Fig. 2

Duplicate gene retention model for the Atlantic salmon (Salmo salar). Shown in each box is a gene tree marked with a colored circle to indicate a duplication event. Blue circles indicate a 3R WGD event, orange circles indicate a Post3R-Pre4R lineage specific duplication event, green circles indicate a 4R WGD event, and red circles indicate a Post4R lineage specific duplication. Taxa are colored based upon the figure color legend. a Gene tree illustrating a 3R WGD with a Post3R-Pre4R duplication, leading to three 4R WGDs and six Post4R duplications along the S. salar lineage. b Gene tree showing a 3R WGD with a Post3R-Pre4R duplication and three 4R duplication events. c Gene tree with a 3R WGD, with a Post3R-Pre4R duplication and no 4R WGD with three Post4R lineage specific duplications. d Gene tree with a 3R WGD, with a Post3R-Pre4R duplication, and no 4R WGD or Post4R duplications. e Gene tree with a 3R duplication, with two 4R WGDs, and four Post4R lineage specific duplications. f Gene tree with a 3R duplication, with two 4R WGDs and no lineage specific duplications. g Gene tree with a 3R duplication, no 4R WGD, but two S. salar lineage specific duplications. h Gene tree with a 3R duplication only. i Gene tree lacking a 3R duplication with a Post3R-Pre4R duplication, with two 4R WGDs, and four lineage specific Post4R duplications. j Gene tree with a Post3R-Pre4R duplication, and two 4R WGDs. k Gene tree with a Post3R-Pre4R duplication and no 4R WGDs, with two Post4R lineage specific duplications. l Gene tree with a Post3R-Pre4R duplication only. m Gene tree with a 4R WGD and two Post4R lineage specific duplications. n Gene tree with a 4R WGD only. o Gene tree with a single Post4R lineage specific duplication. p Gene tree with no duplications; topology of the gene tree matches the species tree. Figure Color Legend: Lepisosteus oculatus (Spotted gar), Danio rerio (Zebrafish), Oreochromis niloticus (Nile tilapia), Takifugu rubripes (Pufferfish), Esox lucius (Northern pike), Salmo salar (Atlantic salmon), Oncorhynchus mykiss (Rainbow trout), 3R WGD duplication, Post3R-Pre4R duplication, 4R WGD duplication, Post4R duplication