The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.

中文翻译：

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分子功能的系统发育普查将现代嗜热古菌确定为最古老的细胞生命形式。

尽管付出了巨大的努力来解开宇宙生命之树的根源，但多样化生命的起源仍然是个谜。在这里，我们重建了直接从基因本体论 (GO) 定义的基因组普查中描述分子功能进化和物种进化的系统发育。我们对跨越生命的三个超级界（古细菌、细菌和真核生物）中的生物的 249 个自由生活基因组进行了采样，并使用丰富的 GO 术语作为分子特征来生成有根的系统发育树。结果揭示了古细菌的早期嗜热起源，随后是微生物超级王国中的基因组减少事件。真核基因组显示出非凡的功能多样性，并富含数百种在无核微生物细胞中未检测到的新型分子活动。值得注意的是，大多数这些新功能出现在进化的后期，与真核超级王国的多样化同步。GO 术语在超级王国中的分布证实，古生菌似乎是最简单和最古老的细胞生命形式，而真核生物是最多样化和最新的。