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

在这个星球上，我们发现了适应各种栖息地的物种。对于在当地适应其家园环境的物种和个体种群来说，情况也是如此。如何实现和维持适应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--即在其家乡环境中做得更好--需要多个突变的联合作用。当环境之间的持续迁移带来非适应性等位基因并通过重组打破适应性等位基因组合时，这可能是具有挑战性的。因此，适应不仅取决于存在什么等位基因，而且取决于它们如何在基因组中打包在一起。当DNA片段倒置时，就会发生染色体倒置。作为副产品，这防止了倒置和未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徙时，倒置可以用来促进适应，但由于缺乏生态学知识或所研究的类群中存在已知的倒置，这一点尚未得到经验验证。最近，我们发现向日葵(向日葵属)的37个大倒位是多态的，并且这些倒位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，可以扩大我们对反转为什么会出现以及它们现在正在做什么的理解。一个令人惊讶的事实是，向日葵的倒位非常古老，往往比它们所在的物种更古老。一种可能性是，它们是通过杂交从其他物种转移过来的。我们将通过对潜在捐赠者物种的基因组进行测序，并将它们与已知的倒置序列进行比较来测试这一点。这就提出了一个问题，这些古老的倒置也存在于其他物种中吗？为了回答这个问题，我们将开发一种新的方法，通过比较参考基因组序列来检测古代倒置。流动的沙丘对任何植物来说都是一种恶劣的景观，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代倒置来实现的。这些倒置在沙丘适应中一直都很重要吗？还是后来它们被用于这一功能？我们将使用数量遗传学来回答这个问题，以追踪适应功能何时起源。最后，对其他适应沙丘的物种进行基因组测序，将发现相同的倒置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整个生命树的基因组结构差异，这里提出的工作将把向日葵作为一个生态和基因组模型来更广泛地理解倒置的进化作用。

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.