biology

1. PHYLOGENETICS
by wajahat ali

2. WHY WE NEED PHYLOGENETICS???
 Because morphology does not gives us info about
taxonomy
 Second morphology changes under environmental
influence
 We will place species on the basis of difference or
similarity based on gene in phylogenetics
 We should also know about divergence time?
 >from where a species separates from its ancestor
 We also estimate the time of new specie..
 Second we also know about the divergence or
convergence

3. MOLECULAR PHYLOGENETICS
 Definition
 Study of evolutionary relationship among biological
entitise (individual specie)by using combination of
molecular data( such as DNA protien )and statistical
technique
 Through statistical techniques we will find
evolutionary relationship
 History?
 You should know lawmarkism,darwanism and new
darwanism

4. PHYLOGENETIC TREE
 In phylogenatic tree we called the point of emerging
new branches the ‘node’
 Node is the point of divergence
 Cladograme
 Graphical representation of phylogenatic tree is
called cladograme (def must)
 Taxonomy
 Nomenclature+classification
 Phlogenetics?
 Nomenclature+classification+evolutionary patterns
and relationship among organisms

5.  Systematics?
 Taxonomy+phylogenetics
 Holotype+paratype
 Holotype(is a sequence specimen of organism on
which the follower description of specie isbased)
 >>that will single organism as arepresentative
 Paratype(aik ko representative man lia dosron ko
member)
 Aur member is mai paratype hain aur
representative holotype

6.  1st sapmling
 2nd preservation and taging(date+name of collector)
 1 Tapological concept of specie
 2 Phenetc concept
 3 Biological concept of species
 Allopatric and sympatric mai difference
 >>Allopatric
 Due to barrier species become reproductively isolate
 >Sympatric
 >Due to change in genetic makeup species become change from
each other

7.  Temporal isolation
 Habitate isolation
 Gametic isolation
 Post zygotic barrier
 Mting season also separate the specie and make a
new species
 Mutation(crossingfore)
 Advantage of molecular data
 1..no confusion
 2..no can change it
 There is regulation in molecular trade
 We can also estimate it quantitatively

8.  We cant explain qualitaive analysis
 4..homology esessment is easier
 5th exactly calulate molecular distence
 6th Molecular data are abuntent
 Thus, phylogenetics is mainly concerned with the
relationships of an organism to other organisms
 according to evolutionary similarities and
differences
>>Phylogenetics is the area of research concerned
with finding the genetic connections
and relationships between species

10. ORTHOLOGY VS PARALOGY
 Two genes are said to be paralogous
 If they are derived from a duplication
 Orthologous :if they are derived from speciation
events

11. CLASSES OF ALGORITHMS FOR PHYLOGENY
 Parsimony
 Distance method
 Likelihood
 Bayesian methods
 UPGMA??
 Unweighted pair group method with algorthims
 Mean this is the simplest method for phylogenatic
reconstruction

12. BOOTSTRAPPING PHYLOGENIES
 This is the test of your hypothesis
 Used to give you feel that how good is your inferred
tree
 Characters are resampled
 It is very viable and widely used technique
 If the estimated tree is inconsistent all the bootstrap
in the world wont help you

13. PROCESS OF MAKING PHYLOGENETIC TREE
 1..Sampling
 2..Random sampling(invasive or non invasive)
 >Preservation and tagging
 3..Genetic analysis
 4..DNA extraction(methods for organic extraction)
 (I).. cell lysis
 (II).. Purification
 (III)..precipitation
 (IV)..washing
 (V)..dilution
 5..gell electrphoresis(confirmation)

14. PROCESS REMAINING
 6..Primer desighning and selection
 7..blast tool
 8..PCR amplification
 9..confirmation
 10..sequencing