BACKGROUND Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions. RESULTS In this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals. CONCLUSIONS Our results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.

中文翻译：

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蛋白质进化的模块化性质：真核生物中的结构域重排率。

背景技术模块化对于进化创新很重要。现有单元的重组以形成具有新功能的更大的复合体，无需从头开始创建新元素。在蛋白质中，可以在蛋白质结构域水平上观察到这一原理，蛋白质结构域是功能性亚基，它们定期重新排列以获得新功能。结果 在这项研究中，我们以前所未有的深度和广度分析了导致五个主要真核生物进化枝（脊椎动物、昆虫、真菌、单子叶植物和真双子叶植物）中新域排列的机制。这首次允许直接比较不同进化枝之间的重排率，并在域重排的背景下确定谱系特定和一般进化模式。我们通过重建祖先域内容并结合可行的单步事件（例如融合或裂变）来分析系统发育树的排列变化。使用这种方法，我们通过追溯它们的前体来解释多达 70% 的重排。我们发现，总体上的速率，特别是给定进化枝的这些速率之间的比率，在所有进化枝中都是高度一致的。与先前的研究一致，融合是导致新领域安排的最常见事件。与其他进化枝相比，真菌中的谱系特定模式显示出异常高的损失率，这支持了最近强调损失对进化创新的重要性的研究。此外，我们的方法允许我们将系统发育树中特定节点的域出现与重要的功能发展联系起来，例如哺乳动物毛发的起源。结论 我们的结果表明，域重排基于一组规范的突变事件，其发生率位于相对狭窄和一致的范围内。此外，获得的关于这些比率的知识为系统发育和同源性分析的先进的基于域的方法提供了基础，这些方法补充了当前的基于序列的方法。