Phylogenomic approaches to inferring ancient relationships among eukaryotes

在过去的几十年里，基因和基因组学数据的计算分析表明，最熟悉的生物“王国”-动物，真菌和植物-只代表生命多样性的一个小角落。生物世界中最深刻的进化分歧是在细菌、细菌和真核生物之间。真核生物包括所有含细胞核的复杂细胞生物：动物、植物、真菌和大量同样重要的“王国”，其中大多数是微生物。我们现在知道，真核生物基本上是嵌合的：15亿多年前，一种与古细菌有关的细胞作为共生体吸收了一种细菌细胞，而这种第二种细胞最终成为被称为线粒体的能量产生细胞器。尽管如此，我们对早期真核生物进化的理解仍然存在根本性的差距，例如，这种细菌共生体是否是具有复杂代谢的自由生活形式，或者已经是简化的寄生虫，以及真核生物如何首先多样化为今天地球上的几十个“王国”。

In the last few decades, computational analysis of genes and genomics data have shown that the most familiar biological ‘kingdoms’ - animals, fungi and plants - represent only a tiny corner of the diversity of Life. The deepest evolutionary divergences in the living world are between Bacteria, Archaea and ‘Eukaryotes’. Eukaryotes includes all the nucleus-containing complex-celled organisms: animals, plants, fungi and a huge number of equally important ‘kingdoms’ that are mostly microbes. We now know that eukaryotes are fundamentally chimeric: More than 1.5 billion years ago, a cell related to Archaea took up a bacterial cell as a symbiont, and this second cell eventually became energy-producing organelles known as mitochondria. Still, fundamental gaps remain in our understanding of early eukaryote evolution, for example, whether this bacterial symbiont was a free-living form with a complex metabolism, or already a simplified parasite, and how eukaryotes first diversified into the dozens of ‘kingdoms’ on Earth today.