Term phylogeny/phylogenetic derived from Greek word- race, origin or lineage.
For trees displayed in a rectangular fashion (as in Figure A), evolutionary distances are
represented by horizontal branches. One can work out the inferred evolutionary distance
between two taxa by adding up all the horizontal branch lengths that join them. The order
and length of the vertical branches does not mean anything – these are just organised to
make the tree readable. Trees can also be shown in a radial or star fashion (Figure B),
where all of the branches correspond to evolutionary distances. Figure A shows a rooted
rectangular tree, where the position of the inferred common ancestor of all the bacteria is
known. To make a rooted tree, researchers usually include an extra, distantly-related
strain as an outgroup. In an outbreak, a rooted tree can be useful as it enables us to
determine the order of infections in a transmission chain. However, for bacterial studies
an unrooted tree, with no extra outgroup strain, is often sufficient (Figure B).
kimura model
According to this model
transitions that are
represented by
Alpha, they are more
prevalent than
transversions that are
represented by
a beta
According to juke cantor model all
nucleotides have equal substitution rate, so a
to g substitution or a to c or a to t, g to c, g to
t and so on and so forth all these
substitutions they have equal substitution
rates.
Dissimilarity between two sequences are considered here to construct a
phylogenetic tree.
It shows evolutionary distance between two or more sequences. Less intensive than
character based methods.
But very accurate as mutations are taken into account.
Tree got by this method is a dendogarm (clusters) based on hierarchical clustering.
Unweighted-Pair-Group Method with Arithmetic mean (UPGMA)
Oldest and simplest distance matrix method.
Originally proposed in the early 1960s to help with the evolutionary analysis of
morphological characters.
requires data that can be condensed to a measure
of genetic distance between all pairs of taxa being
considered.
assumes constant evolution.
With passage of time in many organisms change
occurs in DNA, RNA and protein –constant.
Multiple alignment are used.
Branch length in tree will be same as rate of
evolution is kept constant.
Molecular clock Hypothesis (branch length tells
time period).
Neighbour Joining Methods
Here, constant rate of evolution is not assumed.
No. of mutation rate=No. of branches length.
No. of branches length is directly proportional to rate of evolution. Thus branches
length varies.
Used for larger data. Computationally suited.
Maximum Likelihood (ML)
This is a character based approach which uses probability models to choose a best
tree that has the highest probability or likelihood of reproducing the observed data.
It finds a tree that most likely reflects the actual evolutionary process.
There are few disadvantages for maximum parsimony method and maximum
likelihood method covers up for same.
ML is an exhaustive method that searches every possible tree topology and
considers every position in an alignment, not just informative sites.
By employing a particular substitution model that has probability values of residue
substitutions, ML calculates the total likelihood of ancestral sequences evolving to
internal nodes and eventually to existing sequences.
After computing for all possible tree paths with different combinations of
ancestral sequences, the tree path having the highest likelihood score is the final
topology at the sites.
Tree with highest likelihood score among all others is chosen as the best tree,
which is the ML tree.
Advantages of ML
ML is based on well founded statistics method.
It is mathematically more rigorous than MP and also most consistent of all
methods.
ML uses full sequence information, not just informative sites and hence more
robust.
ML employs substitution models.
Can be applied to nucleiotide and amino acids sequences and other datas.
Disadvantages of ML
Choosing an unrealistic substitution model may lesd to an incorrect tree.
Because of exhaustive nature of ML method, when the number of taxa increases to
modest size, it becomes impossible to use.
Violations of assumed model can lead to incorrect trees.
To overcome problems, several alternative approaches have been proposed like
genetic algorithms and Bayesian inferences.
