Mid-point rooting of Unrooted tree

Midpoint Rooting. As its name suggests, Midpoint rooting attempts to root the tree in its middle point. It does this by calculating all of the tip-to-tip distances and selecting the longest - A to E in the tree above. The root is then placed exactly half-way between these two tips. If the tree is behaving and the rates of evolution are pretty constant throughout, this point should represent the ancestral point. It is therefore useful in situations where the actual root is not known but the assumption of a reasonably constant “clock-like“ rate of evolution is quite sound. The other situation it generally works well for is when a tree is fairly balanced with some closely-related clades separated by a long branch in the middle - if midpoint rooting places the root far away from any nodes, it is less likely to be wrong (i.e. moving it a little due to rate discrepancies would not make any difference). The main problem with midpoint rooting is that it is very susceptible to large deviations from a constant evolutionary rate, especially if these are not “balanced“, i.e. they only occur on one side of the actual root. The other time midpoint rooting tends to go wrong is when it places the root in amongst a rather dense set of short branches, where quite small deviations will place the root on another branch. For these reasons, whenever possible, outgroup rooting is generally the method of choice. #MolecularClock #GeneCkock #evolutionaryClock #PrincipleOfParsimony #phylogenicTree #outgroups #ingroup #Homology #Homoplasy #cladogram #Phylogram #domain #kingdom #phylum #Class #genus #ScientificNames #taxonomicHierarchy #species #phyliogeneticTree #Evolution #speciation #diagram #branchingInAPhylogeneticTree #Genetics #bilology #taxonomy #populationGenetics #hawaiiIslands #founderEffect #geneticDrift #bioinformatics #outapomorphy #synapomorphy