Fig. 4: Hagfish and lamprey share a whole-genome triplication.

a, Phylogenetic support of gnathostome and cyclostome genes for 1R and 2R. Elephant shark, hagfish, lamprey or both cyclostomes’ genes (both hagfish and lamprey genes included) were analysed as test genes in the context of spotted gar and chicken gene phylogenies by each AC (using amphioxus genes) and orthologous sea cucumber genes (outgroup). Left: possible positions where test genes can branch, supporting or not 1R or/and 2R (see legend). Middle and right: statistics of supporting (blue) or not supporting (orange) gene phylogenies from each species’ tested genes. All phylogenetic trees are available in Supplementary Files 5–8. b, Formula to calculate the OR between two chromosomes. Dark cyan denotes genes from the AC, retained in modern chromosomes; white indicates gene loss. c, OR values distribution between WGD-generated paralogous (ohnologous) chromosomes in chicken (top left) and spotted gar (top right), and the artificially split chromosomes in chicken (bottom left) and spotted gar (bottom right). Dashed lines mark OR = 0.15. d, OR values distribution between putative ohnologous chromosomes in hagfish (top left) and lamprey (top right), and the artificially split chromosomes in hagfish (bottom left) and lamprey (bottom right). e, OR values distribution between chicken and spotted gar (top) and between hagfish and lamprey (bottom) orthologous chromosomes. f, Numbers of mutually ohnologous chromosomes in cyclostome genomes that correspond to each one of the 16 reconstructed ACs. g, Retention profile clustering analysis of cyclostome chromosomes deriving from AC2. Retained genes are denoted by dark cyan lines. Five putative orthologous chromosome pairs are defined. Note that AC17 was excluded from the analyses depicted in c–f because of the low number of genes we recovered (20 genes). Animal illustrations kindly provided by Tamara de Dios Fernández; chicken, spotted gar, lamprey and hagfish illustrations reproduced with permission from ref. ¹³³.