Maximum Phylogenetic Tree
Maximum likelihood methods have been developed in order to construct the most probable phylogenetic tree. The earliest methods of calculating the maximum likelihood used gene frequency data, and more recent approaches involve algorithms of amino acid and nucleotide sequences. The general equation for the likelihood L of a phylogenetic tree is defined as the probability of observing the data in a given tree under a specific substitution pattern, L=(data│tree). The tree with the highest L value is the most probable tree out of all of the possible tree constructions. The likelihood of a tree is calculated by forming one of the possible unrooted trees from different aligned taxa sequences. Then, the likelihood of each individual site is calculated,
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However, some of the elements, such as branch lengths, must be approximated because exact values are unknown. Thus, the maximum likelihood tree may not be the same under all circumstances. Unrooted trees can be rooted by including an outgroup. An effective outgroup is a taxa that is related to the other species on the tree but has clearly branched off earlier than any of the other taxa. Outgroups must not be too distantly related, otherwise the relative evolutionary distance between the outgroup and the ingroup is difficult to estimate and topological errors in the tree arise. It is possible to include more than one outgroup to improve construction of the tree. Although, if multiple distant outgroups are used the validity of the tree decreases because of the long branch attraction phenomenon.
When there are no outgroups a hypothetical root can be positioned half-way between the longest distance of two OTUs. This approximation is valid if the rate of evolution is assumed to be consistent over all of the branches. The placement of a root on an unrooted tree can significantly change the direction of evolutionary history of the group of taxa. For instance, a four-taxon tree can be described by five different rooted trees, where the evolutionary time of divergence is changed by each root
However, some of the elements, such as branch lengths, must be approximated because exact values are unknown. Thus, the maximum likelihood tree may not be the same under all circumstances. Unrooted trees can be rooted by including an outgroup. An effective outgroup is a taxa that is related to the other species on the tree but has clearly branched off earlier than any of the other taxa. Outgroups must not be too distantly related, otherwise the relative evolutionary distance between the outgroup and the ingroup is difficult to estimate and topological errors in the tree arise. It is possible to include more than one outgroup to improve construction of the tree. Although, if multiple distant outgroups are used the validity of the tree decreases because of the long branch attraction phenomenon.
When there are no outgroups a hypothetical root can be positioned half-way between the longest distance of two OTUs. This approximation is valid if the rate of evolution is assumed to be consistent over all of the branches. The placement of a root on an unrooted tree can significantly change the direction of evolutionary history of the group of taxa. For instance, a four-taxon tree can be described by five different rooted trees, where the evolutionary time of divergence is changed by each root