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Phylogenetics

Phylogenetics is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations), which is discovered through molecular sequencing data and morphological data matrices.

Phylogenies: The sequence of events involved in the evolutionary development of species or a taxonomic group of organisms.

Terminology:

ptr node: a node represents a taxonomic unit. This can be a taxon (an existing species) or an ancestor (unknown species : represents the ancestor of 2 or more species).

ptr branch: defines the relationship between the taxa in terms of descent and ancestry.

ptr topology: is the branching pattern.

ptr branch length: often represents the number of changes that have occurred in that branch.

ptr root: is the common ancestor of all taxa.

ptr distance scale: scale which represents the number of differences between sequences (e.g. 0.1 means 10 % differences between two sequences)

The tree terminology

Figure : The tree terminology.

Possible ways of drawing a tree:

Trees can be drawn in different ways. There are trees with unscaled branches and with scaled branches.

ptr Unscaled branches: the length is not proportional to the number of changes. Sometimes, the number of changes are indicated on the branches with numbers. The nodes represents the divergence event on a time scale.

ptr Scaled branches: the length of the branch is proportional to the number of changes. The distance between 2 species is the sum of the length of all branches connecting them.

Is is also possible to draw these trees with or without a root. For rooted trees, the root is the common ancestor. For each species, there is a unique path that leads from the root to that species. The direction of each path corresponds to evolutionary time. An unrooted tree specifies the relationships among species and does not define the evolutionary path.

unscaled branches

Methods of phylogenetic analysis:

There are two major groups of analyses to examine phylogenetic relationships between sequences:

ptr Phenetic methods: trees are calculated by similarities of sequences and are based on distance methods. The resulting tree is called a dendrogram and does not necessarily reflect evolutionary relationships. Distance methods compress all of the individual differences between pairs of sequences into a single number.

ptr Cladistic methods: trees are calculated by considering the various possible pathways of evolution and are based on parsimony or likelihood methods. The resulting tree is called a cladogram. Cladistic methods use each alignment position as evolutionary information to build a tree.

Phenetic methods based on distances:

ptr Starting from an alignment, pairwise distances are calculated between DNA sequences as the sum of all base pair differences between two sequences (the most similar sequences are assumed to be closely related). This creates a distance matrix.

ptr All base changes can be considered equally or a matrix of the possible replacements can be used.

ptr Insertions and deletions are given a larger weight than replacements. Insertions or deletions of multiple bases at one position are given less weight than multiple independent insertions or deletions.

ptr it is possible to correct for multiple substitutions at a single site.

ptr From the obtained distance matrix, a phylogenetic tree is calculated with clustering algorithms. These cluster methods construct a tree by linking the least distant pair of taxa, followed by successively more distant taxa.

ptr UPGMA clustering (Unweighted Pair Group Method using Arithmetic averages) : this is the simplest method

ptr Neighbor Joining: this method tries to correct the UPGMA method for its assumption that the rate of evolution is the same in all taxa.

Cladistic methods based on Parsimony:

For each position in the alignment, all possible trees are evaluated and are given a score based on the number of evolutionary changes needed to produce the observed sequence changes. The most parsimonious tree is the one with the fewest evolutionary changes for all sequences to derive from a common ancestor. This is a more time-consuming method than the distance methods.

Cladistic methods based on Maximum Likelihood:

This method also uses each position in an alignment, evaluates all possible trees, and calculates the likelihood for each tree using an explicit model of evolution (<-> Parsimony just looks for the fewest evolutionary changes). The likelihood's for each aligned position are then multiplied to provide a likelihood for each tree. The tree with the maximum likelihood is the most probable tree. This is the slowest method of all but seems to give the best result and the most information about the tree.

Theoretical problems with evolutionary changes between sequences

ptr Transitions : substitutions from A to G ; G to A ; C to T ; T to C.

ptr Transversions : substitutions from G to C ; C to G ; T to A ; A to T.

ptr Deletions : removal of one or more nucleotides.

ptr Insertion : addition of one or more nucleotides.

ptr Inversion : rotation of 180 °C of a double stranded DNA segment compromised of of 2 or more base pairs.

mutations

Figure shows that there is a chance that many more mutations occur than visible at a certain time. Even the best evolutionary models can't solve this problem..

homologous DNA

Figure: Two homologous DNA sequences which descended from an ancestral sequence and accumulated mutations since their divergence from each other. Note that although 12 mutations have accumulated, differences can be detected at only three nucleotide sites. (from Fundamentals of Molecular Evolution, Wen-Hsiung Li and Dan Graur, 1991)