Cephalochordates, urochordates, and vertebrates evolved from a common ancestor 
over 520 million years ago. To improve our understanding of chordate evolution 
and the origin of vertebrates, we intensively searched for particular genes, 
gene families, and conserved noncoding elements in the sequenced genome of the 
cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. 
Special attention was given to homeobox genes, opsin genes, genes involved in 
neural crest development, nuclear receptor genes, genes encoding components of 
the endocrine and immune systems, and conserved cis-regulatory enhancers. The 
amphioxus genome contains a basic set of chordate genes involved in development 
and cell signaling, including a fifteenth Hox gene. This set includes many genes 
that were co-opted in vertebrates for new roles in neural crest development and 
adaptive immunity. However, where amphioxus has a single gene, vertebrates often 
have two, three, or four paralogs derived from two whole-genome duplication 
events. In addition, several transcriptional enhancers are conserved between 
amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, 
urochordate genomes have lost many genes, including a diversity of homeobox 
families and genes involved in steroid hormone function. The amphioxus genome 
also exhibits derived features, including duplications of opsins and genes 
proposed to function in innate immunity and endocrine systems. Our results 
indicate that the amphioxus genome is elemental to an understanding of the 
biology and evolution of nonchordate deuterostomes, invertebrate chordates, and 
vertebrates.