The Great Tit HapMap Project

大山雀单体型图项目

• 批准号: NE/J012599/1
• 负责人: J Slate
• 金额: $ 6.62万
• 依托单位: University of Sheffield
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ012599%2F1
• 关键词: Great; Tit; HapMap; Project

Most people interested in science are aware that the last decade has witnessed dramatic advances in genomics tools and techniques.Excitingly, these new technologies are not limited to humans or classical model organisms like fruitflies and yeasts, but can now be applied to organisms which have long interested ecologists but which, until now, lacked genetics tools. We have taken advantage of the opportunities afforded by so-called next generation sequencing to develop genomics resources for the great tit.Great tits (Parus major) are one of the most widely studied invertebrates because they are common and readily breed in artifical nest boxes. As a result a number of long term studies of great tit populations have been conducted across Europe, some of which have been ongoing for more than 50 years and include data on tens of thousands of individual birds.These long-term datasets are rich resources for studying important ecological questions such as: How organisms adapt to climate change, How organisms allocate resources to breeding and other activities, How species evolve in the face of natural selection. Using funds won from the European Research Council (ERC) and the Netherlands government, we have begun to map genes responsible for variation in life history and morphological traits in two of the most intensively studied populations - at Wytham Woods in the UK and de Hoge Veluwe in The Netherlands. By working as a UK-Dutch collaboration we have pooled genomics resources and developed a tool called a SNP chip which allows us to type more than 9000 genetic markers in each of our study populations. We have now typed more than 2000 Dutch birds and 2700 UK birds with this chip. In this proposal, we request funds to type a further 16 great tit populations (50 birds per population). Why do we want to do this? The main reason is that by typing the same genetic markers in lots of different populations we can characterise genetic variation across the entire species range in order to learn more about the species evolutionary history. Projects of this nature are sometimes called HapMap Projects because they involve the mapping of markers linked along a chromosome (HAPlotypes). The best known HapMap project has been conducted in humans and has led to great insight into how our species colonised the world after migrating from Africa, how different populations are related to each other, and how genes have enabled us to adapt to e.g. different environmental conditions, novel challenges such as emerging diseases, changes in diet etc. By carrying out a Great Tit HapMap Project we can address similar questions in this widely studied ecological model organism. This also means we can extend the findings from the Wytham and de Hoge Veluwe populations to ask fundamental questions about evolutionary genetics. For example: Do the same genes explain adaptation in different populations? Do beneficial genes that arise in one population rapidly spread to other populations? Do the genes that explain variation within a population also explain differences between populations? Does migration between populations play a major role in maintaining genetic diversity? Does this gene flow help or hinder local adaptation?There is perhaps no other vertebrate for which multiple long-term ecological datasets and such extensive genomics resources are available. Therefore, the great tit is an ideal organism in which to perform the first 'natural population' HapMap Project.

大多数对科学感兴趣的人都知道，过去十年，基因组学工具和技术取得了巨大的进步。令人兴奋的是，这些新技术不仅限于人类或果蝇和酵母等经典模式生物，而且现在可以应用于生态学家长期感兴趣但迄今缺乏遗传学工具的生物。我们利用所谓的下一代测序提供的机会开发大山雀的基因组学资源。大山雀（Parus major）是研究最广泛的无脊椎动物之一，因为它们很常见，很容易在人工巢箱中繁殖。因此，欧洲各地对大山雀种群进行了大量的长期研究，其中一些研究已经持续了50多年，包括数万只鸟类的数据。这些长期数据集是研究重要生态问题的丰富资源，例如：生物如何适应气候变化，生物如何分配资源进行繁殖和其他活动，物种如何在自然选择中进化。利用从欧洲研究理事会（ERC）和荷兰政府获得的资金，我们已经开始绘制两个最深入研究的种群--英国的怀瑟姆森林和荷兰的德霍格韦卢韦--的生活史和形态特征变异的基因图谱。通过与英国和荷兰的合作，我们汇集了基因组学资源，并开发了一种名为SNP芯片的工具，该工具使我们能够在每个研究人群中对9000多个遗传标记进行分类。我们现在已经用这个芯片输入了2000多只荷兰鸟和2700只英国鸟。在这项提案中，我们要求提供资金，以确定另外16个大山雀种群（每个种群50只鸟）。我们为什么要这样做？主要原因是，通过在许多不同的种群中对相同的遗传标记进行分型，我们可以在整个物种范围内对遗传变异进行分析，以便更多地了解物种的进化历史。这种性质的项目有时被称为HapMap项目，因为它们涉及沿着染色体（HAPlotypes）沿着连接的标记的定位。最著名的HapMap项目是在人类身上进行的，它使我们深入了解了我们的物种如何从非洲迁移到世界上，不同的人群如何相互关联，以及基因如何使我们适应不同的环境条件，新的挑战，如新出现的疾病，通过实施大山雀单体型图项目，我们可以解决这种广泛研究的生态模式生物的类似问题。这也意味着我们可以扩展Wytham和de Hoge Veluwe人群的发现，以询问有关进化遗传学的基本问题。例如：相同的基因能解释不同种群的适应性吗？在一个种群中出现的有益基因会迅速传播到其他种群吗？解释种群内变异的基因是否也能解释种群间的差异？种群间的迁移在维持遗传多样性方面是否起着重要作用？这种基因流动是帮助还是阻碍了当地的适应？可能没有其他脊椎动物可以获得多个长期生态数据集和如此广泛的基因组学资源。因此，大山雀是执行第一个“自然群体”HapMap项目的理想生物体。

项目成果

Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.

• DOI: 10.1093/gbe/evx213
• 发表时间: 2017-11-01
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Corcoran P;Gossmann TI;Barton HJ;Great Tit HapMap Consortium;Slate J;Zeng K
• 通讯作者: Zeng K

Response to Perrier and Charmantier: On the importance of time scales when studying adaptive evolution.

对 Perrier 和 Charmantier 的回应：论研究适应性进化时时间尺度的重要性。

• DOI: 10.1002/evl3.112
• 发表时间: 2019
• 期刊: Evolution letters
• 影响因子: 5
• 作者: Bosse M

Evolutionary signals of selection on cognition from the great tit genome and methylome.

• DOI: 10.1038/ncomms10474
• 发表时间: 2016-01-25
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Laine VN;Gossmann TI;Schachtschneider KM;Garroway CJ;Madsen O;Verhoeven KJ;de Jager V;Megens HJ;Warren WC;Minx P;Crooijmans RP;Corcoran P;Great Tit HapMap Consortium;Sheldon BC;Slate J;Zeng K;van Oers K;Visser ME;Groenen MA
• 通讯作者: Groenen MA