Figure 1.

Zebrafish is currently evolutionarily distant from all other available fish genomes. (A) Phylogeny with branch lengths and clade groupings (solid lines only). The ‘mousefish’, a desirable but currently unavailable teleost genome at human—mouse distance, is discussed in the text. Apart from zebrafish, frog (1.49 subs/site to chicken), lamprey (1.76 subs/site to zebrafish), amphioxus (>2.5 subs/site to lamprey) and C. elegans (1.07 subs/site to Caenorhabditis remanei) are also shown to have phylogenetically isolated genomes. Molecular distances were taken from the UCSC genome browser (28) for the hg18, braFlo1 and ce10 assemblies. (B) Evolutionary distances (neutral substitutions per site) between zebrafish (left) and human (right) to other sequenced species. In contrast to human, the zebrafish genome occupies a phylogenetic outgroup position with the closest sequenced teleosts at a distance of 1.25–1.41 subs/site, which exceeds the distance between the human and chicken genome (1.08 subs/site). (C) The portion of CNEs conserved to mouse that can be discovered in comparisons between human and evolutionarily more distant species can be used to estimate the fraction of zebrafish CNEs visible using the current availability of genomes.