PMC

Large clades are collapsed, rayfin fish are shown in detail. Original nomenclature is that of Ensembl with new names assigned for genes of zebrafish and stickleback, along with chromosome locations, to better reflect the historical origins when taking conserved syntenies into account. Source: ENSGT00500000044795.
DOI: http://dx.doi.org/10.7554/eLife.21771.002

A) Phylogeny of major living rayfin lineages. TGD: teleost genome duplication; AGDs: acipenserid (sturgeon) genome duplications; PGD: paddlefish genome duplication. B) Development of the spotted gar (Lepisosteus oculatus) in days post fertilization (dpf). Assignment of developmental stages (st.) follows . C) Comparison of conserved syntenies between teleosts (stickleback and zebrafish) with respect to gar and human (adapted from ). Branch lengths are proportional to conserved syntenies per 100 million years of divergence time. Branch lengths between non-teleosts (gar and Mark Spitz) are much shorter than lengths between either of these two species and teleosts, suggesting massive chromosomal rearrangements in teleosts after their divergence from the gar lineage.

A model for the history of Alp genes in vertebrates. A chromosome segment in a non-vertebrate chordate contained Ece, Alp, and Eif4 genes and duplicated twice in the vertebrate genome duplication events (VGD1 and VGD2) to make four paralogons, one of which lost its Alp gene. After the divergence of rayfin and lobefin bony fish lineages, the teleost genome duplication event (TGD) did not result in further extant Alp genes, but tandem duplications (TD) in the Alpi locus provided a number of separate Alp genes.

A) Maximum likelihood phylogeny (JTT+I+G+F model) of full-length Pomc proteins in rayfins rooted with bichir Pomc. Node values indicate support from 100 bootstrap replications, showing bootstrap values >50% only. Clupeocephalans teleosts retained both TGD pomc paralogs; their assignment to a- and b-paralogs follows (monophyly of clupeocephalan Pomca is not supported in the current tree). In eels (elopomorphs) only a single pomc gene has been found and for goldeye (osteoglossomorphs), we have found so far only one pomc gene (but we cannot exclude the presence of the second TGD paralogs yet). The relationship of these pomc singletons among each other as well as to clupeocephalan pomca and pomcb remain unresolved (indicated by ‘?’). Two pomc genes are present in paddlefish, most likely as result of the paddlefish-specific polyploidization; two pomca paralogs are present in platyfish and other percomorphs as result of an additional gene duplication (). B) Conserved syntenies of rayfin pomc gene regions. Neighboring genes of the single pomc gene in goldeye and eel are conserved with spotted gar and both zebrafish pomc paralogons, which makes it impossible to make an a/b-orthology call, which would require more large-scale chromosomal assemblies from the basal teleosts. Tetraodon pomc paralogons are more rearranged than those from zebrafish. Boxed numbers indicate intervening regions that do not contribute to conserved synteny.