A consensus tree gives an estimate for the level of support for each clade in the final tree. It is built by combining clades which occurred in at least a certain percentage of the resampled trees. This percentage is called the consensus support threshold.
Therefore the bootstrap consensus tree is the consensus tree of our re-samplings of our initial tree. It should be similar, but can be different from our initial tree. The more similar the trees of different analyses are (ML, MP, NJ, baysian) the more likely our tree is true.
A 100% support threshold results in a “Strict consensus tree” which is a tree where the included clades are those that are present in all the trees of the original set. A 50% threshold results in a “Majority rule consensus tree” that includes only those clades that are present in the majority of the trees in the original set. A threshold less that 50% gives rise to a “Greedy consensus tree”. In constructing a “Greedy consensus tree” clades are first ordered according to the number of times they appear (i.e. the amount of support they have), then the consensus tree is constructed progressively to include all those clades whose support is above the threshold and that are compatible with the tree constructed so far.
The length of the consensus tree branches is computed from the average over all trees containing the clade. The lengths of tip branches are computed by averaging over all trees.
Reconcile clades from different trees
Conservative estimate of phylogeny that emphasizes points of agreement
Agreement among data sets is more important than agreement within data sets
Defensible and pragmatic starting point, especially if we are proposing a new classification or testing a hypothesis
Each distinct component (clade) is given a unique number
Different algorithms/methods work with these numbers (have different rules)
Strict Consensus: only those components (clades) shared by all trees are considered; components must be exactly replicated among all trees. It is the sost restrictive approach.
Consensus n-Trees: accepts all nodes/resolutions that are present in n% or more of the trees. Usually n=50 and referred to as majority rule consensus.
Adam's Consensus: pulls down components to the first node to which there will be no conflict. It is the most unrestrictive approach and preserves structure.
Sometimes a tree-building method may result in many equally optimal trees. A consensus tree can be built by showing the commonly resolved bifurcating portions and collapsing the ones that disagree among the trees, which results in a polytomy. Combining the nodes can be done either by strict consensus or by majority rule. In a strict consensus tree, all conﬂicting nodes are collapsed into polytomies. In a consensus tree based on a majority rule, among the conﬂicting nodes, those that agree by more than 50% of the nodes are retained whereas the remaining nodes are collapsed in to multifurcation.