Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies
Year: 2012
Type: dissertation
Abstract: Phylogenomics is a biological discipline which can be understood as the intersection of the fields of genomics and evolution. Its main focuses are the analyses of genomes through the evolutionary lens and the understanding of how different organisms relate to each other. Moreover, phylogenomics allows to make accurate functional annotations of newly sequenced genomes. This discipline has grown in response to the deluge of data coming from different genome projects. To achieve their objectives, phylogenomics heavily depends on the accuracy of different methods to generate precise phylogenetic trees. Phylogenetic trees are the basic tool of this field and serve to represent how sequences or species relate to each other through common ancestry. During my thesis, I have centered my efforts in improving an automated pipeline to generate accurate phylogenetic trees and its posterior publication through a public database. Among the efforts to improve the pipeline, I have specially focused on the problem of multiple sequence alignment post-processing, which has been shown to be central to the reliability of subsequent analyses. Subsequently I have applied this pipeline, and a battery of other phylogenomics tools, to the study of the phylogenetic position of Microsporidia, a group of fast-evolving intracellular parasites. Due to their special genomic features, Microsporidia evolution constitutes one of the classical examples of challenging problems for phylogenomics. Finally, I have also used the pipeline as a part of a newly designed method for selecting robust combinations of phylogenetic gene markers. I have used this method for selecting optimal gene sets to assess the phylogenetic relationships within fungi and cyanobacteria, showing that the potential of these genes as phylogenetic markers goes well beyond the species used for their selection.
Authors: Capella Gutiérrez, Salvador Jesús
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2527209860