Reconstrução de cenários evolutivos de sistemas genéticos em larga escala: introduzindo o algoritmo Bridge

Abstract

Methods for reconstructing evolutionary scenarios are important tools that help to better understand biological systems under the perspective of its origins and evolution. The primary concept for understanding them lies in the relationships established by comparing genomes from different species to form gene families known as Orthologous Groups (OGs). Orthologs are genes from distinct species derived from their last common ancestor (LCA), tipically having similar functions in each organism. By observing the phyletic pattern of an OG in a species tree, it is possible to calculate the LCA where most probably the trait represented by the OG emerged. Although this process can be trivial when applied to a single gene, it remains chalenging for large-scale queries. The bridge algorithm, structured as a R software package, allows to interrogate several hundreds to thousands of OGs at once, assigining evolutionary roots to each OG. This thesis constitutes a comprehensive reference to the method of rooting orthologous genes employed by the bridge algorithm, presenting detailed logic, implementation, accuracy, and performance