Phylogenomics and the evolution of duplicated genes in Drosophila species

SERRA F, HUERTA-CEPAS J, T GABALDON & H DOPAZO

Malaga, España

Jornada; X jornadas de bioinformática; 2010

Red Nacional de Bioinformática

Phylogenomics and the Evolution of Duplicated Genes in Drosophila species Phylogeny and adaptation are classical areas of research in the study of evolution and biodiversity. The "omic" framework leads these fields to reach the genome-wide level of analysis. Here, we advance in the study of the complete set of phylogenies - phylogenomics-, and the analysis of adaptation of paralogous sequences in the genome of the classical model of animal genetics: Drosophila melanogaster. A total of 15 genomes (12 Drosophilas and 3 outgroup species) were used to obtain the D. melanogaster phylome. This phylome provides more than 12,000 phylogenetic trees. As was previously noted [1, 2] only a minor proportion of topologies (less than 1,000) fitted the known tree of Drosophila species [3]. Although it is widely recognized that topological differences between species and gene trees has a variable number of evolutionary explanations, we test for possible functional interpretations in the data set [4]. Finally, from a set of more than 400 gene duplications we test for positive selection and relaxation of selective constraints using phylogenetic-based maximum likelihood codon models. According to the expected in different evolutionary models of duplications [5], relaxation of the selective constraints was a frequent process observed in the evolution of paralogous genes. References 1. Huerta-Cepas et al. The human phylome. Genome Biol (2007) vol. 8 (6) pp. R 2. Castresana, J. Topological variation in single-gene phylogenetic trees. Genome Biol (2007) vol. 8 (6) pp. 216 3. Drosophila 12 Genomes Consortium et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) vol. 450 (7167) pp. 203-18 4. Medina et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res (2010) vol. 38 Suppl pp. W210-3 5. Innan and Kondrashov. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) vol. 11 (2) pp. 97-108