Phylogenetic data analyses

1. Phylogenetic data analyses
Md. Dilshad Karim
ID: 19BMBJD07M
Dept. of Biochemistry and Molecular Biology
BAU, Mymensingh

2. Outlines
• Phylogenetic tree
• History
• Purposes of phylogenetic tree
• Parts of a phylogenetic tree
• Types of a phylogenetic tree
• Analysis methods of phylogenetic tree
• Phylogenetic tree construction (of HIV
online based method)
• Applications of phylogenetic tree
• Limitations of phylogenetic tree

3. Phylogenetic tree
• A branching diagram.
• Showing the inferred evolutionary relationships
among various biological species.
• Based upon similarities and differences in their
physical or genetic characteristics.
• Each node with progenies represents the inferred
most recent common ancestor of the progenies.

4. History
• Early representations of "branching“ phylogenetic trees include a
"paleontological chart" showing the geological relationships
among plants and animals in the book Elementary Geology, by
Edward Hitchcock in 1840.
• Charles Darwin in 1859 also produced one of the first illustrations
and crucially popularized the notion of an evolutionary "tree" in
his seminal book The Origin of Species.

5. Purposes to analysis phylogenetic tree
• Understanding human origin.
• Understanding biogeography.
• Understanding the origin of particular traits.
• Understanding the process of molecular evaluation.
• Origin of disease e.g. where did humans get AIDs from?
• The aim of phylogenetic tree construction, is to find the
tree which.
• best describes the relationships between objects in a set.
Usually the objects are species.
• Understanding the processes of molecular evolution.

6. Parts of a phylogenetic tree
• The tree is constructed using a system of nodes and branches.
• Node refers to any terminating end of a branch (a line). External nodes represent the
final taxon (singular form of taxa) while internal nodes represent a common ancestor
that underwent some speciation event.
• As a result, speciation events give rise to divergent lineages of taxa and are
represented by horizontal branches.
• These diverging lines of taxa stem from a common ancestor, resulting in a
relationship called sister taxa (such as taxon A and taxon B), meaning that they share
the closest evolutionary relationship because they stem from the same common
ancestor.
• Taxa outside of that common ancestor are referred to as outgroups as they are more
evolutionarily distant in relation than sister taxa are to one another, due to a more
distant common ancestor.

7. Figure: Parts of phylogenetic tree.

8. Types of Phylogenetic Tree
Rooted Tree:
• Make inferences about the most
common ancestor of the leaves or
branches of the tree.
• Most commonly the root is
referred to as an “outgroup”.
Unrooted Tree:
• Make an illustration about the
leaves or branches, but not make
assumption regarding a common
ancestor.

9. The “Rooted” Vs. “Unrooted” Tree
Rooted tree Unrooted tree
Which shows the ancestry relationship Which only shows the relatedness of
organisms
Contains a root, internal nodes, leaf
nodes
Contains leaf nodes and internal nodes
Contains related organisms as well as an
extra, distantly-related organism for the
root
Only contains related organisms
Shows the recent common ancestor Does not show any common ancestor
Each root to a node shows the
evolutionary path
Does not specify the evolutionary path
Shows the ancestral state of organisms or
genes at the bottom to the terminal
branches
Does not show the ancestral state

10. Analysis methods of phylogenetic tree
• Distance matrix
• Maximum parsimony
• Minimum distance

11. Distance matrix
• Using a sequence alignment, pairwise distances are calculated.
• Creates a distance matrix.
• A phylogenetic tree is calculated with clustering algorithms,
using the distance matrix.
• Examples of clustering algorithms include the unweighted pair
group method using arithmetic averages (UPGMA) and
neighbor joining clustering.

12. Maximum parsimony
• All possible trees are determined for each position of the sequence
alignment.
• Each tree is given a score based on the number of evolutionary step
needed to produce said tree.
• The most parsimonious tree is the one that has the fewest.
evolutionary changes for all sequences to be derived from a common
ancestor.
• Usually several equally parsimonious trees result from a single run.

13. Maximum likelihood
• Creates all possible trees like maximum parsimony method but
instead of retaining trees with shortest evolutionary steps……
• Employs a model of evolution whereby different rates of transition
ration can be used.
• Each tree generated is calculated for the probability that it reflects.
each position of the sequence data.
• Calculation is repeated for all nucleotide sites.
• Finally, the tree with the best probability is shown as the maximum
likelihood tree - usually only a single tree remains.
• It is a more realistic tree estimation because it does not assume equal
transition-transversion ratio for all branches.

14. Comparison of Methods
Distance Maximum parsimony Maximum likelihood
Uses only pairwise
distances
Uses only shared
derived characters
Uses all data
Minimizes distance
between nearest
neighbors
Minimizes total
distance
Maximizes tree likelihood
given specific parameter
values
Very fast Slow Very slow
Easily trapped in local
optima
Assumptions fail when
evolution is rapid
Highly dependent on
assumed evolution model
Good for generating
tentative tree, or choosing
among multiple trees
Best option when
tractable (<30 taxa,
homoplasy rare)
Good for very small data
sets and for testing trees
built using other methods

15. Phylogenetic tree construction (of HIV online based method)
• All complete genome sequences of HIV(minimum 10 sequence) were
collected from gene bank of NCBI.
• Sequences were annotated in FASTA format.
• By using ClastalW software enter into the MSA tools.
• Then we enter our 10 genome sequences of HIV in the input box of
MUSCLE & submit for result.
• Wait for few minutes we get alignment of sequences.(*- means
maximum similarity of the sequences; .- means two nucleotide
changes; :- means one nucleotide changes).
• We get the phylogenetic tree of our desired sequences.

16. NCBI
Popular resources
Nucleotide
Search HIV genome
sequence
Select 10 individual
sequence
Create file in FASTA format
ClastalW2
MSA tools
MUSCLE
Enter input sequence &
submit
Result
Phylogenetic tree
Steps

17. Results
• We have found alignment & phylogenetic tree after completing our procedure.
• The phylogenetic tree indicates the relationship among different HIV genome
sequences.

18. Applications of phylogenetic tree
• Find out the evolutionary history.
• Can measure phylogenetic diversity using phylogenetic trees.
• Search for natural products.
• Infectious bacteria and viruses to trace their evolutionary
histories.
• Find out what trends they've undergone in their history.
• To guide our search for new species.
• Find out how our species spread geographically in their
evolution.
• To tell us when taxa originated and where.

19. Limitations of phylogenetic tree
• Inaccurate evolutionary history.
• The data used is little noisy.
• Problem facing in single type of character basing.
• Hoopla's would be unlikely from natural selection.
• Length of branch doesn’t mean the timing passed.