaptation to short term environmental change. We will do so by making replicated introductions of marine three-spined stickleback into freshwater ponds, and recording changes in the DNA code and its expression during the earliest stages of adaptation. Stickleback are small fish, common in oceans across the northern hemisphere. They have colonised and adapted to freshwater innumerable times, establishing populations in lakes and rivers after the end of the last ice age. Changes in the DNA of stickleback that have accrued during this 10,000 years of long-term adaptation to freshwater have been exceptionally well documented. It is also well known that stickleback can adapt very quickly to freshwater, with significant changes in phenotype, and even some genes, occurring within one to ten years. However, the patterns of short-term changes in the DNA and its expression are poorly understood. We will document how the expression of genes alters following introduction to freshwater, and what kinds of changes take place in the underlying DNA. By quantifying correlations between the ability of fish to control the salt in their body when put in seawater, and variations in their underlying DNA, we will identify parts of the genome that control this ability. We will compare patterns of change across ponds to determine the extent to which these occur in parallel, or are idiosynchratic, shedding light on the extent to which evolution is predictable, another long-running controversy in biology, palaeontology and philosophy. Our work will provide a model for understanding how organisms in general could adapt to rapid environmental change.