Evolutionary Trees
Important terminologies
- Rooted trees – this tree type shows evolutionary relationships, direction of evolution and the ancestral state
- Unrooted trees – this tree type only shows the Phylogenetic relationships.
- Common ancestor – Simply to choose a point (hypothetical point) on the tree as representing the earliest time in the evolutionary history of the sequence data.
- Midpoint rooting – It is the designing a point in the middle of a branch as the common origin of the sequences; first find two most distantly related sequences (sequences with the longest branch lengths) and get the middle, this point is know as the mid point.
- In-group taxa – the group of taxa or organisms being study in order to reconstruct their evolutionary relationships.
- Out-group taxa – is the organisms or taxon that is more distantly related to each taxon of the in-group taxa than each other taxon of the in-group taxa. most of the time it used as the reference group.
- Cladogram: It is a branching diagram that only shows the hypothesized phylogenetic relationships of a group of organisms (taxa).
- Phylogram: It represents the phyologenetic relationships btween taxa, conveys a sense of distance time or rate of evolution. branches are drawn proportional to the amount of inferred character change.
Maximum Parsimony(MP), Maximum Likelihood(ML), and Bayesian can produced multiple equal optimal trees all having same length. In these trees, tree topology may be slightly different because relationships of taxa may be different, in order to avoid this problem Consensus trees are build. These trees are build by combining all equal optimal trees.
Types of consensus trees
- Strict
- Majority rule
- Adams
- Combinable Components
Strict consensus trees
Contains only monophyletic clades that are present on all the trees. Monphyletic clades (natural clades) is the group of organisms (taxa) that include all the descendants of a common ancestor.
Majority rule consensus tree
Grouping of taxa that occurs more than 50% in trees (cladograms); it makes conflicts with the other cladograms consensus tree such as adams, combinable components, therefore it helps to identify the uncertainty in the phylogenetic relationships.
Adams consensus tree
In this method places the taxa that conflict, at the node, this method is useful when one taxon make conflicts in all the trees.
Determining the support of the node of phylogenetic tree.
In phylogenetic tree building number of steps (changes) along the branches indicate the evolutionary relationships between taxa because of the branches with the steps are supported by the more data; However reliability of the trees also influenced by the data quality, evolutionary model.
Methods also to detect the support of the clades:
- Bootstrapping
- Decay indices (Bremer support)
- Jackknifing
Bootstrapping
Bootstrapping is a method for check the reliability of the data.
The pseudoreplicate datasets are created by random sampling of the original character matrix to create new character matrices in same size as the original one. i.e generate multiple trees form pseudoreplicates dataset.
Positive Points of Bootstrap analysis
- It is statistical method for obtain the estimate error.
- Used to evaluate the reliability of the tree.
- Used to examine how often particular cluster is appearing in a tree when characters are re-sampled.