Deyasi Krishanu, Banerjee Anirban, Deb Bony
Department of Mathematics and Statistics, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741 246, India.
J Biosci. 2015 Oct;40(4):799-808. doi: 10.1007/s12038-015-9562-0.
Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of 79 fully sequenced organisms and compared their architectures. We used spectral density of normalized Laplacian matrix for comparing the structure of networks. The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a split network is constructed to analyse the phylogeny from these distances. In our analysis, we focused on the species that belong to different classes, but appear more related to each other in the phylogeny. We tried to explore whether they have evolved under similar environmental conditions or have similar life histories. With this focus, we have obtained interesting insights into the phylogenetic commonality between different organisms.
为了研究不同生物之间的系统发育关系，人们开发了许多方法来寻找它们之间的共性。代谢网络的结构也揭示了关于物种代谢能力以及它们进化所处栖息地的宝贵见解。我们构建了79种全基因组测序生物的代谢网络，并比较了它们的结构。我们使用归一化拉普拉斯矩阵的谱密度来比较网络结构。该矩阵的特征值不仅反映了网络的全局结构，还反映了由不同的图进化过程（如图案复制或连接）产生的局部拓扑结构。基于谱密度的差异度量用于量化各种代谢网络之间的距离，并构建分裂网络以从这些距离分析系统发育关系。在我们的分析中，我们专注于属于不同类别的物种，但在系统发育中彼此似乎更相关的物种。我们试图探究它们是否在相似的环境条件下进化或具有相似的生活史。基于这一重点，我们获得了关于不同生物之间系统发育共性的有趣见解。
