3.4 Genome Evolution and Estimation of Evolutionary Rate
To clarify M. japonicus genome evolution, 46,975 gene families were clustered from 21 species. To reveal the phylogenetic relationships among M. japonicus and other species, 174 single-copy ortholog families derived from the 21 species were identified and the protein sequences of these orthologs were aligned. The maximum-likelihood method was used to performed phylogenetic analysis. According to the phylogenetic analysis, M. japonicus might have started to diverge from other species of shrimp approximately 119 million years ago (Figure 5).