Consensus Smoothing does not fix the larger problem of distinguishing between long distances. For example, branches of length 12, 24, or 48 are all very likely to result in no gene tree discordance given 1000 genes; thus, even with smoothing, it remains impossible to distinguish between branches with these very different distances. This limitation makes it impossible to compute distances that reflect the true topology from limited data when the species tree includes adjacent long branches (resembling the saturation problem in phylogenetics ). We can construct examples when all gene trees are likely identical, yet our smoothed distances are misleading (Additional file 1: Section 2.2; Figure S7). However, long branches are easy to recover because they appear in most gene trees. A simple majority rule (50 %) consensus of gene trees would return all long branches. Thus, we simply compute the majority consensus and resolve its polytomies using DISTIQUE (Additional file 1: Algorithms S2 and S3). Because the majority consensus is proved not positively misleading under the MSC , our method remains statistically consistent.