Addressing the problem of deep coalescence in ancient radiations: Resolving the explosive radiation of the Lophotrochozoa.

解决古代辐射中的深层合并问题：解决冠轮动物的爆炸性辐射。

基本信息

批准号：
BB/R016240/1
负责人：
Maximilian Telford
金额：
$ 54.71万
依托单位：
University College London
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2018
资助国家：
英国
起止时间：
2018 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FR016240%2F1
关键词：
Addressing problem deep coalescence ancient

项目摘要

Using molecular data (sequences of genes and proteins) to resolve the relationships between living organisms has been a major international research goal for over 25 years. Our improved knowledge of the relationships between species has already radically affected our understanding of how the great diversity of life evolved. Recently, completing this project seemed in reach, thanks to plentiful molecular data from the so called next generation sequencing. Despite the ready availability of data, some major parts of the tree of life have nevertheless proved impossible to resolve.While this is a general problem affecting many different groups of organisms we will focus on resolving the relationships between a significant part portion of the animal kingdom. One of the most striking features of the animal tree is the short time frame over which the constituent major groups (phyla such as chordates, annelids, arthropods and molluscs) diverged from one another over half a billion years ago in so-called rapid, or even explosive radiations. Rapid radiations can cause two problems. First is a lack of phylogenetic signal due to the limited opportunity to accumulate genetic changes that identify individual groups. Second is the insidious problem of Incomplete Lineage Sorting (ILS) or deep coalescence. Due to polymorphism in the ancestral species, gene sequences may not all coalesce within each species but earlier causing gene-trees to diverge from the actual species-trees. Put more simply, ILS results in different genes telling us different things about the relationships of the organisms.Recent efforts to solve these problems focussed on compiling very large genomic datasets that were concatenated into a single data set and analysed as single supergenes. This approach masks the incongruence between genes we expect to exist and may lead to positively misleading estimates. To solve this final and most recalcitrant aspects of the animal phylogeny we must use methods designed to deal with data incongruence.Within the animals we will focus specifically on resolving the relationships between the phyla within the Lophotrochozoa. This is one of three ancient groups of bilaterally symmetrical animals. Lophotrochozoa contains approximately half of animal phyla including flatworms, annelids, and molluscs.Our ultimate goals are I. to use the example of the Lophotrochozoa to better understand the processes involved in rapid radiations and how best to resolve them. II. to use our understanding to reconstruct the phylogenetic relationships between the animal phyla in the Lophotrochozoa. These practical goals will result in the phylogenetic framework that is the essential foundation for understanding the evolution of this major portion of animal diversity. Our work should give us insight into the processes at work during an ancient, explosive radiation. Such radiation events have repeatedly had a major impact on the evolution of life meaning that developing methods to address such questions will be of broad use. The easy problems having been solved, many remaining phylogenetic questions across the tree of life will involve similar rapid radiations.

使用分子数据（基因和蛋白质的序列）解决生物体之间的关系已成为25年以上的主要国际研究目标。我们对物种之间关系的改进知识已经从根本上影响了我们对生活多样性如何发展的理解。最近，由于来自所谓的下一代测序的大量分子数据，完成该项目似乎已经触及了。尽管已经准备好数据，但事实证明，生命之树的某些主要部分无法解决。尽管这是影响许多不同生物群体的一般问题，但我们将重点侧重于解决动物王国的重要部分之间的关系。动物树最引人注目的特征之一是成分主要群体（类似于弦弦，Annelids，Annelids，Annelids和Molluscs）在超过50亿年前在所谓的快速，甚至爆炸性的辐射中彼此之间的分歧。快速辐射会导致两个问题。首先是由于有限的遗传变化识别单个组的遗传变化的机会有限，因此缺乏系统发育信号。第二是谱系分类（IL）或深层结合的阴险问题。由于祖先物种的多态性，基因序列可能并非所有物种内的融合，而是较早导致基因树与实际物种树的差异。简而言之，ILS导致不同的基因告诉我们有关生物关系关系的不同事物。解决这些问题的努力集中在编译非常大的基因组数据集中，这些数据集被串联为单个数据集并被分析为单个超级基因。这种方法掩盖了我们期望存在的基因之间的不一致，并可能导致积极的误导估计。为了解决动物系统发育的最终和大多数顽固的方面，我们必须使用旨在处理数据不一致的方法。在动物中，我们将专门针对解决Lophotrochozoa中的门之间的关系。这是三个古老的双侧对称动物之一。 Lophotrochozoa包含大约一半的动物门，包括扁虫，Annelids和Molluscss。我们的最终目标是I。要以Lophotrochozoa的示例来更好地了解快速辐射的过程以及如何最好地解决它们。 ii。利用我们的理解来重建lophotrochozoa中动物门之间的系统发育关系。这些实际目标将导致系统发育框架，这是理解这一主要部分动物多样性的发展的基础。我们的工作应该使我们深入了解古老的爆炸性辐射期间工作过程。这样的辐射事件反复对生活的演变产生了重大影响，这意味着开发解决此类问题的方法将广泛使用。解决的简单问题已经解决，整个生命树中的许多系统发育问题将涉及类似的快速辐射。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

缺乏对 Deuterostomia 的支持促使重新解释第一个 Bilateria

DOI：
10.1101/2020.07.01.182915
发表时间：
2020
期刊：
影响因子：
0
作者：
Kapli P
通讯作者：
Kapli P

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria.

DOI：
10.1126/sciadv.abe2741
发表时间：
2021-03
期刊：
Science advances
影响因子：
13.6
作者：
Kapli P;Natsidis P;Leite DJ;Fursman M;Jeffrie N;Rahman IA;Philippe H;Copley RR;Telford MJ
通讯作者：
Telford MJ

DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.

DOI：
10.1093/sysbio/syad036
发表时间：
2023-11-01
期刊：
Systematic biology
影响因子：
6.5
作者：
通讯作者：

Systematic errors in orthology inference and their effects on evolutionary analyses.

DOI：
10.1016/j.isci.2021.102110
发表时间：
2021-02-19
期刊：
iScience
影响因子：
5.8
作者：
Natsidis P;Kapli P;Schiffer PH;Telford MJ
通讯作者：
Telford MJ

Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent.

DOI：
10.1093/molbev/msac161
发表时间：
2022-08-03
期刊：
MOLECULAR BIOLOGY AND EVOLUTION
影响因子：
10.7
作者：
Flouri, Tomas;Huang, Jun;Jiao, Xiyun;Kapli, Paschalia;Rannala, Bruce;Yang, Ziheng
通讯作者：
Yang, Ziheng