Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries. However, mounting evidence from comparative genomics indicates that this paradigm is often violated. Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes. Nonvertical evolution might be more restricted in eukaryotes than in prokaryotes, yet it is not negligible and can be common in certain groups. Recognition of such processes brings about the need to incorporate this complexity into our models, as well as to conceptually reframe eukaryotic diversity and evolution. Here, I review the recent work from genomics studies that supports the effects of nonvertical modes of evolution including introgression, hybridization, and horizontal gene transfer in different eukaryotic groups. I then discuss emerging patterns and effects, illustrated by specific examples, that support the conclusion that nonvertical processes are often at the root of important evolutionary transitions and adaptations. I will argue that a paradigm shift is needed to naturally accommodate nonvertical processes in eukaryotic evolution.

中文翻译：

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真核生物非垂直进化的模式和影响：范式转变

真核物种及其基因组的进化传统上被理解为一个垂直过程，其中遗传物质沿谱系从父母传给后代，并且遗传交换被限制在物种边界内。然而，越来越多的来自比较基因组学的证据表明这种范式经常被违反。不同谱系之间的水平基因转移和交配模糊了物种边界，并挑战了物种及其基因组进化历史的重建。非垂直进化在真核生物中可能比在原核生物中受到更多限制，但它不可忽略并且在某些群体中可能很常见。对此类过程的认识需要将这种复杂性纳入我们的模型，并在概念上重新构建真核生物多样性和进化。这里，我回顾了基因组学研究的近期工作，这些研究支持非垂直进化模式的影响，包括基因渗入、杂交和不同真核生物群体中的水平基因转移。然后，我讨论了新出现的模式和影响，通过具体的例子来说明，支持非垂直过程通常是重要进化转变和适应的根源的结论。我认为需要范式转变来自然地适应真核进化中的非垂直过程。这支持了以下结论：非垂直过程通常是重要的进化转变和适应的根源。我认为需要范式转变来自然地适应真核进化中的非垂直过程。这支持了以下结论：非垂直过程通常是重要的进化转变和适应的根源。我认为需要范式转变来自然地适应真核进化中的非垂直过程。