Genomic and gene regulatory basis of rapid evolutionary diversification of a multifunctional trait

进化创新可以由多种机制产生，如基因内突变、蛋白质编码基因从非编码DNA重新进化、基因复制、转座元件的插入以及基因转录率的变化（即调控变化）。进化创新对于研究对生物体至关重要但进化迅速的复杂表型特征尤其有趣。昆虫的表皮碳氢化合物（CHC）特征就是其中之一。chc基本上覆盖了所有昆虫的身体，防止水分流失，并在化学通讯中发挥作用。在亲缘关系密切的物种之间，甚至在同种性别或社会昆虫种姓之间，CHC谱可能会发生巨大变化，这表明潜在的遗传机制是多种多样的。有趣的是，在膜翅目昆虫中，相似的CHC表型反复进化。尽管对一般CHC生物合成途径有一定的了解，但我们对种内和种间CHC变异和新表型背后的分子进化机制仍然知之甚少。我们的项目旨在确定CHC多样化的基因组，转录组学和表观遗传学基础。我们将研究13对密切相关但化学成分不同的物种，涵盖了几乎所有主要的针叶膜翅目（刺蜂、蚂蚁和蜜蜂）。性别和种姓差异还将在这26个物种中的10个物种中进行研究。应用跨物种比较基因组方法，我们将评估基因拷贝数变异、编码序列的非同义变化、可选择的mRNA剪接和其他促进表型差异的调控变化的相对重要性。我们将研究基因拷贝数变异是否由异位重组或转座因子的活性促进。最后，我们将评估CHC生物合成基因的亚群是否已经进化成超协调的共调节单元，这可能解释了快速的表型变异和相似表型的重复进化。为此，我们将获得组织特异性转录组。我们还将通过ATAC-seq将开放染色质图谱与通过全基因组亚硫酸氢盐测序的甲基化模式进行对比，以确定表观遗传机制在调节CHC变异中的作用。我们假设近亲物种之间的CHC分布差异与同种性别或种姓之间的差异是由类似的机制驱动的。我们预计基因组机制，如核苷酸差异和基因拷贝数变异（包括新功能化），是导致远亲物种之间差异的主要原因。我们的研究结果将有助于更好地理解塑造高度可变但至关重要的表型性状进化的分子机制。因此，我们将对多种基因组和基因调控机制的相互作用如何促进进化创新和多样化获得新的见解。

Evolutionary innovation can result from various mechanisms, such as mutations within genes, de novo-evolution of protein-coding genes from non-coding DNA, gene duplication, insertions of transposable elements, and changes in the transcription rate of genes (i.e., regulatory change). Evolutionary innovation is particularly interesting to study on complex phenotypic traits that are vital for the organism, yet evolve rapidly. One such trait is the cuticular hydrocarbon (CHC) profile of insects. CHCs cover the body of essentially all insects, protecting against water loss and functioning in chemical communication. CHC profiles can vary drastically between closely related species or even between conspecific sexes or social insect castes, suggesting a versatile underlying genetic machinery. Interestingly, in the insect order Hymenoptera, similar CHC phenotypes have evolved repeatedly. Despite some understanding of the general CHC biosynthesis pathways, we still know little about the molecular evolutionary mechanisms behind intra- and interspecific CHC variation and novel phenotypes. Our project aims at identifying the genomic, transcriptomic, and epigenetic underpinnings of CHC diversification. We will study 13 pairs of closely related yet chemically different species that cover almost all major lineages of aculeate Hymenoptera (stinging wasps, ant, and bees). Sex and caste differences will additionally be studied in ten of these 26 species. Applying a cross-species comparative genomic approach, we will assess the relative importance of gene copy number variation, non-synonymous changes in coding sequences, alternative mRNA splicing, and other regulatory changes for fostering phenotypic divergence. We will investigate whether gene copy number variation has been promoted by ectopic recombination or the activity of transposable elements. Finally, we will evaluate whether subgroups of CHC biosynthesis genes may have evolved into superordinated co-regulated units, potentially explaining rapid phenotypic variation and repeated evolution of similar phenotypes. To this end, we will obtain tissue-specific transcriptomes. We will also contrast open chromatin maps via ATAC-seq to methylation patterns via whole genome bisulfite sequencing to determine the role of epigenetic mechanisms in regulating CHC variation. We hypothesize that CHC profile divergence between closely related species is driven by similar mechanisms as the divergence between conspecific sexes or castes. We expect genomic mechanisms, such as nucleotide divergence and gene copy number variation (incl. neofunctionalization), to primarily cause divergence between distantly related species. Our results will contribute to a better understanding of the molecular mechanisms that shape the evolution of a highly variable yet vital phenotypic trait. Thus, we will gain new insights into how the interplay of multiple genomic and gene regulatory mechanisms enables evolutionary innovation and diversification.