The immense morphological and phenotypic diversity within eukaryotes coincides with large-scale differences in genic repertoires, including the presence of thousands of new genes in every genome. New genes arise through duplication and divergence of existing coding sequences or de novo from noncoding sequences. These processes together cause individual genomes to contain up to one-third of orphan genes without any detectable homology in other lineages. Recently, deep taxon phylogenomics, the genome comparisons of extremely closely related species, provided novel insight into the evolutionary dynamics of such rapidly evolving genes. This review focuses on deep taxon phylogenomics and its importance in studying the evolution of new genes and discusses challenges and opportunities.

中文翻译：

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新基因起源和深分类群系统学：机遇与挑战。

真核生物内巨大的形态和表型多样性与基因库中的大规模差异相吻合，包括每个基因组中都有成千上万的新基因的存在。新基因通过现有编码序列的重复和发散或从非编码序列的重新产生而产生。这些过程共同导致单个基因组包含多达三分之一的孤儿基因，而在其他谱系中没有任何可检测的同源性。最近，深分类生物系统发育组学，即极为密切相关的物种的基因组比较，为这种快速进化的基因的进化动力学提供了新颖的见解。这篇综述着重于深层分类系统发育学及其在研究新基因进化中的重要性，并讨论了挑战和机遇。