Fibroblast growth factors (Fgfs) encode small signaling proteins that help 
regulate embryo patterning. Fgfs fall into seven families, including FgfD. 
Nonvertebrate chordates have a single FgfD gene; mammals have three (Fgf8, 
Fgf17, and Fgf18); and teleosts have six (fgf8a, fgf8b, fgf17, fgf18a, fgf18b, 
and fgf24). What are the evolutionary processes that led to the structural 
duplication and functional diversification of FgfD genes during vertebrate 
phylogeny? To study this question, we investigated conserved syntenies, patterns 
of gene expression, and the distribution of conserved noncoding elements (CNEs) 
in FgfD genes of stickleback and zebrafish, and compared them with data from 
cephalochordates, urochordates, and mammals. Genomic analysis suggests that 
Fgf8, Fgf17, Fgf18, and Fgf24 arose in two rounds of whole genome duplication at 
the base of the vertebrate radiation; that fgf8 and fgf18 duplications occurred 
at the base of the teleost radiation; and that Fgf24 is an ohnolog that was lost 
in the mammalian lineage. Expression analysis suggests that ancestral 
subfunctions partitioned between gene duplicates and points to the evolution of 
novel expression domains. Analysis of CNEs, at least some of which are candidate 
regulatory elements, suggests that ancestral CNEs partitioned between gene 
duplicates. These results help explain the evolutionary pathways by which the 
developmentally important family of FgfD molecules arose and the deduced 
principles that guided FgfD evolution are likely applicable to the evolution of 
developmental regulation in many vertebrate multigene families.