GBE Punctuated Emergences of Genetic and Phenotypic Innovations in Eumetazoan, Bilaterian, Euteleostome, and Hominidae Ancestors Yvan Wenger and Brigitte Galliot* Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland *Corresponding author: E-mail:
[email protected]. Accepted: September 12, 2013 Data deposition: Sequences of the 6,071 Hydra-human orthologs were deposited at European Nucleotide Archive (ENA), sequencing project PRJEB446, individual accession numbers HAAD01000001–HAAD01006071. Sequences of the 45,269 Hydra RNA-seq transcripts were also de- posited at European Nucleotide Archive (ENA) sequencing project PRJEB445, individual accession numbers HAAC01000001–HAAC01045269. Abstract Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans,