Phylogenetic Analysis data

• Taxa – The group of organisms, that are classified based on the evolutionary relationships.
• Characters – specific traits or features that can be used to distinguish between different taxa.

The characters that used for building the phylogenetic trees

1. Classical phylogenetic analysis uses morphological features – number of legs, anatomy
2. Modern phylogenetic analysis uses molecular information –

• Bio-molecular sequences (DNA, RNA)
• DNA fragements (AFLPs, RFLPs)
• Biochemical features

Phylogenetic data can be classified into two types

1. Distance data -Measure the distance between the objects; these data are usually derived from the sequences data. E.g – distance (man,monkey) = 120. distance data Metrix is constructed using pairwise comparison.
2. Discrete data – Each characters have finite number of states. Character species Matrix is constructed using present and absence of the data. E.g – DNA has four states – A,C,T,G, numbers of legs of mammals – 2,3,4,5…

Molecular phylogenetic Analysis data

There are two broad categories of the molecular data; Protein data & DNA base markers there data can be used in both taxonomic low levels and taxonomic high-level

1. Protein data are two main categories : isoezymes and amino acids.
2. DNA based makers can be categories base on the dependency of the PCR technique.

• PCR independent techniques – RFLP (Restriction Fragment Length Polymorphism)
• PCR dependent techniques – RAPD (Randomly Amplified Polymorphic DNA),AFLP (Amplified Fragment Length Polymorphism), SSR (Simple Sequence Repeat) and Direct DNA sequencing

History of the Molecular markers in Phylogeny

1. Revolution 1 – 1975 – DNA sequencing – Sanger sequencing is used for direct examination of the DNA sequences.
2. Revolution 2 – 1985 – Polymerase Chain Reaction (PCR) – Produce large amount of fragments in very short time such as DNA fingerprinting, RAPDs, AFLP, transposable elements
3. Revolution 3 – 2005 – Next generation sequencing – allow to generation of massive amount of data that can be used for construct the whole genome phylogenies.