Gene family expansion and contraction
The expansion and contraction of gene families were analysed using CAFE
v4.2.1 (De Bie et al. 2006). The sequences were first clustered using
MCL (Enright et al. 2002) following the CAFE developers’ instructions
(https://iu.app.box.com/v/cafetutorial-files ) and filtering the
gene families using a custom python script
(cafe_filterin_blast_dump.py) to exclude gene families that contain
at least one or more species with ≥ 100 genes. An ultrametric tree was
produced with r8s v1.81 (Sanderson 2003) using the phylogenetic tree
produced in our phylogenomic analysis and the divergence time forThunnus thynnus and Oreochromis niloticus taken from
TIMETREE
(http://www.timetree.org/).
Finally, CAFE was run with conditional P-values, for each gene family
below 0.01.