One of the key questions of evolution is to answer how the morphological complexity takes place among extant animals including vertebrates. The subphylum Vertebrata is characterized by the appearance of critical morphological innovations such as an elaborate segmented brain, neural crest cells, neurogenic placodes, and endoskeleton (Shimeld and Holland, 2000). Several decades of developmental genetic studies have led to the important discovery that most animals from different taxa share a bunch of regulatory and tissue-specific genes known as “genetic toolkit,” which controls animal body pattern (Carroll, 2000). Therefore, the molecular phylogeny of these toolkit genes will provide us an insight into the evolutionary origin of morphological novelties. Whole genome duplication (WGD) could not only enrich the genomic complexity, but also generate new functions of duplicated genes by co-option (Ohno, 1970; True and Carroll, 2002; Dehal and Boore, 2005; Conant and Wolfe, 2008; Cañestro et al., 2013). WGD occurred around the origin of vertebrate lineage, has been shown to be related to vertebrate morphological innovations (Manzanares et al., 2000; True and Carroll, 2002). For example, the origin of vertebrate cartilage was found to be attributable to the duplication of chordate fibrillar collagen genes (Wada et al., 2006; Zhang et al., 2006), and the emergence of vertebrate vascular vessels to the duplication of kank genes (Hensley et al., 2016).