Runt Gene Evolution 44. Meulemans D, McCauley D, Bronner-Fraser M (2003) Id expression in amphioxus and lamprey highlights the role of gene cooption during neural crest evolution. Dev Biol 264: 430–442. 45. Baker CV, Bronner-Fraser M (1997) The origins of the neural crest. Part II: an evolutionary perspective. Mech Dev 69: 13–29. 46. Ra¨hr H (1982) Ultrastructure of gill bars of Branchiostoma lanceolatum with special reference to gill skeleton and blood vessels (Cephalochordata). Zoomorphology 99: 167–180. 47. Huang G, Xie X, Han Y, Fan L, Chen J, et al. (2007) The identification of lymphocyte-like cells and lymphoid-related genes in amphioxus indicates the twilight for the emergency of adaptive immune system. PLoS ONE 2: e206. 48. Avaron F, Hoffman L, Guay D, Akimenko MA (2006) Characterization of two new zebrafish members of the hedgehog family: atypical expression of a zebrafish indian hedgehog gene in skeletal elements of both endochondral and dermal origins. Dev Dyn 235: 478–489. 49. Meulemans D, Bronner-Fraser M (2007) Insights from amphioxus into the evolution of vertebrate cartilage. PLoS ONE 2: e787. 50. Shimeld SM (1999) The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev Genes Evol 209: 40–47. 51. Dyer MA, Farrington SM, Mohn D, Munday JR, Baron MH (2001) Indian hedgehog activates hematopoiesis and vasculogenesis and can respecify prospective neurectodermal cell fate in the mouse embryo. Development 128: 1717–1730. 52. Holland ND, Holland LZ (1993) Embryos and larvae of invertebrate deuterostomes. In: Stern CD, Holland PWH, eds (1993) Essential developmental biology: a practical approach. Oxford: IRL Press. pp 21–32. 53. Triglia T, Peterson MG, Kemp DJ (1988) A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res 16: 8186. 54. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23: 403–405. 55. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540–552. 56. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755. 57. Albrecht AN, Schwabe GC, Stricker S, Boddrich A, Wanker EE, et al. (2002) The synpolydactyly homolog (spdh) mutation in the mouse – a defect in patterning and growth of limb cartilage elements. Mech Dev 112: 53–67. 58. Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, et al. (2002) Human chromosome 21 gene expression atlas in the mouse. Nature 420: 582–586. 59. Stock M, Schafer H, Stricker S, Gross G, Mundlos S, et al. (2003) Expression of galectin-3 in skeletal tissues is controlled by Runx2. J Biol Chem 278: 17360–17367. 60. Jeffery WR (2006) Ascidian neural crest-like cells: phylogenetic distribution, relationship to larval complexity, and pigment cell fate. J Exp Zoolog B Mol Dev Evol 306: 470–480. PLoS Genetics | www.plosgenetics.org 13 March 2008 | Volume 4 | Issue 3 | e1000025