Cordero Otto X, Snel Berend, Hogeweg Paulien
Theoretical Biology and Bioinformatics, University of Utrecht, 3584 CH Utrecht, The Netherlands.
Genome Res. 2008 Mar;18(3):462-8. doi: 10.1101/gr.6815508. Epub 2008 Jan 29.
We study gene family coevolution on a tree of life based on a large-scale ancestral gene content reconstruction, which includes gene duplication and deletion events. The insights obtained from this study are threefold: (1) Global properties, such as the distribution of coevolution partners and the formation of disconnected clusters of coevolving families, can be an inevitable consequence of evolution along a tree. (2) Concerted family expansion (gene duplication) and contraction (gene deletion) reflect functional constraints and therefore lead to better function prediction. (3) "Long-range" coevolutionary relationships, caused mostly by large family expansions or contractions, reveal high-level evolutionary organization of cellular processes in prokaryotes.
我们基于大规模的祖先基因含量重建，在生命之树上研究基因家族的共同进化，其中包括基因复制和缺失事件。这项研究获得的见解有三个方面：（1）全局特性，如共同进化伙伴的分布以及共同进化家族的不相连簇的形成，可能是沿着一棵树进化的必然结果。（2）协同的家族扩张（基因复制）和收缩（基因缺失）反映了功能限制，因此有助于更好地进行功能预测。（3）主要由大家族扩张或收缩引起的“远程”共同进化关系，揭示了原核生物中细胞过程的高级进化组织。
