Basics of constructing Phylogenetic tree.ppt

basics of constructing Phylogenetic tree

1. 1
Constructing Phylogenetic tree

2. What Is Phylogentic tree?
Itisdefinedasadiagrammaticrepresentationofevolutionaryrelationships
amonglivingorganisms.Thisdiagrammaticrepresentationrepresentshow
differentspeciesevolvedfromaseriesofcommonancestors.
Thephylogenetictreecanalsobedefinedasthetwo-dimensionalgraph
representingtheevolutionaryrelationshipbetweenanorganismfrom
variousotherorganisms.

3. 3
Phylogenetics is the science of the pattern of evolution
Evolutionary biology versus phylogenetics
-Evolutionary biology is the study of the processesthat generate diversity
-Phylogenetics is the study of the patternof diversity produced by those
processes

4. Phylogentictree
Node:a branchpointin a tree (a presumed ancestral OTU)
Branch:defines the relationship between the taxa in terms of descent and ancestry
Topology:the branching patterns of the tree
Branch length(scaled trees only): represents the number of changes that have occurred in
the branch
Root:the common ancestor of all taxa
Clade:a group of two or more taxa or DNA sequences that includes both their common
ancestor and all their descendents
Operational Taxonomic Unit (OTU):taxonomic level of sampling selected by the user to be
used in a study, such as individuals, populations, species, genera, or bacterial strains

5. True Clade
5
•A true cladeis a monophyletic group that contains a common
ancestor and all of its descendants.
•A paraphyletic group is one that has a common ancestor but does
notcontain all of the descendants.
•A polyphyletic group does not have a unique common ancestor for
all the descendants.

6. 6
The central problem of phylogenetics:
1. How do we determine the relationships between species?
2. Use evidence from shared characteristics, not differences
3. Use homologies, not analogies
4. Use derived condition, not ancestral
a. synapomorphy -shared derived characteristic
b. plesiomorphy -ancestral characteristic
Cladisticsis phylogenetics based on synapomorphies.
1. Cladistic classification creates and names taxa based only on
synapomorphies.
2. This is the principle of monophyly
3. monophyletic, paraphyletic, polyphyletic
4. Cladistics is now the preferred approach to phylogeny

7. Phylogenetic trees
There are many ways of drawing a treeA
E
D
C
B
=A EDCB E DC B A =
E CD BA A EDCB A EDCB
= =A EDCB
no meaning

8. A EDCB A EDCB Bifurcation
Trifurcation
=/
BifurcationversusMultifurcation(e.g.Trifurcation)
Multifurcation(alsocalledpolytomy):anodeinatreethatconnectsmorethanthree
branches.Amultifurcationmayrepresentalackofresolutionbecauseoftoofewdata
availableforinferringthephylogeny(inwhichcaseitissaidtobeasoft
multifurcation)oritmayrepresentthehypothesizedsimultaneoussplittingofseveral
lineages(inwhichcaseitissaidtobeahardmultifurcation).
Phylogenetic trees

9. Trees can be scaled or unscaled (with or without branch lengths)A
E
D
C
B A
E
D
C
B A
E
D
C
B A
E
D
C
B unit unit
Phylogenetic trees
Phylogramisatype
ofphylogenetictree
thatrepresentsthe
evolutionary
relationshipsamong
organismsbyshowing
boththebranching
patternandtheamount
of evolutionary
divergence.
Phylogramsarescaled,
whichmeansthatthe
branchlengthsare
proportionaltothe
amount of
evolutionary
divergence.
Cladogramisatype
ofphylogenetictree
thatdisplaysonlythe
branchingpatternof
evolutionary
relationshipsamong
organisms.
Cladograms are
unscaled,which
meansthatthebranch
lengthsdonotreflect
theamountof
evolutionary
divergencebetween
taxaoroperational
taxonomic units
(OTUs).

10. Trees can be unrooted or rooted
D
A C
B
Unrooted tree
A CB D
Root
Rooted tree
D
A C
B
Root
A CB D
Root
Root
Phylogenetic trees
Unrootedtreesdo
not have a
specifiedrootnode
andshowonlythe
branchingpattern
oftheevolutionary
relationships
amongtaxaor
OTUs,withoutany
informationabout
their common
ancestor.
Rootedtreesare
treesthathavea
specifiedroot
node, which
representsthe
common
ancestorofall
theorganismsin
thetree.

11. Trees can be unrooted or rootedUnrootedtree
A C
B D
4
3
5
2
1
These trees showfive different evolutionary relationships among the taxa!Rooted tree 1
B
A
C
D Rooted tree 2
A
B
C
D Rooted tree 3
A
B
C
D Rooted tree 4
C
D
A
B Rooted tree 5
D
C
A
B
Phylogenetic trees

12. How to root?
Use information from ancestorsA C
B D
4
3
5
2
1
Use statistical tools will root trees automatically (e.g.
mid-point rooting)A
B
C
D
10
2
3
5
2 d(A,D) = 10 + 3 + 5 = 18 Midpoint = 18 / 2 = 9
Phylogenetic trees

13. Using
“outgroups”A C
B D
4
3
5
2
1 outgroup
How to root?
Phylogenetic trees
-the outgroup should be a taxon known to be less closely related to the rest of
the taxa (ingroups)
-it should ideally be as closely related as possible to the rest of the taxa while
still satisfying the above condition

14. Exercise: rooted/unrooted; scaled/unscaledA EDCB A
E
D
C
B A
E
D
C
B A
E
D
C
B A
E
D
C
B A EDCB
A
ED
C
B
F
Phylogenetic trees

15. What are useful characters?
Use homologies, not analogies!
-Homology:common ancestry of two or more character
states
-Analogy:similarity of character states not due to
shared ancestry
-Homoplasy:a collection of phenomena that leads to
similarities in character states
for reasons other than inheritance from a common
ancestor
(e.g.convergence, parallelism, reversal)
Homoplasy is huge problem
in morphology data sets!
Cactaceae
(cactus spines are
modified leaves)
Euphorbiaceae
(euphorb spines are
modified shoots)
Phylogenetic trees

16. 1. Using Homologous Features
16
•Once a group splits into two distinct groups they evolve independently of one
another. However, they retain many of the features of their common ancestor.
•Any feature shared by two or more species andinherited from a common
ancestor are said to be homologous.
•Homologous features can be heritable traits, such as anatomical structures,
DNA sequences, or similar proteins.
Phylogenetic trees

17. Ancestral vs. Derived Traits
•During the course of evolution,
traits change. The original
shared trait is termed the
ancestral trait and the trait
found in the newly evolved
organism being examined is
termed the derived trait.
•Any feature shared by two or
more species that is inherited
from a common ancestor is said
to be homologous.
The limbs above are homologous
structures, having similar bones.
Phylogenetic trees

18. Analogous Structures
•Analogous structures are those that
are similar in structure but are not
inherited from a common ancestor.
•While the bones found in the wings
of birds and bats are homologous,
the wing itself is analogous. The
wing structure did not evolve from
the same ancestor.
The physics necessary for flight is the
selection pressure responsible for the
similar shape of the wings. Examine
airplane wings! Analogous structures
should NOT be used in establishing
phylogenies .
Phylogenetic trees

19. 19

20. 2. Using Molecular Clocks
The molecular clock hypothesis argues that DNA and protein
sequences mutate at a constant rate over time among different
organisms and that the number of genetic differences between
organisms can give us an estimation of when they last shared a
common ancestor.
Genomic sequencing, computer software and systematics are
able to identify these molecular homologies. The more closely
related two organisms are, the more their DNA sequences will
be alike.
The colored boxes represent DNA homologies.
Phylogenetic trees

21. The molecular clock is a method used to estimate the amount of time needed for a certain
amount of evolutionary change. This is done by analyzing biomolecular data, such as the
number of changes or substitutions in nucleotide sequences of DNA and RNA, or the amino
acid sequence of proteins. Substitution is a type of mutation where one nucleotide is replaced by
another.
Asuming that the nucleotide or amino acid sequences mutate at a constant rate, the number of
substitutions over time is equivalent to the evolutionary rate. For this reason, the molecular
clock is also known as the gene clock or the evolutionary clock.
2. Using Molecular Clocks
Phylogenetic trees

22. 22
Answer: https://www.thetech.org/ask-a-
geneticist/articles/2019/ho w-build-phylogenetic-tree/
How do scientists construct phylogenetic trees and know the
degree of relatedness between living organisms by DNA?
Do they just look for similarities between the whole genomes?
Or just specific genes? Or RNA? Or what exactly?”
Phylogenetic trees

23. 23
Phylogenetic trees

24. 24
The methods to construct phylogenetic trees can be classified into two major types:
1. Distance-based methods
Distance-based tree construction methods involve calculating evolutionary distances
between sequences by using substitution models, which are then used to construct a
distance matrix. Using the distance matrix, a phylogenetic tree is constructed. The
two popular distance-based methods are UPGMA and NJ.
Phylogenetic trees
Methods to construct phylogenetic trees

25. 25
2.Character-BasedMethods
Character-basedmethodsinvolveanalyzingsequencedatabydirectlyexaminingthe
sequencecharacters,ratherthanrelyingonpairwisedistancecomparisons.These
methodsevaluateallsequencesatoncebyanalyzingonecharacterorsiteatatime.
Character-basedmethodsaregenerallyconsideredmoreaccuratethandistance-
basedmethods.However,character-basedmethodsaremorecomputationally
intensiveandrequiremoresophisticatedstatisticalmodels.
Themaximumparsimony(MP)andmaximumlikelihood(ML)methodsarethetwo
mostcommonlyusedcharacter-basedtreeconstructionmethods.
Phylogenetic trees
Methods to construct phylogenetic trees