Searching For Modular Structure In Complex Phenotypes: Inferences From Network Theory

dc.creatorIvan Perez S.
dc.creatorde Aguiar M.A.M.
dc.creatorGuimaraes Jr. P.R.
dc.creatordos Reis S.F.
dc.date2009
dc.date2015-06-26T13:35:06Z
dc.date2015-11-26T15:33:58Z
dc.date2015-06-26T13:35:06Z
dc.date2015-11-26T15:33:58Z
dc.date.accessioned2018-03-28T22:42:34Z
dc.date.available2018-03-28T22:42:34Z
dc.identifier
dc.identifierEvolutionary Biology. , v. 36, n. 4, p. 416 - 422, 2009.
dc.identifier713260
dc.identifier10.1007/s11692-009-9074-7
dc.identifierhttp://www.scopus.com/inward/record.url?eid=2-s2.0-72249090842&partnerID=40&md5=02dfda56d2c5fddf4c08997c9f643faf
dc.identifierhttp://www.repositorio.unicamp.br/handle/REPOSIP/92154
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/92154
dc.identifier2-s2.0-72249090842
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1262879
dc.descriptionThe notion of modularity has become a unifying principle to understand structural and functional aspects of biological organization at different levels of complexity. Recently, deciphering the modular organization of molecular systems has been greatly aided by network theory. Nevertheless, network theory is completely absent from the investigation of modularity of complex macroscopic phenotypes, a fundamental level of organization at which organisms experience and interact with the environment. Here, we used geometric descriptors of phenotypic variation to derive a network representation of a complex morphological structure, the mammalian mandible, in terms of nodes and links. Then, by integrating the network representation and description with random matrix theory, we uncovered a modular organization for the mammalian mandible, which deviates significantly from an equivalent random network. The modules revealed by the network analysis correspond to the four morphogenetic units recognized for the mammalian mandible on a developmental basis. Furthermore, these modules are known to be affected only by particular genes and are also functionally differentiated. This study shows that the powerful formalism of network theory can be applied to the discovery of modules in complex phenotypes and opens the possibility of an integrated approach to the study of modularity at all levels of organizational complexity. © Springer Science+Business Media, LLC 2009.
dc.description36
dc.description4
dc.description416
dc.description422
dc.descriptionAdams, D.C., Rohlf, F.J., Slice, D.E., Geometric morphometrics: Ten years of progress following the 'revolution' (2004) The Italian Journal of Zoology, 71, pp. 5-16
dc.descriptionAlbert, R., Barabási, A.L., Statistical mechanics of complex networks (2002) Review of Modern Physics, 74, pp. 47-97
dc.descriptionAtchley, W.R., Hall, B.K., A model for development and evolution of complex morphological structures (1991) Biological Review, 66, pp. 101-157
dc.descriptionBatagelj, V., Mrvar, A., (2008) Pajek 1. 23 Software, , http://vlado.fmf.uni-lj.si/pub/networks/pajek/
dc.descriptionBookstein, F.L., (1991) Morphometric Tools for Landmark Data: Geometry and Biology, , London: Cambridge University Press
dc.descriptionCheverud, J.M., Modular pleiotropic effects of quantitative trait loci on morphological traits (2004) Modularity in Development and Evolution, pp. 132-153. , G. Schlosser and G. P. Wagner (Eds.), Chicago: Chicago University Press
dc.descriptionCheverud, J.M., Routman, E.J., Irschick, D.K., Pleiotropic effects of individual gene loci on mandibular morphology (1997) Evolution, 51, pp. 2004-2014
dc.descriptionDanon, L., Duch, J., Diaz-Guilera, A., Arenas, A., Comparing community structure identification (2005) Journal of Statistical Mechanics, , P09008
dc.descriptionDavidson, E.H., Levine, M., Properties of developmental gene regulatory networks (2008) Proceedings of the National Academy of Sciences of the United States of America, 105, pp. 20063-20066
dc.descriptionde Aguiar, M.A.M., Bar-Yam, Y., Spectral analysis and the dynamic response of complex networks (2005) Physical Review, E71, p. 6106
dc.descriptionEhrich, T.H., Vaughn, T.T., Koreishi, S.F., Linsey, R.B., Pletscher, L.S., Cheverud, J.M., Pleiotropic effects on mandibular morphology I. Developmental morphological integration and differential dominance (2003) Journal of Experimental Zoology Molecular and Developmental Evolution, 296 B, pp. 58-79
dc.descriptionGalewski, T., Mauffrey, J.F., Leite, Y.L.R., Patton, J.L., Douzery, E.J.P., Ecomorphological diversification among South American spiny rats (Rodentia: Echimyidae): A phylogenetic and chronological approach (2005) Molecular Phylogenetics and Evolution, 34, pp. 601-615
dc.descriptionGuimerà, R., Amaral, L.A.N., Functional cartography of complex metabolic networks (2005) Nature, 433, pp. 895-900
dc.descriptionGuimerà, R., Sales-Pardo, M., Amaral, L.A.N., Modularity from fluctuations in random graphs and complex networks (2004) Physical Review E, 70, p. 025101
dc.descriptionHall, B.K., Unlocking the black box between genotype and phenotype: Cell condensations as morphogenetic (modular) units (2003) Biology and Philosophy, 18, pp. 219-247
dc.descriptionHallgrimsson, B., Lieberman, D.E., Young, N.M., Parsons, T., Wat, S., Evolution of covariance in the mammalian skull (2007) Novartis Foundation Symposium, 284, pp. 164-190
dc.descriptionHintze, A., Adami, C., Evolution of complex modular biological networks (2008) PLoS Computational Biology, 4, pp. e23
dc.descriptionKlingenberg, C.P., Mebus, K., Auffray, J.-C., Developmental integration in a complex morphological structure: How distinct are the modules in the mouse mandible? (2003) Evolution and Development, 5, pp. 522-531
dc.descriptionKlingenberg, C.P., Zaklan, S.D., Morphological integration between developmental compartments in the Drosophila wing (2000) Evolution, 54, pp. 1273-1285
dc.descriptionKreimer, A., Boresntein, E., Gophna, U., Ruppin, E., The evolution of modularity in bacterial metabolic networks (2008) Proceedings of the National Academy of Sciences of the United States of America, 105, pp. 6976-6981
dc.descriptionLevin, S.A., The problem of pattern and scale in ecology (1992) Ecology, 73, pp. 1943-1967
dc.descriptionLevin, S.A., Complex adaptive systems: Exploring the known, the unknown and the unknowable (2003) Bulletin of the American Mathematical Society, 40, pp. 3-19
dc.descriptionMa'ayan, A., Insights into the organization of biochemical regulatory networks using graph theory analyses (2009) Journal of Biological Chemistry, 284, pp. 5451-5455
dc.descriptionMarroig, G., Cheverud, J.M., A comparison of phenotypic variation and covariation patterns and the role of phylogeny, ecology and ontogeny during cranial evolution of New World monkeys (2001) Evolution, 55, pp. 2576-2600
dc.descriptionMehta, M.L., (2004) Random Matrices, , New York: Academic Press
dc.descriptionMitteroecker, P., Bookstein, F., The ontogenetic trajectory of the phenotypic covariance matrix, with examples from craniofacial shape in rats and humans (2009) Evolution, 63, pp. 727-737
dc.descriptionNewman, M.E.J., Modularity and community structure in networks (2006) Proceedings of the National Academy of Sciences of the United States of America, 103, pp. 8577-8582
dc.descriptionOksanen, J., Kindt, R., Legendre, P., O'Hara, B., Simpson, G.L., Stevens, M.H.H., Vegan: Community ecology package (2008) R Package Version 1. 11-4, , http://cran.r-project.org
dc.descriptionPalla, G., Vattay, G., Spectral transitions in networks (2006) New Journal of Physics, 8, p. 307
dc.descriptionPeres-neto, P.R., Jackson, D.A., How well do multivariate data sets match? The advantages of a procrustean superimposition approach over the Mantel test (2001) Oecologia, 129, pp. 169-178
dc.descriptionPerez, S.I., Diniz-Filho, J.A.F., Rohlf, F.J., dos Reis, S.F., Morphological diversification among South American spiny rats (Rodentia: Echimyidae): Ecological and phylogenetic factors (2009) Journal of the Linnean Society, 96, pp. 646-660
dc.descriptionPorto, A., de Oliveira, F.B., Shirai, L.T., de Conto, V., Marroig, G., The evolution of modularity in the mammalian skull I: Morphological integration patterns and magnitudes (2008) Evolutionary Biology, 35, pp. 1-18
dc.descriptionRaff, R.A., (1996) The Shape of Life: Genes, Development, and the Evolution of Animal Form, , Chicago: University of Chicago Press
dc.descriptionRavasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., Barabási, A.L., Hierarchical organization of modularity in metabolic networks (2002) Science, 297, pp. 1551-1555
dc.descriptionRohlf, F.J., (2007) Tps Series Softwares, , http//life.bio.sunysb.edu/morph/
dc.descriptionSales-pardo, M., Guimerà, R., Moreira, A.A., Amaral, L.A.N., Extracting the hierarchical organization of complex systems (2007) Proceedings of the National Academy of Sciences of the United States of America, 104, pp. 15224-15229
dc.description(2004) Modularity in Development and Evolution, , G. Schlosser and G. P. Wagner (Eds.), Chicago: Chicago University Press
dc.descriptionSheets, H.D., (2003) IMP-Integrated Morphometrics Package, , Department of Physics, Canisius College, Buffalo, New York
dc.descriptionSteinhauser, D., Krall, L., Müssig, C., Büssis, D., Usadel, B., Correlation networks (2008) Analysis of Biological Networks, pp. 305-333. , B. H. Junker and F. Schreiber (Eds.), New Jersey: Wiley
dc.descriptionWagner, G.P., On the eigenvalues of genetic and phenotypic dispersion matrices: Evidence for a nonrandom organization of quantitative character variation (1984) Journal of Mathematical Biology, 21, pp. 77-95
dc.descriptionWagner, G.P., Homologues, natural kinds and the evolution of modularity (1996) American Zoologist, 36, pp. 36-43
dc.descriptionWagner, G.P., Pavlicev, M., Cheverud, J.M., The road to modularity (2007) Nature Reviews. Genetics, 8, pp. 921-931
dc.descriptionWang, Z., Zhang, J., In search of the biological significance of modular structures in protein networks (2007) PLoS Computational Biology, 3 (6), pp. e107
dc.descriptionWinther, R.G., Varieties of modules: Kinds, levels, origins, and behaviours (2001) Journal of Experimental Zoology Molecular and Developmental Evolution, 291, pp. 116-129
dc.languageen
dc.publisher
dc.relationEvolutionary Biology
dc.rightsfechado
dc.sourceScopus
dc.titleSearching For Modular Structure In Complex Phenotypes: Inferences From Network Theory
dc.typeArtículos de revistas


Este ítem pertenece a la siguiente institución