Scribd
Upload
251 views25 pages

Phylogenetic Analysis

Phylogenetic analysis involves determining evolutionary relationships among organisms based on shared characteristics like genetic and anatomical similarities. A phylogenetic tree visually depicts these relationships, with branches indicating how groups of organisms are more closely related through common ancestors over time. Key terms include phylogeny, genealogy, lineage, and clade. Methods for constructing phylogenetic trees include distance matrix, maximum parsimony, and maximum likelihood approaches, which analyze sequence alignments to search for the optimal tree topology that models the evolutionary history of the organisms.

Uploaded by

RONAK LASHKARI
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
251 views25 pages

Phylogenetic Analysis

Phylogenetic analysis involves determining evolutionary relationships among organisms based on shared characteristics like genetic and anatomical similarities. A phylogenetic tree visually depicts these relationships, with branches indicating how groups of organisms are more closely related through common ancestors over time. Key terms include phylogeny, genealogy, lineage, and clade. Methods for constructing phylogenetic trees include distance matrix, maximum parsimony, and maximum likelihood approaches, which analyze sequence alignments to search for the optimal tree topology that models the evolutionary history of the organisms.

Uploaded by

RONAK LASHKARI
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 25

Phylogenetic analysis

What Is Phylogeny?
• Phylogeny is the study of relationships among different groups of
organisms and their evolutionary development.
• Phylogeny attempts to trace the evolutionary history of all life on the
planet.
• It is based on the phylogenetic hypothesis that all living organisms
share a common ancestry.
• The relationships among organisms are depicted in what is known as a
phylogenetic tree.
• Relationships are determined by shared characteristics, as indicated
through the comparison of genetic and anatomical similarities.
Phylogenetic Tree
• A phylogenetic tree, or cladogram, is a schematic diagram used as a
visual illustration of proposed evolutionary relationships among taxa.
• Phylogenetic trees are diagrammed based on assumptions of cladistics, or
phylogenetic systematics. Cladistics is a classification system that
categorizes organisms based on shared traits, as determined by genetic,
anatomical, and molecular analysis.
• The main assumptions of cladistics are:
1. All organisms descend from a common ancestor.
2. New organisms develop when existing populations split into two groups.
3. Over time, lineages experience changes in characteristics.
Phylogeny-Terms
• Phylogeny- the evolutionary history of a group of organisms/ study of the
genealogy and evolutionary history of a taxonomic group.

• Genealogy- study of ancestral relationships and lineages.

• Lineage- A continuous line of descent; a series of organisms or genes


connected by ancestor/ descendent relationships.

• Relationships are depicted through a diagram better known as a


phylogram
Evolution
• Changes in the genetic makeup of populations- evolution, may occur
in lineages over time.
• Descent with modification
• Evolution may be recognized as a change from a pre-existing or
ancestral character state (plesiomorphic) to a new character state,
derived character state (apomorphy).
• 2 mechanisms of evolutionary change-
1. Natural selection – non-random, directed by survival of the fittest
and reproductive ability-through Adaptation
2. Genetic Drift- random, directed by chance events
Cladistics
• Classification based on phylogeny
• Phylogenetic systematics- Cladistics
Lineage- A continuous line of descent; a series of organisms or genes
• Connected by ancestor/descendent relationships.
• Relationship is depicted as phylogenetic tree/cladogram
• A tree-like network that expresses such ancestor-descendant
• Relationships (Cladistic relationship ) is called a cladogram.
Cladogram -Branching diagram shows the sequence of evolutionary
• Change in characters, the number of changes associated with each lineage, and
the sequence of lineage branching
• The branches of a cladogram represent time (unlike a phenogram).
What is clade?
• A clade is a group which includes a common ancestor and all the
descendants (living and extinct) of that ancestor.
• Members of a clade will possess common characteristics as a result of
their shared evolutionary lineage.
• Clades can be organized into branching diagrams (cladograms) in
order to show evolutionary relationships.
Phylogenetic approach
• A taxon (pl. taxa) is any group of organisms that is given a formal
taxonomic name.
• Monophyletic taxon is one that includes a group of organisms
descended from a single ancestor.
• Polyphyletic taxon is composed of unrelated organisms descended
from more than one ancestor.
Phylogeographic tree is a mathematical model of evolution
Parts of a phylogenetic tree
Branch
Node

Root

Ingroup

Outgroup
Tree structure
• A tree can be also presented in a text format: (A(B(C,D)))
• The graphic structure can be difficult to interpret (2-dimentional)
Methods
• Distance matrix
• Maximum parsimony
• Minimum distance
Distance matrix
• A distance matrix is calculated from the sequence dataset
• Algorithms: Fitch-Margoliash, Neighbor-Joining or UPGMA in tree
building
• Simple, finds only one tree
• Somewhat old-fashioned (OK if your alignment is good and
evolutionary distances are short)
Maximum parsimony
• Finds the optimum tree by minimizing the number of evolutionary
changes
• No assumptions on the evolutionary pattern
• May oversimplify evolution
• May produce several equally good trees
Maximum likelihood
• The best tree is found based on assumptions on evolution model
• Nucleotide models more advanced at the moment than aminoacid
models
• Programs require lot of capacity from the system
Algorithms used for tree searching
• Exhaustive search: all possibilities → best tree → requires lots of time
and computer resources
• Branch and Bound: a tree is built according to the model given → the
tree is compared to the next tree while its constructed → if the first
tree is better the second tree is abandoned → third tree… → best
possible tree
• Heuristic Search: only the most likely options → saves time and
resources, does not always result in the best tree
Bootstrapping
• Evaluation of the tree reliability
• n number of trees are built (n=100/1000/5000)
→ How many times a certain branch is reproduced

Values between 1-100 (%)


Analyses
1. Choosing the sequence type
2. Alignment of sequence data
3. Search for the best tree
4. Evaluation of tree reproducibility
Sequence alignment
• Finding similar nucleotide composition for further analysis
• Manually: can take weeks
• ClustalW
• Check the alignment made by ClustalW
• You may have to go back to Chromas to check the sequences once
again
Analysing the aligned sequence matrix
• PHYLIP
• POY
• PAUP, GCG

You might also like

pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy