The evolution of the vertebrate beta globin gene family
This thesis covers different aspects of the evolution of the vertebrate beta globin gene family. A wealth of data on globins has been accumulated over decades of work in diverse areas, this information, together with the use of new methods, allowed a comprehensive analysis of beta globins. First, a review on the current knowledge of gene family evolution is made and the general objectives of the thesis are stated. This introductory chapter is followed by the careful analysis of the beta globin phylogeny comparing different reconstruction methods and discussing the differences between species and gene tree topologies. The molecular evolution of this gene family is investigated using codon models of sequence evolution. Particular emphasis is put on the role of gene conversion and positive selection acting at sites in the genes and along branches in the phylogeny. Also, several models of evolution by gene duplication are tested and results are analysed in the light of the different hypotheses on gene family evolution. The third chapter is devoted to the evolution of the globin protein structure from the analysis of sequence data. The ancestral state reconstruction of structurally relevant amino acids in different globins is conducted and the substitution pathway leading to the observed data is examined. The impact of amino acid changes in the hemoglobin protein is evaluated in terms of structural and functional constraints and the role of positive selection on the protein products of these genes is explored. Also, a possible case of coevolution between residues in the alpha and beta subunits of hemoglobin is proposed. Finally, using new and more sophisticated methods, I estimate dates for gene duplication and gene divergence events in the beta globin family. Two different methods of date estimation based on molecular data are compared and evolutionary rate variation in this gene family is tested.