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Computational phylogenetics
computational phylogenetics uses
algorithms to assemble
phylogenetic trees.
Phylogenetic trees
a phylogenetic tree is a branching
diagram representing evolutionary
relationships between taxa or
biological molecules.
Hedges & Kumar 2009. Timetree of Life. Oxford University Press
depending on the input data and
the algorithm used, trees can be
rooted or unrooted.
Phylogenetic trees
Alpha
Delta
Gamma Beta
Epsilon
Gamma
Beta
Alpha
most recent common ancestor
Delta
Epsilon
Phylogenetic trees
depending on the input data and
the algorithm used, trees can be
scaled to time or not
1Mya
2Mya
3Mya
4Mya
5Mya
Phylogenetic trees
trees can be bifurcating or
multifurcating.
Characters
different types of traits can be used
to infer phylogenies.
Phenotypical data
Morphological traits
Physiological traits
Cytological traits
Behavioural traits
Molecular data
Immunological techniques
Proteines (amino acid sequences)
DNA
DNA-DNA hybridisation
Restriction enzyme sites
Nucleotide sequence comparisons
Characters
Friedman 2008. Nature 454: 209-212.
morphological traits can be
measured in both extant and
extinct taxa.
Characters
10mm
Friedman 2008. Nature 454: 209-212.
Characters
cytogenetic traits include the
number, size and morphology of
the chromosomes, behavior in
meiosis and total DNA content
Zeltnera exaltata
Zeltnera calycosa
Zeltnera venusta
Mansion & Zeltner 2004. Am. J. Botany 91: 2069-2086.
Characters
behavioural characteristics can be
used to build trees.
Elk – Cervus canadensis
Moose – Alces alces
Fallow deer – Dama dama
Cap et al. 2008 Cladistics 24: 917-932.
Characters
behavioural characteristics can be
used to build trees.
Elk – Cervus canadensis
Moose – Alces alces
Fallow deer – Dama dama
Cap et al. 2008 Cladistics 24: 917-932.
in immunological taxonomy,
antibody-antigen recognition is
used to estimate relatedness.
Characters
B
A
species A antigens
species A
antibodies
species B
antigens
precipitation
precipitation+++
species C
antigens
C
trees can be build by comparing
amino acid sequences for the same
protein in different species.
Characters
amino acid sequence of aspartate transaminase
1
2
3
4
5
6
7
8
9
1
0
1
1
1
2
4
0
4
1
4
2
4
3
4
4
4
5
4
6
4
7
4
8
4
9
5
0
Bacteria
P
L
F
D
F
A
Y
Q
G
F
A
R
…
K
N
F
G
L
Y
N
E
R
V
G
Yeast
A
L
F
D
T
A
Y
Q
G
F
A
T
…
K
N
A
G
M
Y
G
E
R
V
G
Alfaalfa
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
M
G
L
Y
G
E
R
V
G
Chicken
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
F
G
L
Y
N
E
R
V
G
Rat
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
F
G
L
Y
N
E
R
V
G
Horse
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
F
G
L
Y
N
E
R
V
G
Pig
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
F
G
L
Y
N
E
R
V
G
Human
P
F
F
D
S
A
Y
Q
G
F
A
S
…
K
N
F
G
L
Y
N
E
R
V
G
P=proline, A=alanine, L=leucine, F=tryptophan, D=aspartic acid, T=threonine, S=serine, K=lysine,
N=asparagine, M=methionine, G=glycine, Y=tyrosine, E=glutamic acid, R=arginine, V=valine
DNA hybridisation techniques allow
the comparison of a billion of
nucleotides.
Characters
dissociate into
single strands
dissociate into
single strands
radioactive
labeling
add to
incubation mixture
isolate
hybrid double strands
determine melting
temperature
restriction enzymes cleave DNA at
specific short nucleotide
sequences, producing distinctive
patterns of fragments.
Characters
EcoRI
5’ … N N G A A T T C N N … 3’
3’ … N N C T T A A G N N … 5’
5’ … N N G
3’ … N N C T T A A
restriction enzymes cleave DNA at
specific short nucleotide
sequences, producing distinctive
patterns of fragments.
Characters
EcoRI
HindIII
Hpa1
Bg/II
XbaI
SmaI
EcoRI
Hpa1
Bg/II
XbaI
SmaI
Characters
April 2011:
comparing nucleotide sequences
among species is the most precise
way of inferring phylogenetic
relationships.
135 440 924 sequences
126 551 501 141 bases
since 1995, 180 organisms were
sequenced genome-wide
Characters
Drosophila melanogaster
Ciona intestinalis
Rattus norvegicus
Caenorhabdites elegans
Caenorhabditis briggsae
Arabidopsis thala
Apis mellifera
Anopheles gambiae
Takifugu rubripes
Mus musculus
Canis familaris
Oryza sativa
Pan troglodytes
Tetraodon nigroviridis
Gallus gallus
Homo sapiens
Populus trichocarpa
Characters
Nuclear DNA
Mitochondrial DNA
Microsatellites
some types of DNA evolve faster
than others.
• easy to isolate
• evolves at a faster rate
• e.g. CAACAACAA…
• evolve at an even faster rate
Character coding
state 0
a
continuous quantitative characters
are often reverted into discrete
ones, e.g. by gap coding.
state 1
b
c
state 2
d
Inferring phylogenies
Parsimony methods
Distance methods
Maximum likelihood methods
Bayesian inference methods
different approaches exist for
inferring phylogenies
Testing phylogenies
specific hypotheses about trees,
evolutionary models and clocks can
be tested statistically.
Testing models, trees and clocks
Bootstrap, jackknife and permutation tests