Detection of Selection and Codon Evolution in Phylogenomic Datasets

Abstract

The detection of positive selection across genomes, as well as the detection of patterns of codon usage bias, have been a crucial aspect in the study of adaptive evolution, but the molecular basis of adaptation still remains elusive. This dissertation focused on detecting signals of positive selection and codon usage bias across the genomes of different cellular compartments in various organisms. Datasets of nuclear genomes from Basidiomycota fungi, of oak chloroplast genomes, and of European sardine mitochondrial genomes were analysed. Using two Basidiomycota datasets (’basidioPAML’ and ’basidioPAML_Hv’), the influence of alignment filtering tools in the detection of positive selection was analysed, but all of the approaches produced highly variable results, with moderate to high false discovery rates. In the ’PSB’ Basidiomycota dataset, significant signals of positive selection were detected in 6382 codons across 732 nuclear genes, particularly within the Pucciniales lineage, highlighting the adaptive pressures driving their global diversification as highly specialized plant parasites. Three distinct codon usage bias patterns were identified in the third dataset, mainly influenced by differential codon usage of serine, which illustrate the evolutionary diversity within the lineage. In the chloroplast dataset, 13 codons in 9 different genes showed significant positive selection signals, with polymorphisms associated to two distinct Quercus suber haplogroups which suggests a possible influence of balancing selection on these haplogroups. No codon usage bias was detected between lineages in this dataset, although codon usage differed between genes. In the mitochondrial dataset of Sardina pilchardus, selective signals were found in 5 codons of 4 different genes involved in environmental response mechanisms. Overall, these results emphasize the importance of analysing positive selection and codon usage bias to obtain valuable insights into the genetic mechanisms that enable species to adapt to environmental changes.