Dollo parsimony and the reconstruction of genome evolution

The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to a substantial simplification of evolutionary analysis and provides for unambiguous reconstruction of evolutionary scenarios, which may not be attainable with other methods. In this chapter, applications of Dollo parsimony are described for the quantitative analysis of the dynamics of genome evolution. Dollo parsimony is the method of choice for reconstructing evolution of the gene repertoire of eukaryotic organisms because although multiple, independent losses of a gene in different lineages are common, multiple gains of the same gene are improbable. This contrasts with the situation in prokaryotes where the widespread occurrence of horizontal gene transfer makes multiple gains possible, thereby invalidating the Dollo principle. The chapter applies Dollo parsimony to reconstruct the scenario of evolution for the genomes of crown-group eukaryotes by assigning the loss of genes and emergence of new genes to the branches of the phylogenetic tree, and delineate the minimal gene sets for various ancestral forms. A similar analysis, with rather unexpected results, was performed to infer gain versus loss of introns in conserved eukaryotic genes. The applicability of the Dollo principle for these and other problems in evolutionary genomics is discussed.