Computational phylogeneticscomputational phylogenetics uses algorithms to assemble phylogenetic trees.

a phylogenetic tree is a branching diagram representing evolutionary relationships between taxa or biological molecules.

Phylogenetic trees

Hedges & Kumar 2009. Timetree of Life. Oxford University Press

depending on the input data and the algorithm used, trees can be rooted or unrooted.

Alpha BetaDelta Gamma Epsilon

Phylogenetic trees

Gamma

Delta

Alpha

Beta

Epsilon

most recent common ancestor

depending on the input data and the algorithm used, trees can be scaled to time or not

Phylogenetic trees

1Mya

2Mya

3Mya

4Mya

5Mya

trees can be bifurcating or multifurcating.

Phylogenetic trees

Characters different types of traits can be used to infer phylogenies.

Phenotypical data

Molecular data

Morphological traitsPhysiological traitsCytological traitsBehavioural traits

Immunological techniquesProteines (amino acid sequences)DNA DNA-DNA hybridisation Restriction enzyme sites Nucleotide sequence comparisons

Characters

Friedman 2008. Nature 454: 209-212.

Characters morphological traits can be measured in both extant and extinct taxa.

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 venusta

Zeltnera calycosa

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.

Characters in immunological taxonomy, antibody-antigen recognition is used to estimate relatedness.

species B antigens

species C antigens

species A antigens

species A antibodies

precipitation

precipitation+++

AB C

Characters trees can be build by comparing amino acid sequences for the same protein in different species.

1 2 3 4 5 6 7 8 9 10

11

12

40

41

42

43

44

45

46

47

48

49

50

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

amino acid sequence of aspartate transaminase

Characters DNA hybridisation techniques allow the comparison of a billion of nucleotides.

dissociate into single strands

dissociate into single strands

add to incubation mixture

isolate hybrid double strands

determine melting temperature

radioactivelabeling

Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments.

N

N

N

N

G

C

A

T

A

T

T

A

C

G

N

N

N

N

…

…

3’

5’

…

…

5’

3’

T

A

A A T C

G

N

N

N

N

…

…

3’

5’

N

N

N

N

G

C

…

…

5’

3’ A AT T

EcoRI

Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments.

EcoRI HindIII Hpa1 Bg/II XbaI SmaI EcoRI Hpa1 Bg/II XbaI SmaI

Characters comparing nucleotide sequences among species is the most precise way of inferring phylogenetic relationships.

April 2011: 135 440 924 sequences 126 551 501 141 bases

Characters since 1995, 180 organisms were sequenced genome-wide

Drosophila melanogaster Rattus norvegicus Caenorhabditis briggsae Apis mellifera Takifugu rubripes Canis familaris Oryza sativa Tetraodon nigroviridis

Ciona intestinalis Caenorhabdites elegans Arabidopsis thala Anopheles gambiae Mus musculus Pan troglodytes Gallus gallus Homo sapiens

Populus trichocarpa

Characters some types of DNA evolve faster than others.

Nuclear DNAMitochondrial DNAMicrosatellites • easy to isolate

• evolves at a faster rate

• e.g. CAACAACAA…• evolve at an even faster rate

Character coding continuous quantitative characters are often reverted into discrete ones, e.g. by gap coding.

a b c d

state 0 state 1 state 2

Inferring phylogenies different approaches exist for inferring phylogenies

Parsimony methodsDistance methodsMaximum likelihood methodsBayesian inference methods

Testing phylogenies specific hypotheses about trees, evolutionary models and clocks can be tested statistically.

Testing models, trees and clocksBootstrap, jackknife and permutation tests