Because the conservation of gene order can also provide clues to the evolution of gene regulation, we next attempted to trace the evolution of these paralogous segments by examining the genome of the tunicate C. intestinalis [11] and the most "primitive" compact vertebrate genome sequenced to date, T. rubripes [14]. Although not fully assembled, examination of the genome of T. rubripes confirmed the presence of chromosomal segments paralogous to those found in higher vertebrates (Fig. 2). For instance, the orthologues of GPRK2L and RGS12 are found on T. rubripes scaffold 290 (emb|CAAB01000290.1), and within 300 kb of each other in human 4p16. The T. rubripes orthologues of FGFR3, LETM1 and WHSC1 are located on the same 166 kb genomic scaffold 251 (emb|CAAB01000166.1). Significantly, the three human orthologues of these genes are also located within 300 kb of each other on 4p16. Furthermore, TACC3 and FGFRL map to the overlapping scaffolds 1184/4669 (emb|CAAB01004668). Similarly, elements of these gene clusters, extending from HMP19 to GPRK6 in human chromosome 5q34-ter are also found in the pufferfish, with the T. rubripes orthologues of NSD1, FGFR4 and a RAB-like gene mapping on scaffold 407 (emb|CAAB01000407). However, there is no evidence for a gene corresponding to a TACC4 gene in any of these clusters.