Architecture and evolution of gene regulatory networks underlying environmental responses in butterflies

这个项目研究了非洲蝴蝶如何根据不同的环境条件调整它们的形态、行为和生命周期。这种现象被称为表型可塑性，并通过严格调节的发育和调节级联来完成。它已经在全球许多生物中进化，因为几乎所有的环境都表现出可变性，特别是在季节之间。虽然我们对生态的相关性有很好的理解，但我们对可塑性的机制只有一个基本的理解。当环境发生变化时，哪些基因和途径能够感知环境并产生不同的表型？这些基因如何在基因调控网络（grn）中相互作用？当物种入侵新的栖息地或面临环境变化时，这些grn是如何进化的？可塑性如何影响未来的适应，比如对气候变化的适应？为了填补这一空白，我们使用了一个已建立的系统，该系统结合了生态相关性，实验可追溯性和基因组资源-非洲双环蝶。这些物种在从森林入侵的季节性热带稀树草原上反复进化出翅膀模式、行为和生命周期的可塑性。实验室实验已经揭示了表皮甾体激素信号是导致不同成人表型的发育途径之间的关键开关。然而，这种开关与环境敏感grn之间的机制关系尚不清楚，这些grn的进化起源和动力学也不清楚。通过实验室实验和计算分析各种双环属野生种群的序列数据，我们将研究可塑性的发育、进化和基因组学。具体而言，我们将(i)测试外皮甾体激素、幼年激素和胰岛素信号在组织和可塑性阶段特异性中的作用，（ii）鉴定和表征与发育可塑性相关的不同基因和grn，并在物种间进行比较，以发现可塑性的起源，（iii）通过与非塑性祖先物种的保守过程进行比较，推断可塑性grn的重复进化和趋同基因组变化。将从非洲（肯尼亚、喀麦隆、南非和加纳）的野生种群中收集不同种类的双环蝶，并将在实验室中在各种季节性环境的受控条件下饲养，以产生季节性表型，包括旱季、雨季和中间形式。这些数据以及不同季节条件下的特定阶段（幼虫和蛹）激素滴定实验（包括表皮类固醇激素、幼年激素和胰岛素）将使与表型和激素信号相关的环境线索相互关联。此外，阶段特异性激素水平操纵实验将揭示它们在发育可塑性中的作用。对这些实验室培养的个体（受控条件和激素操纵）进行比较RNA序列转录组分析，将确定与激素信号相关的基因和调控途径。这些数据将与不同双环属植物的全基因组测序数据一起用于系统基因组学方法，以形成祖先状态重建，并确定与可塑性起源和进化相关的趋同基因组变化。

This project investigates how African butterflies tune their morphology, behaviour and lifecycle to varying environmental conditions. This phenomenon is called phenotypic plasticity and is accomplished via tightly regulated developmental and regulatory cascades. It has evolved in many organisms across the globe as almost all environments show variability, in particular between seasons.While we have a good understanding of the ecological relevance, we only have a rudimentary mechanistic understanding of plasticity. What are the genes and pathways that sense the environment and produce a different phenotype when the environment changes? How do these genes interact in gene regulatory networks (GRNs)? How have these GRNs evolved when species invade new habitats or are faced with environmental changes? How does plasticity affect future adaptation, for instance to climate changes?To fill this gap, we use an established system that combines ecological relevance, experimental tractability and genomic resources-African Bicyclus butterflies. These species have repeatedly evolved plasticity in wing pattern, behaviour and life cycle upon invasions of seasonal savannahs from forests. Laboratory experiments have revealed Ecdysteroid hormone signalling as a key switch between developmental pathways leading to alternative adult phenotypes. However, the mechanistic relationship between this switch and environment-sensitive GRNs is unknown, as are theevolutionary origin and dynamics of these GRNs.With lab experiments and computational analyses of sequence data from wild populations of various Bicyclus species, we will study the development, evolution and genomics of plasticity. Specifically, we will (i) test the role of ecdysteroid hormone, juvenile hormone and insulin signalling in tissue and stage-specificity of plasticity, (ii) identify and characterise different genes and GRNs associated with developmental plasticity and compare these across species to find the origin of plasticity, and (iii) infer the repeated evolution and convergent genomic changes of plasticity GRNs by comparisons with conserved processes in non-plastic ancestor species.Different species of Bicyclus butterflies will be collected from wild populations in Africa ( Kenya, Cameroon, South Africa and Ghana) and will be lab-reared in controlled conditions spanning the range of seasonal environments to produce seasonal phenotypes including dry season, wet season and intermediate forms. These data along with stage-specific (larva and pupa) hormone titration experiments (involving ecdysteroid hormone, juvenile hormone and insulin) on different seasonal conditions will correlate the environmental cues associated with the phenotype and the hormone signalling. Further, stage-specific hormone level manipulation experiments will decipher their roles in developmental plasticity. Comparative RNA seq transcriptome analysis of these lab-reared (controlled condition and hormone manipulated) individuals will identify the genes and regulatory pathways correlated with the hormone signalling. These data along with whole-genome sequencing data of different Bicyclus species will be used in phylogenomic approaches to form an ancestral state reconstruction and identify convergent genomic changes associated with the origin and evolution of plasticity.