Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea.
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Biochimie. 2014 Apr;99:129-37. doi: 10.1016/j.biochi.2013.11.019. Epub 2013 Dec 4.
The reconstruction of phylogenetic trees from molecular data requires selecting models of molecular evolution that adequately describe known processes of change. Operationally, these models optimize molecular changes along branches of the trees. The underlying processes must be realistic and must comply with well-supported biological assumptions. In a recent paper, a new model of proteome evolution that penalizes growth of the protein world provides an 'upside down' phylogeny and identifies a very complex ancestor of diversified life. Here we show that the model is phylogenetically self-inconsistent and at odds with considerable background knowledge, including the scale-free property of domain networks, genomic scaling laws, and the principle of continuity that supports the tenets of ideographic analysis and evolutionary thinking. While technical and conceptual limitations invalidate the main conclusions of the study, including the existence of bottlenecks in protein evolution caused by planetary cataclysms, we use the example to highlight the complexities and pitfalls of retrodiction in phylogenetic and phylogenomic analyses and reexamine the framework of ideographic exploration that is used in scientific inquiry.
从分子数据重建系统发育树需要选择能够充分描述已知进化过程的分子进化模型。这些模型通过优化树枝上的分子变化来操作。基础过程必须是现实的，并且必须符合得到充分支持的生物学假设。在最近的一篇论文中，一种新的蛋白质组进化模型对蛋白质世界的增长进行了惩罚，该模型提供了一个“颠倒”的系统发育关系，并确定了多样化生命的一个非常复杂的祖先。在这里，我们表明该模型在系统发育上是自相矛盾的，与大量背景知识相冲突，包括结构域网络的无标度特性、基因组缩放定律以及连续性原则，这些都支持了表意分析和进化思维的原则。虽然技术和概念上的限制使该研究的主要结论无效，包括由行星灾难引起的蛋白质进化瓶颈的存在，但我们使用该示例来突出系统发育和系统发育基因组分析中的回溯复杂性和陷阱，并重新审视用于科学探究的表意探索框架。
