Can phenotypic plasticity and DNA methylation promote adaptive radiation?

生物如何适应新的环境？从长远来看，这将需要基因(或偶尔是文化)改变，但生物学家开始认真对待基因组已经进化到允许有机体的发育对环境做出反应的想法。这一过程可能是在基础水平上进行的，DNA本身的结构会发生化学变化，以表观遗传标记的形式出现，从而增强或抑制单个基因的表达。大多数情况下，这些是作为正常发育过程的一部分，在个体有机体的不同组织和生命阶段有所不同的短期变化，但现在已经知道，有时它们可以由环境诱导，有时甚至会持续几代人。这种表观遗传变化能否帮助生物体应对新的环境挑战，甚至通过后来的基因变化，使它们进化成新的物种，这一过程被称为“基因同化”？对于理解生物多样性的起源及其在不断变化的世界中的维护来说，这些是重要的问题。我们的目标是研究这些问题，重点是一种小型鱼类--东方喜鱼--它属于爆炸性进化多样化最壮观的例子之一--非洲五大湖慈嘴鱼，它们在几百万年的时间里进化成了数千个物种。慈鱼的喉部有第二组(咽部)下巴，它们用来处理食物，而外部(口腔)下巴专门用于捕捉猎物。许多关系密切的慈鱼物种有着微妙的不同的下巴结构，这使得它们可以吃不同的东西。这有助于种群适应不同的环境，并允许不同的物种生活在一起，开发不同的资源。我们计划观察东方幸福的三对密切相关的种群：在每一对种群中，一个种群主要以软性食物-浮游生物或植物材料为食，而另一个种群在其食物中包括硬壳猎物，如蜗牛，这反映在它们更有力的下巴上。我们的目标是看看这些颌骨结构的差异在多大程度上可以由环境诱导的灵活性来解释，又有多少是遗传的。我们将在水族馆中测试活鱼，看看种群之间的解剖差异是否真的改善了它们捕获和处理不同种类猎物的方式。我们将看到基因差异是否会导致解剖学上的差异，其方向与环境引起的变化是相同的。我们将调查基因组的结构，看看表观遗传变化是否与不同的饮食和结构有关，并试图确定不同的种群对是否以类似的方式分化。我们的目标是测试颌骨中关键基因的活动是否与表观遗传变化有关。这些实验将基于对在研究水族馆中饲养的鱼的调查，这些鱼以不同的饲料喂养，以模仿它们在野外经历的硬食物和软食物。这使得我们可以用硬饲料喂养来自软饮食群体的鱼，反之亦然。特别好的洞察力来自于在6个月后将一窝鱼分开，其中一半用硬食喂养，另一半用软食喂养，从而控制了遗传的影响。通过这种方式饲养几代人，我们将能够看到基因组的表观遗传变化是否可以持续几代人。这项研究有可能在最基本的层面上揭示令人兴奋的新见解，了解生物体如何迅速适应环境。这些发现和技术将在一系列物种和情况下得到应用，并可能揭示物种将如何应对由人类通过气候变化、污染和外来物种引入而造成的环境变化的挑战。

How do living things adapt to a new environment? In the long-run this will need genetic (or occasionally cultural) changes, but biologists are beginning to take seriously the idea that the genome has evolved to allow an organism's development to be responsive to the environment. This process may operate at a fundamental level, with chemical changes to the structure of the DNA itself in the form of 'epigenetic' marks which can enhance or inhibit the expression of individual genes. Mostly, these are short-term changes that vary among tissues and life-stages in an individual organism as part of the normal process of development, but it is now known that sometimes they can be induced by the environment and occasionally even persist across generations. Can this type of epigenetic change help organisms cope with new environmental challenges or even lead to them evolving into new species through later genetic changes, a process called 'genetic assimilation'? These are important questions for understanding the origins of biodiversity and its maintenance in a changing world. We aim to investigate these questions focussing on a small fish- the Eastern Happy- which belongs to one of the most spectacular examples of explosive evolutionary diversification, the African Great Lakes cichlid fishes, which have evolved into thousands of species in a few million years. Cichlid fishes have a second set of (pharyngeal) jaws in their throats that they use for processing their food, while the external (oral) jaws are specialised for capturing prey. Many closely-related cichlid species have subtly different jaw structures allowing them to feed on different things. This helps populations adapt to different environments, and allows different species to live together, exploiting different resources. We plan to look at three closely-related pairs of populations of the Eastern Happy: in each pair one population feeds mostly on soft food- plankton or plant material, but the other includes hard-shelled prey such snails in its diet, and this is reflected in their more powerful jaws. We aim to see how much of these difference in jaw structures can be explained by environmentally-induced flexibility and how much is genetic. We will test live fish in aquaria to see whether the anatomical differences among populations really do improve how they capture and process different kinds of prey. We will see whether genetic differences cause anatomical variation in the same direction as the environmentally-induced changes. We will investigate the structure of the genomes to see whether epigenetic changes are associated with divergent diets and structures, and try to determine if different population pairs are diverging in similar ways. We aim to test if the activities of key genes in the jaws are associated with epigenetic changes. These experiments will be based around investigations of fish reared in research aquaria, fed on different diets to mimic the hard and soft-diets they experience in the wild. This allows us to feed fish from soft-diet populations on hard diets and vice versa. Particularly good insights will come from splitting a single brood of fish after 6th months and rearing one half on hard diet and the other half on a soft diet, thus controlling for the effects of genetics. By rearing several generations in this way, we will be able to see whether epigenetic changes to the genome can persist over several generations. This study has the potential to reveal exciting new insights at the most fundamental level into how organisms adapt rapidly to their environments. The findings and techniques will have applications across a range of species and situations and perhaps cast light on how species will respond to the challenges of the environmental changes being caused by humans, through climate change, pollution and the introduction of alien species.