URMITE, UM63, CNRS 7278, IRD 198, INSERM U1095, Aix Marseille Université Marseille, France.
Front Cell Infect Microbiol. 2012 Aug 28;2:113. doi: 10.3389/fcimb.2012.00113. eCollection 2012.
Darwin's theory about the evolution of species has been the object of considerable dispute. In this review, we have described seven key principles in Darwin's book The Origin of Species and tried to present how genomics challenge each of these concepts and improve our knowledge about evolution. Darwin believed that species evolution consists on a positive directional selection ensuring the "survival of the fittest." The most developed state of the species is characterized by increasing complexity. Darwin proposed the theory of "descent with modification" according to which all species evolve from a single common ancestor through a gradual process of small modification of their vertical inheritance. Finally, the process of evolution can be depicted in the form of a tree. However, microbial genomics showed that evolution is better described as the "biological changes over time." The mode of change is not unidirectional and does not necessarily favors advantageous mutations to increase fitness it is rather subject to random selection as a result of catastrophic stochastic processes. Complexity is not necessarily the completion of development: several complex organisms have gone extinct and many microbes including bacteria with intracellular lifestyle have streamlined highly effective genomes. Genomes evolve through large events of gene deletions, duplications, insertions, and genomes rearrangements rather than a gradual adaptative process. Genomes are dynamic and chimeric entities with gene repertoires that result from vertical and horizontal acquisitions as well as de novo gene creation. The chimeric character of microbial genomes excludes the possibility of finding a single common ancestor for all the genes recorded currently. Genomes are collections of genes with different evolutionary histories that cannot be represented by a single tree of life (TOL). A forest, a network or a rhizome of life may be more accurate to represent evolutionary relationships among species.
达尔文的物种进化理论一直备受争议。在这篇综述中，我们描述了达尔文的《物种起源》一书中的七个关键原则，并试图展示基因组学如何挑战这些概念中的每一个，以及如何提高我们对进化的认识。达尔文认为，物种进化是由正向定向选择所决定的，确保“适者生存”。物种的最发达状态的特征是复杂性的增加。达尔文提出了“通过修改进行的进化”理论，根据该理论，所有物种都是从一个单一的共同祖先通过逐渐的微小修改其垂直遗传而进化而来的。最后，进化过程可以用树的形式来描述。然而，微生物基因组学表明，进化最好被描述为“随着时间的推移而发生的生物学变化”。变化的模式不是单向的，不一定有利于增加适应性的有利突变，而是由于灾难性的随机过程而受到随机选择的影响。复杂性不一定是发展的完成：几个复杂的生物体已经灭绝，许多微生物包括具有细胞内生活方式的细菌，都拥有高度有效的基因组。基因组通过大规模的基因缺失、重复、插入和基因组重排事件而进化，而不是渐进的适应过程。基因组是动态的和嵌合的实体，具有来自垂直和水平获取以及从头基因创造的基因库。微生物基因组的嵌合特征排除了为当前记录的所有基因找到一个单一共同祖先的可能性。基因组是具有不同进化历史的基因集合，不能用单个生命之树 (TOL) 来表示。生命的森林、网络或根茎可能更能准确地表示物种之间的进化关系。
