Rooting the eukaryotic radiation with new models of gene and genome evolution
用基因和基因组进化的新模型来扎根真核辐射
基本信息
- 批准号:NE/P00251X/1
- 负责人:
- 金额:$ 39.35万
- 依托单位:
- 依托单位国家:英国
- 项目类别:Research Grant
- 财政年份:2017
- 资助国家:英国
- 起止时间:2017 至 无数据
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
The origin of eukaryotes from their prokaryotic progenitors was one of the most formative transitions in the history of life, catalysing the blossoming of eukaryotic biodiversity into the astonishing range of forms we see today, from the largest organisms on our planet - blue whales, giant sequoias, fungal networks extending for miles underground - to microscopic plankton that jostle with bacteria in the world's oceans. Explaining the leap in cellular complexity during the prokaryote-to-eukaryote transition is one of the outstanding challenges in 21st-century biology.The common structure of all eukaryotic cells testifies to their shared ancestry, but our understanding of the kind of cell that ancestral eukaryote was - where it lived, what it ate, the kinds of biochemical reactions it could perform - is in disarray. Whole-genome data have enabled us to resolve the more recent divergences in eukaryotic evolution, but we still have a very poor understanding of the deeper relationships between the main groups at the base of the evolutionary tree. In particular, the root of the tree - the starting point of the eukaryotic radiation - remains mired in controversy and debate.The problem is that traditional rooting methods rely on the use of an outgroup: to find the root of the tree of mammals, for example, we might include birds in the analysis, and then use our a priori knowledge to place the root on the branch between the two groups. This approach breaks down when applied to the eukaryotic radiation: including our closest prokaryotic relatives greatly reduces the proportion of the eukaryotic genome that can be analysed, and the enormous evolutionary distance to the prokaryotic outgroup obscures the relationships among the different eukaryotic lineages. As a result, recent analyses of the eukaryotic root disagree strongly on its position, despite using similar datasets and analytical approaches. In this project, we will tackle these difficulties head-on to definitively resolve the root of the eukaryotic tree by applying new outgroup-free rooting approaches, including some pioneered by members of the project team, to the most up-to-date, representative sampling of eukaryotic genomic diversity yet assembled. We will use the resulting phylogenomic framework to map the points in evolutionary history at which the unique cellular and genomic traits of modern eukaryotes first evolved, establishing a timescale for the evolution of key eukaryotic innovations. By mapping these traits onto the tree, we will reconstruct a detailed cellular and genomic model of the ancestral eukaryote - an organism which may have lived up to two billion years ago - in order to establish its lifestyle, ecology, and metabolism, and to test hypotheses of how that founding lineage gave rise to the staggering diversity of eukaryotic life we see today. The work we are proposing is fundamental discovery science: the ultimate goal is to understand our own origins, to bring clarity to a poorly-understood period in the history of life vitally important for making sense of the biodiversity we see around us today, and in doing so to establish a new state-of-the-art for phylogenetic rooting with broad applicability to other major evolutionary transitions across the tree of life. But there is also real potential for broader socio-economic impact. Some of the groups that branch near the base of eukaryotic tree are parasitic, and so establishing how these evolved from their free-living ancestors will provide new, much-needed insights into the adaptation of eukaryotic parasites such as Trypanosoma (sleeping sickness) and Giardia to their hosts. As part of the research programme, we will host summer internships for motivated students on biohacking (DIY computational biology), providing a taste of scientific discovery and teaching the crucial computational, statistical and scientific skills needed to identify and nurture the next generation of scientific leaders.
真核生物从原核生物祖先的起源是生命历史上最具形成性的转变之一,催化了真核生物多样性的蓬勃发展,成为我们今天看到的惊人的形式,从我们星球上最大的生物体-蓝鲸,巨型红杉,真菌网络延伸到地下数英里-到世界海洋中与细菌竞争的微观浮游生物。解释原核生物向真核生物转变过程中细胞复杂性的飞跃是21世纪生物学面临的突出挑战之一。所有真核细胞的共同结构证明了它们的共同祖先,但我们对真核生物祖先是哪种细胞的理解--它生活在哪里,吃什么,它能进行什么样的生化反应--却一片混乱。全基因组数据使我们能够解决真核生物进化中最近的分歧,但我们仍然对进化树底部的主要群体之间的深层关系了解甚少。特别是树根--真核辐射的起点--仍然深陷争议和争论之中。问题在于传统的生根方法依赖于使用外群:为了找到哺乳动物这棵树的树根,例如,我们可能会将鸟类纳入分析,然后利用我们的先验知识将树根放置在两个群体之间的分支上。当应用到真核辐射时,这种方法就失败了:包括我们最近的原核亲戚大大减少了可分析的真核基因组的比例,而与原核外群的巨大进化距离模糊了不同真核谱系之间的关系。因此,最近对真核根的分析强烈反对其立场,尽管使用了类似的数据集和分析方法。在这个项目中,我们将通过应用新的无外群生根方法(包括项目团队成员开创的一些方法)来解决这些困难,以确定真核树的根,以最新的,具有代表性的真核基因组多样性采样尚未组装。我们将使用由此产生的基因组框架来绘制现代真核生物独特的细胞和基因组特征首次进化的进化历史点,为关键的真核生物创新的进化建立时间尺度。通过将这些特征映射到树上,我们将重建一个详细的原始真核生物的细胞和基因组模型-一种可能生活在20亿年前的生物体-以建立其生活方式,生态学和新陈代谢,并测试关于创始谱系如何产生我们今天看到的惊人的真核生物多样性的假设。我们提出的工作是基础发现科学:最终目标是了解我们自己的起源,澄清生命历史上一个不太了解的时期,这对于理解我们今天看到的生物多样性至关重要,并在这样做的过程中建立一个新的最先进的系统发生学根源,广泛适用于生命之树的其他主要进化过渡。但也有真实的潜力产生更广泛的社会经济影响。在真核生物树的底部附近有一些分支是寄生的,因此,确定这些分支是如何从它们自由生活的祖先进化而来的,将为真核寄生虫(如锥虫(昏睡病)和贾第虫)适应宿主提供新的、急需的见解。作为研究计划的一部分,我们将为生物黑客(DIY计算生物学)的积极学生举办暑期实习,提供科学发现的味道,并教授识别和培养下一代科学领导者所需的关键计算,统计和科学技能。
项目成果
期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Gene transfers can date the tree of life.
- DOI:10.1038/s41559-018-0525-3
- 发表时间:2018-05
- 期刊:
- 影响因子:16.8
- 作者:Davín AA;Tannier E;Williams TA;Boussau B;Daubin V;Szöllősi GJ
- 通讯作者:Szöllősi GJ
Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.
- DOI:10.1111/jeu.12524
- 发表时间:2018-11
- 期刊:
- 影响因子:0
- 作者:Bass D;Tikhonenkov DV;Foster R;Dyal P;Janouškovec J;Keeling PJ;Gardner M;Neuhauser S;Hartikainen H;Mylnikov AP;Berney C
- 通讯作者:Berney C
Supplemental Figures_1-8.pdf from Molecular palaeontology illuminates the evolution of ecdysozoan vision.
来自分子古生物学的补充Figures_1-8.pdf 阐明了蜕皮动物视觉的进化。
- DOI:10.6084/m9.figshare.7365041
- 发表时间:2018
- 期刊:
- 影响因子:0
- 作者:Fleming J
- 通讯作者:Fleming J
Clarifying the Relationships between Microsporidia and Cryptomycota.
- DOI:10.1111/jeu.12519
- 发表时间:2018-11
- 期刊:
- 影响因子:0
- 作者:Bass D;Czech L;Williams BAP;Berney C;Dunthorn M;Mahé F;Torruella G;Stentiford GD;Williams TA
- 通讯作者:Williams TA
Gene transfers, like fossils, can date the Tree of Life
- DOI:10.1101/193813
- 发表时间:2017-09
- 期刊:
- 影响因子:0
- 作者:Adrián A. Davín;Éric Tannier;T. Williams;B. Boussau;V. Daubin;G. Szöllősi
- 通讯作者:Adrián A. Davín;Éric Tannier;T. Williams;B. Boussau;V. Daubin;G. Szöllősi
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Tom Williams其他文献
No Name, No Voice, Less Trust: Robot Group Identity Performance, Entitativity, and Trust Distribution
无名字、无声音、信任度较低:机器人群体身份表现、实体性和信任分布
- DOI:
- 发表时间:
2023 - 期刊:
- 影响因子:0
- 作者:
Alexandra Bejarano;Tom Williams - 通讯作者:
Tom Williams
Understanding Roboticists' Power through Matrix Guided Power Analysis
通过矩阵引导功率分析了解机器人专家的功率
- DOI:
- 发表时间:
2024 - 期刊:
- 影响因子:0
- 作者:
Tom Williams - 通讯作者:
Tom Williams
Robot Co-design Can Help Us Engage Child Stakeholders in Ethical Reflection
机器人协同设计可以帮助我们让儿童利益相关者参与道德反思
- DOI:
10.1109/hri53351.2022.9889430 - 发表时间:
2022 - 期刊:
- 影响因子:0
- 作者:
Terran Mott;Alexandra Bejarano;Tom Williams - 通讯作者:
Tom Williams
Seasonal Movements, Aggregations and Diving Behavior of Atlantic Bluefin Tuna (Thunnus thynnus) Revealed with Archival Tags
档案标签揭示了大西洋蓝鳍金枪鱼 (Thunnus thynnus) 的季节性活动、聚集和潜水行为
- DOI:
- 发表时间:
2009 - 期刊:
- 影响因子:3.7
- 作者:
Andreas Walli;S. Teo;Andre M. Boustany;C. Farwell;Tom Williams;H. Dewar;E. Prince;B. Block - 通讯作者:
B. Block
Exploring the Naturalness of Cognitive Status-Informed Referring Form Selection Models
探索认知状态知情的参考形式选择模型的自然性
- DOI:
10.18653/v1/2023.inlg-main.19 - 发表时间:
2023 - 期刊:
- 影响因子:0
- 作者:
Gabriel Del Castillo;Grace Clark;Zhao Han;Tom Williams - 通讯作者:
Tom Williams
Tom Williams的其他文献
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