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Using genomes to dissect the speciation process - a comparative approach

使用基因组剖析物种形成过程——一种比较方法

基本信息

批准号：
NE/L011522/1
负责人：
Konrad Lohse
金额：
$ 55.02万
依托单位：
University of Edinburgh
依托单位国家：
英国
项目类别：
Fellowship
财政年份：
2014
资助国家：
英国
起止时间：
2014 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=NE%2FL011522%2F1
关键词：
Using genomes dissect speciation process

项目摘要

Although speciation is one of the most fundamental biological processes, we still know surprisingly little about it. For example, it is not know whether species splits are generally abrupt, which would be expected if speciation mostly occurs as a result of populations becoming separated in different places, or whether speciation generally involves a protracted period of hybridisation which eventually ceases. It is also unclear what type of selection matters most for making species reproductively isolated: species may become isolated from each other simply by adapting to different environments or, alternatively, as a result of selection on traits that only benefit one sex. For example, in many insects, males increase the number of offspring by producing very many or very large sperm, while females have evolved mechanisms to kill, store and select sperm. This sexual antagonism leads to a reciprocal armsrace and rapid evolution of reproductive traits which in itself may be strong enough to drive speciation.Because the genome of an individual is made up of contributions from an enormous number of ancestors, even a small sample of genomes contains a lot of information about the population of ancestors and about when and how fast this ancestral population split into distinct species. Since speciation is a slow process, the only chance to understand how species typically arise in nature is by extracting this genomic information about past speciation events. For example, recent comparisons of individual human genomes have shown that our own genomes are a result of past hybridisation between modern humans and more archaic forms such as Neandertals. The main aim of my project is to use genomic data to estimate speciation histories and find out what factors drive speciation in nature. Comparing speciation histories across many different insect species and between different parts of the genome, will allow me answer fundamental questions about how new species are born. This work comes in two parts. Firstly, I will develop new statistical methods to reconstruct past speciation events from genome data. To make such inferences realistic, many biological processes that effect patterns of diversity in the genome must be incorporated into a mathematical model: During reproduction, genetic material is combined from different parents and passed on to successive generations by chance. While the splitting of populations leads to separated gene pools, individuals from different populations may migrate and hybridise, causing genes to "flow" between diverging species. In particular, I will focus on reconstructing the duration and direction of such gene flow after divergence which gives a measure of how fast speciation has happened. Secondly, I will use these methods to ask how the process of speciation has played out in 40 species of wasps, flies, beetles and butterflies many of which are common in UK. I will sequence multiple individual genomes in 20 pairs of closely related species and compare speciation parameters between species pairs with more and less intensive sexual antagonism, as indicated by their mating behaviour. This will reveal whether sexual antagonism speeds up speciation. A second comparison will explore the link between speciation and ecological specialisation by testing whether species that specialise on a small number of hosts generally evolve from generalists or vice versa. Finally, I will compare the speed at which sex chromosomes and autosomes become distinct during speciation to test whether genes important in speciation accumulate more rapidly on sex chromosomes.This work will build a statistical framework for us to use genome sequences as a window into the past and to understand the role of selection, geography and hybridisation in speciation - an important step towards solving Darwin's mystery of mysteries of how species come about.

虽然物种形成是最基本的生物过程之一，但我们对它的了解仍然少得惊人。例如，我们不知道物种的分裂是否通常是突然的，如果物种的形成主要是由于种群在不同的地方分离而发生的，那么这是可以预料的，或者物种的形成是否通常包括一个最终停止的漫长的杂交时期。同样不清楚的是，哪种类型的选择对物种的繁殖隔离起了最重要的作用：物种可能仅仅通过适应不同的环境而彼此隔离，或者，作为只对一个性别有利的特征的选择的结果。例如，在许多昆虫中，雄性通过产生非常多或非常大的精子来增加后代的数量，而雌性则进化出了杀死、储存和选择精子的机制。这种性对抗导致了相互的军备竞赛和生殖特征的快速进化，这本身就足以推动物种形成。因为一个人的基因组是由大量祖先的贡献组成的，即使是一个很小的基因组样本也包含了很多关于祖先群体的信息，以及这个祖先群体何时以及以多快的速度分裂成不同的物种。由于物种形成是一个缓慢的过程，了解物种如何在自然界中典型出现的唯一机会就是提取过去物种形成事件的基因组信息。例如，最近对人类个体基因组的比较表明，我们自己的基因组是过去现代人与尼安德特人等更古老的物种杂交的结果。我项目的主要目的是利用基因组数据来估计物种形成的历史，并找出自然界中驱动物种形成的因素。比较许多不同昆虫物种的物种形成历史，以及基因组不同部分之间的物种形成历史，将使我能够回答有关新物种如何诞生的基本问题。这项工作分为两部分。首先，我将开发新的统计方法，从基因组数据重建过去的物种形成事件。为了使这样的推论成为现实，许多影响基因组多样性模式的生物过程必须被纳入一个数学模型：在繁殖过程中，来自不同父母的遗传物质被组合在一起，并偶然地传递给后代。虽然种群的分裂导致了基因库的分离，但来自不同种群的个体可能会迁移和杂交，导致基因在不同物种之间“流动”。特别地，我将着重于重建分化后基因流动的持续时间和方向，这可以衡量物种形成发生的速度有多快。其次，我将用这些方法来研究40种黄蜂、苍蝇、甲虫和蝴蝶的物种形成过程，其中许多物种在英国很常见。我将对20对亲缘关系密切的物种的多个个体基因组进行测序，并比较性对抗程度较高和较低的物种对之间的物种形成参数，这是由它们的交配行为所表明的。这将揭示两性对抗是否会加速物种形成。第二个比较将通过测试专门针对少数宿主的物种是否通常从通才进化而来，来探索物种形成和生态特化之间的联系，反之亦然。最后，我将比较性染色体和常染色体在物种形成过程中变得不同的速度，以测试在物种形成中重要的基因是否在性染色体上积累得更快。这项工作将为我们建立一个统计框架，使我们能够利用基因组序列作为了解过去的窗口，并理解选择、地理和杂交在物种形成中的作用——这是解决达尔文关于物种如何产生的奥秘的重要一步。

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）

Whole-genome data reveal the complex history of a diverse ecological community.

DOI：
10.1073/pnas.1800334115
发表时间：
2018-07-10
期刊：
Proceedings of the National Academy of Sciences of the United States of America
影响因子：
11.1
作者：
Bunnefeld L;Hearn J;Stone GN;Lohse K
通讯作者：
Lohse K

Sweeps in time: leveraging the joint distribution of branch lengths.