Department of Zoology, University of Oxford, Oxford, UK.
Philos Trans R Soc Lond B Biol Sci. 2010 Jan 12;365(1537):111-32. doi: 10.1098/rstb.2009.0161.
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.
生物系统发生取决于细胞分裂、停滞、突变分歧、细胞融合（通过性或共生）、侧向基因转移和死亡。生命之树是生物体系统发生历史的有用隐喻，只要我们认识到分支有时会融合。亨尼根分类学仅强调谱系分裂，忽略了其他大多数主要的系统发育过程。尽管在方法论上有用，但它在概念上令人困惑，并损害了分类学，特别是在错误地反对祖先（并系）分类群方面。生命的历史涉及大约 10 种真正的细胞结构重大创新。在膜拓扑学方面，有五种连续的细胞：（i）具有两个边界膜的Negibacteria，（ii）具有一个边界膜而没有内部膜的Unibacteria，（iii）具有内膜和线粒体的真核生物，（iv）具有叶绿体的植物，以及（v）最后，具有内质网内部质体的Chromists。膜化学将Negibacteria 分为更先进的糖细菌（例如蓝细菌和变形菌），它们具有外膜脂多糖，而原始的 Eobacteria 则没有脂多糖（值得更深入的研究）。它还将 Unibacteria 分为 Posibacteria，真核生物的祖先，以及古细菌——真核生物的姐妹（不是祖先）和最年轻的细菌门。厌氧变形菌、需氧蓝细菌、抗干燥的 Posibacteria ，最后是 Neomura（真核生物加上古细菌）相继改造了地球。在身体形态进化中，意外和组织约束与适应性一样重要。
