Gene families with correlated patterns of duplication/loss. Loss and gain patterns over 36 phylogenetic intervals (Figures 2 and 3) were compared between each pair of gene families. A) Gene families with significant correlation of their duplication patterns (see Methods) are connected with a blue line. Gene families with significant correlation of their loss patterns are connected with a red line. B) To partially account for the probable high amount of functional overlap between members of the same gene family, we calculated overall gene family duplication/loss activity over a phylogenetic interval (number of losses subtracted from number of duplications) and compared patterns between gene families over all phylogenetic intervals. Pairs with a significant amount of correlation (see Methods) are connected by blue lines. 15 genes had significant correlation with at least one other gene family. This is much higher than the number found in our randomly shuffled matrices (C, see Methods). C) Histogram representing the numbers of correlations found in 1000 randomly shuffled matrices using the gain minus loss data (see Methods). Most shuffled matrices had 0 or 1 significant correlations, representing 0 or 2 genes, a few had 5 or 6. Arrow represents the number of significant correlations (14) found in the unshuffled gain minus loss data matrix.