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dc.contributor.authorZhou, Wanding
Nakhleh, Luay
dc.date.accessioned 2013-03-19T15:23:53Z
dc.date.available 2013-03-19T15:23:53Z
dc.date.issued 2012
dc.identifier.citation Zhou, Wanding and Nakhleh, Luay. "Convergent evolution of modularity in metabolic networks through different community structures." BMC Evolutionary Biology, 12, (2012) BioMed Central: 181. http://dx.doi.org/10.1186/1471-2148-12-181.
dc.identifier.urihttps://hdl.handle.net/1911/70713
dc.description.abstract Background: It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of themodularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. Results: In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxomony. Conclusions: We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organismメs metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new measures of modularity and network communities that better correspond to functional categorizations.
dc.language.iso eng
dc.publisher BioMed Central
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/
dc.title Convergent evolution of modularity in metabolic networks through different community structures
dc.type Journal article
dc.contributor.funder National Science Foundation
dc.contributor.funder Alfred P. Sloan Foundation
dc.citation.journalTitle BMC Evolutionary Biology
dc.citation.volumeNumber 12
dc.embargo.terms none
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2148-12-181
dc.identifier.pmcid PMC3534581
dc.identifier.pmid 22974099
dc.identifier.grantID CCF-0622037 (National Science Foundation)
dc.identifier.grantID Research Fellowship (Alfred P. Sloan Foundation)
dc.type.publication publisher version
dc.citation.firstpage 181


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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.