Phylogenetics

Phylogenetics
M.Sc.IIsem
Paper-202,unit-V
Dr. Pinky Dwivedi

Phylogenetics
Taxonomy and phylogenetics
Phylogenetic trees
Cladistic versus phenetic analyses
Model of sequence evolution
Phylogenetic trees and networks
Cladistic and phenetic methods
Computer software and demos
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic Inference I
A science primer: Phylogenetics
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
Brown, S.M. (2000) Bioinformatics, Eaton Publishing, pp. 145-160
Brown, S.M.: Molecular Phylogenetics
www.med.nyu.edu/rcr/rcr/course/PPT/phylogen.ppt
Hillis, D.M.; Moritz, G. & Mable, B.K. (1996) Molecular Systematics,
2. Edition, Sinauer Associates, 655 pp.
Mount, D.W. (2001) Bioinformatics,
Cold Spring Harbor Lab Press, pp.237-280
Recommended readings
(very) basic
advanced
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

CS 177 Phylogenetic Inference I
The theory of evolution is the foundation upon which all of modern biology is built
Evolution
From anatomy to behavior to genomics, the scientific method requires an appreciation of
changes in organisms over time
It is impossible to evaluate relationships among gene
sequences without taking into consideration the
way these sequences have been modified over time
Ernst Haeckel (1834-1919)
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

CS 177 Phylogenetic Inference I
Similarity searches and multiple alignments of sequences naturally lead to the question
“How are these sequences related?”
and more generally:
“How are the organisms from which these sequences come related?”
Relationships
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Classifying Organisms
Nomenclature is the science of naming organisms
Evolution has created an enormous diversity, so how do we deal with it?
Names allow us to talk about groups of organisms.
- Scientific names were originally descriptive phrases; not practical
- Binomial nomenclature
> Developed by Linnaeus, a Swedish naturalist
> Names are in Latin, formerly the language of
science
> binomials - names consisting of two parts
> The generic name is a noun.
> The epithet is a descriptive adjective.
- Thus a species' name is two words
e.g. Homo sapiens
Carolus Linnaeus (1707-1778)
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Taxonomy is the science of the classification of organisms
Taxonomy deals with the naming and ordering of taxa.
The Linnaean hierarchy:
1. Kingdom
2. Division
3. Class
4. Order
5. Family
6. Genus
7. Species
T
axonomic Classification
of Man
Homo sapiens
S
uperkingdom: Eukaryota
Kingdom: Metazoa
Phylum: Chordata
Class: Mammalia
Order: Primata
Family: Hominidae
Genus:
S
pecies:
Homo
sapiens
S
ubspecies: sapiens
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Systematics is the science of the relationships of organisms
Systematics is the science of how organisms are related and the evidence for those
relationships
Systematics is divided primarily into phylogenetics and taxonomy
Speciation -- the origin of new species from previously existing ones
- anagenesis - one species changes into another over time
- cladogenesis - one species splits to make two
Reconstruct evolutionary history
Phylogeny
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetics
Review of protein
structures
Need for analyses
of protein
structures
Sources of protein
structure
information
Computational
Modeling
Phylogenetics is the science of the pattern of evolution.
A. Evolutionary biology is the study of the processes that generate diversity, while
phylogenetics is the study of the pattern of diversity produced by
those processes.
B. 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
C. Cladistics is 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
The phylogeny and
classification of life as
proposed by Haeckel
(1866)

Phylogenetics
Evolutionary theory states that groups of similar organisms are descended
from a common ancestor.
Phylogenetic systematics is a method of taxonomic classification based
on their evolutionary history.
It was developed by Hennig, a German entomologist, in 1950.
Willi Hennig (1913-1976)
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetics
Phylogenetics is the science of the pattern of evolution
Evolutionary biology versus phylogenetics
- Evolutionary biology is the study of the processes that generate diversity
- Phylogenetics is the study of the pattern of diversity produced by those processes
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetics
Who uses phylogenetics? Some examples:
Evolutionary biologists (e.g. reconstructing tree of life)
Systematists (e.g. classification of groups)
Anthropologists (e.g. origin of human populations)
Forensics (e.g. transmission of HIV virus to a rape victim)
Parasitologists (e.g. phylogeny of parasites, co-evolution)
Epidemiologists (e.g. reconstruction of disease transmission)
Genomics/Proteomics (e.g. homology comparison of new proteins)
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic trees
The central problem of phylogenetics:
how do we determine the relationships between taxa?
in phylogenetic studies, the most convenient way of presenting evolutionary
relationships among a group of organisms is the phylogenetic tree
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetics
Review of protein
structures
Need for analyses
of protein
structures
Sources of protein
structure
information
Computational
Modeling
Phylogenetics is the science of the pattern of evolution.
A. Evolutionary biology is the study of the processes that generate diversity, while
phylogenetics is the study of the pattern of diversity produced by
those processes.
B. 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
C. Cladistics is 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

Phylogenetic trees
S
pecies A
S
pecies E
S
pecies D
S
pecies C
S
pecies B
Node: a branchpoint in 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
Root
Branch
Clade
Node
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic trees
There are many ways of drawing a tree
A
E
D
C
B
A E
D
C
B
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic trees
=
A E
D
C
B E D
C B A
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
=
E C
D B A

Phylogenetic trees
A E
D
C
B
A E
D
C
B
= =
A E
D
C
B
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
no meaning

Phylogenetic trees
A E
D
C
B A E
D
C
B
Bifurcation
Trifurcation
=
/
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
Bifurcation versus Multifurcation (e.g. Trifurcation)
Multifurcation (also called polytomy): a node in a tree that connects more than three
branches. A multifurcation may represent a lack of resolution because of too few data
available for inferring the phylogeny (in which case it is said to be a soft multifurcation)
or it may represent the hypothesized simultaneous splitting of several lineages (in
which case it is said to be a hard multifurcation).

Phylogenetic trees
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
u
n
i
t
u
n
i
t
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic trees
Trees can be unrooted or rooted
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
D
A C
B
Unrooted tree
A C
B D
Root
Rooted tree
D
A C
B
Root
A C
B D
Root
Root

Phylogenetic trees
Trees can be unrooted or rooted
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
Unrooted tree
A C
B D
4
3
5
2
1
These trees show five 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
Possible evolutionary trees
Taxa (n) Unrooted/rooted
2
2 1/1
3 1/3
4 3/15
4
3
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
Taxa (n):

Phylogenetic trees
Possible evolutionary trees
Taxa (n) rooted
(2n-3)!/(2n-2(n-2)!)
unrooted
(2n-5)!/(2n-3(n-3)!)
2 1 1
3 3 1
4 15 3
5 105 15
6 954 105
7 10,395 954
8 135,135 10,395
9 2,027,025 135,135
10 34,459,425 2,027,025
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetic trees
How to root?
Use information from ancestors
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
In most cases not available
A C
B D
4
3
5
2
1

Phylogenetic trees
How to root?
Use statistical tools will root trees automatically (e.g. mid-point rooting)
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
A C
B D
4
3
5
2
1
This must involve assumptions … BEWARE!
A
B
C
D
10
2
3
5
2
d
(
A
,
D
)
=
1
0
+
3
+
5
=
1
8
M
i
d
p
o
i
n
t=
1
8
/2
=
9

Phylogenetic trees
How to root?
Using “outgroups”
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy
A C
B D
4
3
5
2
1
outgroup
- 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

Phylogenetic trees
Exercise: rooted/unrooted; scaled/unscaled
A E
D
C
B
A
E
D
C
B
A
E
D
C
B
A
E
D
C
B
A
E
D
C
B
A E
D
C
B
A
E
D
C
B
F
Taxonomy and
phylogenetics
Phylogenetic trees
Cladistic versus
phenetic analyses
Homology and
homoplasy

Phylogenetics
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!
But in molecular data sets, too!
Cactaceae
(cactus spines are
modified leaves)
Taxonomy and
phylogenetics
Phylogenetic trees
Homology and
homoplasy
Cladistic versus
phenetic analyses
Euphorbiaceae
(euphorb spines are
modified shoots)

Phylogenetics
Molecular data and homoplasy
260 * 280 * 300 * 320
0841r : CCTTCAATTTTTATT-----------------------AGAGTTTTAGGAGAAATAAGTATGTG : 272
0992r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 213
4062r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGAACAGAGTTTTAGGAGAAATAAGTATGTG : 319
3802r : CCTCCAATTTTTATTAGTTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 282
ph2f : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 306
CCTcCAATTTTTATTag ttgcctactcctttggg acAGAGTTTTAGGAGAAATAAGTATGTG
gene sequences represent character data
characters are positions in the sequence (not all workers agree; some say one
gene is one character)
character states are the nucleotides in the sequence (or amino acids in the case
of proteins)
Problems:
the probability that two nucleotides are the same just by chance mutation is 25%
what to do with insertions or deletions (which may themselves be characters)
homoplasy in sequences may cause alignment errors
Taxonomy and
phylogenetics
Phylogenetic trees
Homology and
homoplasy
Cladistic versus
phenetic analyses

Phylogenetics
Molecular data and homoplasy: Orthologs vs. Paralogs
When comparing gene sequences, it is important to distinguish between identical
vs. merely similar genes in different organisms
Orthologs are homologous genes in different species with analogous functions
Paralogs are similar genes that are the result of a gene duplication
A phylogeny that includes both orthologs and paralogs is likely to be incorrect
Sometimes phylogenetic analysis is the best way to determine if a new gene is an
ortholog or paralog to other known genes
Taxonomy and
phylogenetics
Phylogenetic trees
Homology and
homoplasy
Cladistic versus
phenetic analyses

Phylogenetics
What are useful characters?
Use derived condition, not ancestral
- Synapomorphy (shared derived character): homologous traits share the same
character state because it originated in their immediate common ancestor
- Plesiomorphy (shared ancestral character”): homologous traits share the same
character state because they are inherited from a common distant ancestor
Taxonomy and
phylogenetics
Phylogenetic trees
Homology and
homoplasy
Cladistic versus
phenetic analyses
analogy
synapomorphy
(shared derived
character)
plesiomorphy
(shared ancestral
character)
autapomorphy
(unique derived
character)

Phenetic methods construct trees (phenograms) by considering the current
states of characters without regard to the evolutionary history that brought the
species to their current phenotypes;
phenograms are based on overall similarity
Cladistic methods construct trees (cladograms) rely on assumptions about
ancestral relationships as well as on current data;
cladograms are based on character evolution (e.g. shared derived characters)
Within the field of taxonomy there are two different
methods and philosophies of building phylogenetic trees:
cladistic and phenetic
Cladistics is becoming the method of choice; it is considered to be more powerful
and to provide more realistic estimates, however, it is slower than phenetic algorithms
Phenetics versus cladistics

Phenetics vs. cladistics
An example
characteristics identity
critter A 4 limbs meta.
kidney
hair endothermy vivip. no
cloaca
placental
critter B 4 limbs meta.
kidney
hair endothermy ovip. cloaca echidna
critter C 4 limbs meta.
kidney
feathers endothermy ovip. cloaca bird
ancestor 4 limbs meta.
kidney
no
hair/feathers
ectothermy ovip. cloaca turtle

kidney
cloaca
placental
kidney
kidney
kidney
no
hair/feathers
Phenetic (overall similarity)
A
B
C
overall similarity
C B A
3
4
5

kidney
cloaca
placental
kidney
kidney
kidney
no
hair/feathers
Cladistics (character evolution; e.g. shared derived characters)
A
B
C
shared derived characters
A B C
1
2
1

The problem
- A basic process in the evolution of a sequence is change in that sequence over time
- Now we are interested in a mathematical model to describe that
- It is essential to have such a model to understand the mechanisms of change and is required to
estimate both the rate of evolution and the evolutionary history of sequences
260 * 280 * 300 * 320
0841r : CCTTCAATTTTTATT-----------------------AGAGTTTTAGGAGAAATAAGTATGTG : 272
4062r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGAACAGAGTTTTAGGAGAAATAAGTATGTG : 319
3802r : CCTCCAATTTTTATTAGTTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 282
ph2f : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 306
CCTcCAATTTTTATTag ttgcctactcctttggg acAGAGTTTTAGGAGAAATAAGTATGTG

Pyrimidine (C4N2H4) Purine (C5N4H4)
Nucleotide base + sugar + phosphate
O
sugar
P O
O
-
O
-
PO4
--
Guanine
Adenine
Thymine
Cytosine
5’
3’
3’
3’
3’
3’
5’
3’
3’
3’
3’
3’

A
C T
G






Models of sequence evolution
Examples
Jukes-Cantor model (1969)
All substitutions have an equal probability and
base frequencies are equal

A
C T
G






Examples
Felsenstein (1981)
All substitutions have an equal probability, but there are unequal
base frequencies

A
Purines
Purymidines C T
G






Examples
Kimura 2 parameter model (K2P) (1980)
Transitions and transversions have different probabilities

A
Purines
Purymidines C T
G






Examples
Hasegawa, Kishino & Yano (HKY) (1985)
Transitions and transversions have different probabilities,
base frequencies are unequal

A
C T
G




 
Examples
General time reversible model (GTR)
Different probabilities for each substitution,
base frequencies are unequal

A
C T
G




 
GTR
HKY
A
C T
G






A
C T
G






A
C T
G






A
C T
G






Jukes-Cantor
Felsenstein K2P

More models of sequence evolution …
Currently, there are more than 60 models described
- plus gamma distribution and invariable sites
- accuracy of models rapidly decreases for highly divergent sequences
- problem: more complicated models tend to be less accurate (and slower)
How to pick an appropriate model?
- use a maximum likelihood ratio test
- implemented in Modeltest 3.06 (Posada & Crandall, 1998)

Phylogenetics

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Phylogenetics