Hall Brian K
Department of Biology, Dalhousie University, Halifax, N.S., Canada B3H 471.
Biol Rev Camb Philos Soc. 2003 Aug;78(3):409-33. doi: 10.1017/s1464793102006097.
Homology is at the foundation of comparative studies in biology at all levels from genes to phenotypes. Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. However, given that there is but one tree of life, all organisms, and therefore all features of organisms, share some degree of relationship and similarity one to another. That sharing may be similarity or even identity of structure and the sharing of a most recent common ancestor--as in the homology of the arms of humans and apes--or it may reflect some (often small) degree of similarity, such as that between the wings of insects and the wings of birds, groups whose shared ancestor lies deep within the evolutionary history of the Metazoa. It may reflect sharing of entire developmental pathways, partial sharing, or divergent pathways. This review compares features classified as homologous with the classes of features normally grouped as homoplastic, the latter being convergence, parallelism, reversals, rudiments, vestiges, and atavisms. On the one hand, developmental mechanisms may be conserved, even when a complete structure does not form (rudiments, vestiges), or when a structure appears only in some individuals (atavisms). On the other hand, different developmental mechanisms can produce similar (homologous) features. Joint examination of nearness of relationship and degree of shared development reveals a continuum within an expanded category of homology, extending from homology --> reversals --> rudiments --> vestiges --> atavisms --> parallelism, with convergence as the only class of homoplasy, an idea that turns out to be surprisingly old. This realignment provides a glimmer of a way to bridge phylogenetic and developmental approaches to homology and homoplasy, a bridge that should provide a key pillar for evolutionary developmental biology (evo-devo). It will not, and in a practical sense cannot, alter how homoplastic features are identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution.
同源性是生物学中从基因到表型各个层面比较研究的基础。同源性是由于共同的祖先和世系而产生的相似性，同功性是通过独立进化达成的相似性。然而，鉴于生命之树只有一棵，所有生物，进而生物的所有特征，彼此之间都存在一定程度的关联和相似性。这种相似性可能是结构的相似甚至相同以及拥有最近的共同祖先——比如人类和猿类手臂的同源性——或者它可能反映出某种（通常较小）程度的相似性，比如昆虫翅膀和鸟类翅膀之间的相似性，这两类生物的共同祖先处于后生动物进化史的深处。它可能反映出整个发育途径的共享、部分共享或分歧途径。本综述将被归类为同源的特征与通常被归为同功的特征类别进行比较，后者包括趋同、平行进化、逆转、残迹、痕迹器官和返祖现象。一方面，发育机制可能是保守的，即使完整结构未形成（残迹、痕迹器官），或者结构仅在某些个体中出现（返祖现象）。另一方面，不同的发育机制可以产生相似（同源）的特征。对亲缘关系的接近程度和共享发育程度的联合考察揭示了同源性扩展类别中的一个连续统，从同源性→逆转→残迹→痕迹器官→返祖现象→平行进化，趋同是同功性的唯一类别，这一观点其实相当古老。这种重新排列为在系统发育和发育方法之间架起同源性和同功性的桥梁提供了一线希望，这座桥梁应该为进化发育生物学（演化发育生物学）提供关键支柱。它不会，而且实际上也不能，改变在系统发育分析中识别同功特征的方式。但是将残迹、逆转、痕迹器官、返祖现象和平行进化视为比同功性更接近同源性，应该引导我们去寻找表型形成背后的共同要素（有些人称之为遗传和/或细胞机制的深度同源性），而不是从共享或独立进化的角度来讨论特征。
