(A) A scheme of the pruned ProtoNet tree. The leaves of the tree (marked pink) are representatives of UniRef50. The left axis represents the ProtoLevel (PL) of the clusters. The lowest PL (PL = 0) is associated with the leaves. High PL (up to 100) is reached next to the global ProtoNet tree root. Each Daphnia protein (a-c) was mapped to 'best stable' node of the protein in the ProtoNet (Map10 clusters). The proteins that are mapped to the same node (e.g., node 11) are considered paralogs. Following mapping, we 'climb' the tree to a higher level of the hierarchy (PL = 70). The roots that contain Daphnia proteins are subjected to further analysis. Each ProRoot70 is conjectured to represent a functional family. (B) ProtoLevel of the mapped clusters. Only 129 clusters of Map10 are at PL> 70 (to the right of the red dashed line). These clusters are excluded from the annotation scheme.