有机体巨大的多样性，以及其形态学、生理学和行为的变异的丰富性，全都是亿万年进化的结果。进化历史对每一个个体都已留下了不能去除的影响。我们今天发现的种种模式，只有按照进化论才可能有意义。

……

从更广的水平而言，进化的趋势是使有机体适合度最优，这个生态学家在对有机体结构和行为进行构想假说时提供了有用的工具。［1］

关于evolution，我认为翻译成“演化”更恰当。

那么，什么是演化？

达尔文提出了两个概念，永远驱散了“有意识设计”的论调。这两个概念就是演化与自然选择。达尔文学说最简约的描述就是：基于自然选择的演化理论。

但该学说经常被误解、或故意歪曲。

达尔文的学说包括六个方面：演化、渐进性、物种形成、共同祖先、自然选择、和演化改变的非选择性机制。［2］

按照共同祖先的设想，生物界的演化模式是树形的，但基因水平转移（horizontal gene transfer）的发现，使我们意识到演化是网状的，而非适应性过程（non-adaptiveprocesses）在演化中具有更重要的作用。［3，4］

References：

［1］A.麦肯齐等著，孙儒泳等译.生态学. 北京：科学出版社，2000

［2］科因著，叶盛译.为什么要相信达尔文. 北京：科学出版社，2009

［3］E.V.Koonin. Darwinianevolution in the light of genomics. Nucleic Acids Research, 2009, Vol. 37, No.4 1011–1034

［4］El. Baidouri, et al.Widespreadand frequent horizontal transfers of transposable elements in plants. GenomeResearch 2014 (Article published online before print.)

附：Darwinian evolution in the light of genomics的摘要

ABSTRACT

Comparative genomics andsystems biology offer unprecedented opportunities for testing central tenets ofevolutionary biology formulated by Darwin in the Origin of Species in 1859 and expandedin the Modern Synthesis 100 years later. Evolutionary-genomic studies show thatnatural selection is only one of the forces that shape genome evolution and isnot quantitatively dominant, whereas non-adaptive processes are much moreprominent than previously suspected. Major contributions of horizontal genetransfer and diverse selfish genetic elements to genome evolution undermine theTree of Life concept. An adequate depiction of evolution requires the more complexconcept of a network or ‘forest’ of life. There is no consistent tendency ofevolution towards increased genomic complexity, and when complexity increases,this appears to be a nonadaptive consequence of evolution under weak purifying selectionrather than an adaptation. Several universals of genome evolution werediscovered including the invariant distributions of evolutionary rates amongorthologous genes from diverse genomes and of paralogous gene family sizes, andthe negative correlation between gene expression level and sequence evolutionrate. Simple, non-adaptive models of evolution explain some of theseuniversals, suggesting that a new synthesis of evolutionary biology mightbecome feasible in a not so remote future.