EASTBIO (WCUB) Speciation and sex-biased gene expression in butterflies

尽管男性和女性的大部分基因组相同，但他们的生物学在根本上是不同的。在强烈的自然性选择和性选择下，男性和女性的性二型性特征倾向于相反的擎天柱。在果蝇等模型系统中的研究表明，超过50%的基因表现出性别偏见或性别限制表达，人们认为性别偏见表达已经进化成解决性别对立选择(Ellegren&Parsch 2007)。最近的实证研究表明，性别偏见基因进化速度更快，并且--正如理论模型预测的那样--集中在许多生物体的性染色体上(Ellegren&Parsch 2007)。然而，我们仍然知之甚少，关于性别偏见基因表达随着物种分化而进化的速度有多快，以及性别偏见基因的不同进化动态对物种形成过程有什么连锁影响。例如，一种耐人寻味的可能性是，性别特异基因，由于其较快的进化速度，潜在的参与性别选择和与性染色体的联系，可能会在物种形成的早期阶段不成比例地引发生殖隔离。比较研究表明，物种形成率可能确实与性对抗进化的水平有关。然而，关于基因表达的全基因组数据仅限于少数模型系统，我们目前缺乏性别特异性基因和无偏见基因之间的任何直接比较，因为在物种形成过程中发挥作用的相关力量。对雌性异性恋系统(例如鸟类和蝴蝶)的研究特别有价值，因为将它们与雄性异性恋有机体进行对比，可以让我们找出是什么机制导致性别偏见基因在性染色体上积累(Huylmans等人，2017年)。该项目的目的是利用欧洲蝴蝶的姐妹种作为模型来量化性别偏见和物种特异性的基因表达，并调查物种形成过程中基因表达、选择和基因流之间的相互作用。具体目的是：i)测量物种分化过程中性别特异性表达的翻转。ii)通过对物种形成过程的显式模型拟合，比较物种分化过程中性别偏见基因和无偏见基因之间的进化动态(Lohse等人)。如果性别偏见基因的正选择是由显性突变驱动的，那么测试蝴蝶Z染色体是否如预期的那样丰富了男性偏见基因。首席主管Konrad Lohse在种群遗传学、昆虫物种形成和生物信息学方面具有丰富的经验，并开发了从基因组数据建模分歧和基因流动的推理方法。在与LepBase和Alex Hayward(埃克塞特大学)的合作下，Lohse实验室正在为几对欧洲蝴蝶的姐妹物种生成参考组件基因组范围的多态数据。副主管Mike Ritchie在设计RNAseq实验和物种形成研究方面拥有丰富的经验。学生将获得最先进的基因组学、生物信息学和高级进化遗传学和统计学方面的培训。这还将包括通过EastBio研讨会以及由爱丁堡基因组公司提供的量身定制的生物信息学和编码研讨会进行基本培训。这个项目主要是计算/定量的，但也包括一些实地工作和/或在湿实验室中的一小段时间，以产生RNAseq数据。

Although males and females share most of their genome, their biology differs in fundamental ways. Sexually dimorphic traits are under intense natural and sexual selection favouring opposing optima in males and females. Studies in model systems like Drosophila have shown that over 50% of genes show sex biased or sex limited expression and it is thought that sex-biased expression has evolved to resolve sexually antagonistic selection (Ellegren & Parsch 2007).Recent empirical work has shown that sex-biased genes evolve at faster rates and - as predicted by theoretical models - are concentrated on the sex-chromosomes in a number of organisms (Ellegren & Parsch 2007). However, we still know very little about how quickly sex-biased gene expression evolves as species diverge and what knock-on effects the distinct evolutionary dynamics of sex-biased genes have on the speciation process. For example, an intriguing possibility is that sex-specific genes, by virtue of their faster rates of evolution, potential involvement in sexual selection and linkage to sex chromosomes may disproportionately trigger reproductive isolation in the early stages of speciation. Comparative studies suggest that rates of speciation may indeed be correlated with levels of sexually antagonistic evolution. However, genome-wide data on gene-expression are limited to a small number of model systems and we currently lack any direct comparison between sex-specific and unbiased genes in terms of the relevant forces that act during the speciation process. Studies on female heterogametic systems (e.g. birds and butterflies) are particularly valuable, because contrasting them with male heterogametic organisms allows us to find out what mechanisms cause sex-biased genes to accumulate on the sex-chromosomes (Huylmans et al 2017). The aim of the project is to use sister-species of European butterflies as a model to quantify both sex-biased and species-specific gene expression and investigate the interplay between gene expression, selection and gene-flow during speciation.The specific aims are to:i) Measure the turn-over in sex-specific expression during species divergence.ii) Compare the evolutionary dynamics during species divergence between sex biased genes and unbiased genes by fitting explicit models of the speciation process (Lohse et al. 2016).iii) Test whether butterfly Z chromosomes are enriched for male-biased genes as expected if positive selection at sex-biased genes is driven by dominant mutations.The lead supervisor, Konrad Lohse, brings extensive experience in population genetics, insect speciation and bioinformatics and has developed inference methods to model divergence and gene flow from genomic data. In collaboration with LepBase and Alex Hayward (Exeter University), the Lohse lab is generating reference assemblies genome-wide polymorphism data for several sister species pairs of European butterflies. Co-supervisor Mike Ritchie has extensive experience with designing RNASeq experiments and speciation research. The student will obtain state of the art training in genomics, bioinformatics and advanced evolutionary genetics and statistics. This will also involve basic training through EastBio workshops as well as tailored bioinformatics and coding workshops offered by Edinburgh Genomics. This project is mainly computational/quantitative but also includes some fieldwork and/or a short spell in the wet-lab to generate RNASeq data.