Theoretical Molecular Evolution

• Grant number: 99/09644-9
• Support Opportunities: Research Projects - Thematic Grants
• Start date: March 01, 2000
• End date: August 31, 2004
• Field of knowledge: Physical Sciences and Mathematics - Physics - General Physics
• Principal Investigator: José Fernando Fontanari
• Grantee: José Fernando Fontanari
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil

Abstract

The introduction of molecular methods in the study of evolution has undoubtedly turned this research field into a 'hard' science, in which the relevant parameters can be accurately measured from experimental data, and the theories can be tested against reality. In this project we concentrate on two areas of study, namely, (a) reconstruction of the evolutionary history of genes and organisms (ancestral inference), and (b) prebiotic evolution or the origin of life. Although these areas have traditionally been studied separately, mainly because the origin of life is still a largely speculative issue, we will argue that, from the theoretical side at least, the models used to study the two problems are essentially the same; the main difference being the emphasis given on different characteristics or quantities of the evolutionary process. In this sense we plan to use our experience of 5 years of work on prebiotic evolution to tackle problems on phylogeny and genealogy reconstruction. This sort of problem has great practical importance as, for instance, the elucidation of the origin and natural history of viruses. More pointedly, we will focus on the effects of selection (or differential reproduction) on the statistical properties of genealogical trees such as the adjacency patterns and the distribution of distance between nodes. Although these properties are well understood in the case of neutral evolution, there are very few works that take selection into account. As for the prebiotic evolution theme, we will concentrate mainly on the application of group selection theory ideas to explain the stable coexistence of self-replicating molecules with different rates of replication. This coexistence is essential to the emergence of complex molecular clusters capable of working as a rudimentary metabolism. (AU)

Scientific publications

(15)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MAIA, LEONARDO P.; COLATO, ALEXANDRE; FONTANARI, JOSÉ F.. Effect of selection on the topology of genealogical trees. Journal of Theoretical Biology, v. 226, n. 3, p. 315-320, Feb. 2004. (99/09644-9)

ROSAS‚ A.; FERREIRA‚ CP; FONTANARI‚ JF. Evolution of protein synthesis in a lattice model of replicators. Physical Review Letters, v. 89, n. 18, p. 188101, 2002. (99/09644-9)

STADLER‚ P.F.; HORDIJK‚ W.; FONTANARI‚ J.F.. Phase transition and landscape statistics of the number partitioning problem. Physical Review E, v. 67, n. 5, p. 056701, 2003. (99/09644-9)

ALVES‚ D.; CAMPOS‚ PRA; SILVA‚ ATC; FONTANARI‚ JF. Group selection models in prebiotic evolution. Physical Review E, v. 63, n. 1, p. 011911, 2000. (99/09644-9)

SANTOS‚ D.O.C.; FONTANARI‚ J.F.. Model ecosystems with random nonlinear interspecies interactions. Physical Review E, v. 70, n. 6, p. 061914, 2004. (99/09644-9)

COLATO‚ A.; FONTANARI‚ JF. Soluble model for the accumulation of mutations in asexual populations. Physical Review Letters, v. 87, n. 23, p. 238102, 2001. (99/09644-9)

DE OLIVEIRA‚ V.M.; FONTANARI‚ JF. Random replicators with high-order interactions. Physical Review Letters, v. 85, n. 23, p. 4984-4987, 2000. (99/09644-9)

FONTANARI‚ JF; PERLOVSKY‚ LI. Solvable null model for the distribution of word frequencies. Physical Review E, v. 70, n. 4, p. 042901, 2004. (99/09644-9)

FERREIRA‚ C.P.; FONTANARI‚ J.F.; DOS SANTOS‚ R.M.Z.. Phase transitions in a model for the formation of herpes simplex ulcers. Physical Review E, v. 64, n. 4, p. 041903, 2001. (99/09644-9)

FONTANARI‚ JF; COLATO‚ A.; HOWARD‚ RS. Mutation accumulation in growing asexual lineages. Physical Review Letters, v. 91, n. 21, p. 218101, 2003. (99/09644-9)

DE OLIVEIRA‚ V.M.; FONTANARI‚ JF. Extinctions in the random replicator model. Physical Review E, v. 64, n. 5, p. 051911, 2001. (99/09644-9)

FERREIRA‚ C.P.; FONTANARI‚ JF. Nonequilibrium phase transitions in a model for the origin of life. Physical Review E, v. 65, n. 2, p. 021902, 2002. (99/09644-9)

DE OLIVEIRA‚ V.M.; FONTANARI‚ JF. Complementarity and diversity in a soluble model ecosystem. Physical Review Letters, v. 89, n. 14, p. 148101, 2002. (99/09644-9)

ROSAS‚ A.; NOGUEIRA JR‚ E.; FONTANARI‚ J.F.. Multifractal analysis of DNA walks and trails. Physical Review E, v. 66, n. 6, p. 061906, 2002. (99/09644-9)

MAIA, LEONARDO P.; BOTELHO, DANIELA F.; FONTANARI, JOSÉ F.. Analytical solution of the evolution dynamics on a multiplicative-fitness landscape. Journal of Mathematical Biology, v. 47, n. 5, p. 453-456, Nov. 2003. (99/09644-9)