Why so mixed up? Exploring the history and adaptive significance of pervasive large chromosomal inversions in sunflowers.

在地球上，我们发现了适应各种栖息地的物种。这对物种和个体种群都是正确的，因为它们在当地适应了它们的家庭环境。适应是如何实现和维持的是进化生物学的基本问题之一。研究表明，要使种群适应当地环境——即在其家庭环境中表现更好——就需要多种突变的联合作用。当环境之间存在持续的迁移时，这会带来非适应性等位基因，并通过重组破坏适应性等位基因的组合。因此，适应性不仅取决于存在哪些等位基因，还取决于它们如何在基因组中打包在一起。染色体倒位发生在DNA片段倒位的时候。作为副产品，这可以防止倒置和非倒置片段之间的重组，并可以有效地将等位基因锁定在一起。理论工作预测，当有来自不同环境的迁移时，倒序可以用来促进适应，但由于缺乏生态学知识或已知的倒序研究分类群，这还没有得到实证检验。最近，我们发现向日葵（Helianthus属）具有37个大反转的多态性，并且这些反转与局部适应性状有关（Todesco， Owens等）。自然,2020)。这提供了一个前所未有的机会来扩展我们对反转为什么会出现以及它们现在在做什么的理解。一个令人惊讶的事实是，倒置的向日葵非常古老，通常比它们生长的物种还要古老。一种可能性是它们是通过杂交从其他物种转移过来的。我们将通过对潜在供体物种的基因组进行测序并将其与已知的倒置序列进行比较来验证这一点。这就提出了一个问题，这些古老的倒位是否也存在于其他物种中？为了回答这个问题，我们将开发一种通过比较参考基因组序列来检测古代倒置的新方法。移动的沙丘对任何植物来说都是严酷的环境，但在向日葵中，一些种群已经适应并在这种危险的环境中茁壮成长。我们发现这种适应是通过使用七个古老的倒位来实现的。这些逆温在沙丘适应过程中一直都很重要吗？还是它们后来才被这一功能所取代？我们将用定量遗传学来追踪适应功能的起源。最后，对其他沙丘适应物种的基因组测序将发现相同的倒序是否在整个属中重复使用。现代基因组测序技术越来越多地揭示了生命之树的基因组结构变异，本文提出的工作将使向日葵成为更广泛地理解反转进化作用的生态和基因组模型。

Across the planet we find species adapted to a wide range of habitats. This is true for species as well as individual populations that are locally adapted to their home environment. How adaptation is achieved and maintained is one of evolutionary biology's fundamental questions. Research has shown that for populations to be locally adapted - i.e., do better in their home environment - it requires the combined action of multiple mutations. This can be challenging when there is ongoing migration between environments bringing in non-adaptive alleles and breaking up combinations of adaptive alleles through recombination. Thus, adaptation depends not just on what alleles are present, but how they are packaged together in the genome. Chromosomal inversions occur when stretches of DNA invert. As a by-product, this prevents recombination between inverted and uninverted segments and can effectively lock together alleles. Theoretical work has predicted that inversions can be used to facilitate adaptation when there is migration from different environments, but this hasn't been empirically tested because of a lack of ecological knowledge or known inversions in studied taxa. Recently, we discovered that sunflowers (genus Helianthus) were polymorphic for 37 large inversions and that these inversions were associated with locally adaptive traits (Todesco, Owens et al. Nature, 2020). This provides an unprecedented opportunity to expand our understanding of why inversions appear and what they are doing now. One surprising fact is that sunflower inversions are very old, often older than the species they are found in. One possibility is that they were transferred in from other species through hybridization. We will test this by sequencing the genomes of potential donor species and comparing them to known inversion sequences. This raises the question, are these ancient inversions also found in other species? To answer this, we will develop a new method to detect ancient inversions by comparing reference genome sequences. Shifting sand dunes are a harsh landscape for any plant, but in sunflowers, some populations have adapted and thrive in this treacherous environment. We found that this adaptation was achieved through the use of seven ancient inversions. Were these inversions always important in sand dune adaptation or were they later co-opted for this function? We will answer this question using quantitative genetics to trace when the adaptive functions originated. Lastly, genome sequencing of other sand dune adapted species will find out if the same inversions are reused across the genus. Modern genome sequencing technology is increasingly revealing genome structure variation across the tree of life and the work proposed here will develop sunflowers as an ecological and genomic model for understanding the evolutionary role of inversions more broadly.