Cao et al. (2000) Gene

Phylogeny of Mammals

a good example where molecular sequences have led to a big improvement of our understanding of evolution.

rRNA structure is conserved in evolution.

The sequence changes slowly. Therefore it can be used to tell us about the earliest branches in the tree of life.

69 Mammals with complete motochondrial genomes.

Used two models simulatneously

Total of 3571 sites

= 1637 single sites

+ 967 pairs

Hudelot et al. 2003

Afrotheria / Laurasiatheria

Phylogenetic Methods

• Distances

• Clustering Methods

• Likelihood Methods

• Parsimony

Recommended books:

P. G. Higgs and T. K. Attwood – Bioinformatics and Molecular Evolution

R. Page and A. Holmes – Molecular evolution: a phylogenetic approach

W. H. Li – Molecular evolution

Part of sequence alignment of Mitochondrial Small Sub-Unit rRNA

Full gene is length ~950

11 Primate species with mouse as outgroup

Mouse : Lemur : Tarsier : SakiMonkey : Marmoset : Baboon : Gibbon : Orangutan : Gorilla : PygmyChimp : Chimp : Human :

* 20 * 40 * 60 * CUCACCAUCUCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGG-UAUUAAAGUAAGCAAAAGACUCACCACUUCUUGCUAAUUCAACUUAUAUACCGCCAUCCCCAGCAAACCCUAUUAAGGCCC-CAAAGUAAGCAAAAACCUUACCACCUCUUGCUAAUUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAUAAAGGUUUUAAAGUAAGCACAAGUCUUACCACCUCUUGCC-AU-CAGCCUGUAUACCGCCAUCUUCAGCAAACUCUA-UAAUGACAGUAAAGUAAGCACAAGUCUCACCACGUCUAGCC-AU-CAGCCUGUAUACCGCCAUCUUCAGCAAACUCCU-UAAUGAUUGUAAAGUAAGCAGAAGUCCCACCCUCUCUUGCU----UAGUCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACGAAGUGAGCGCAAAUCUCACCAUCUCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACCUCACCACCCCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCCACGAAGUAAGCGCAAACCUCACCACCUCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACGAAGGCCACAAAGUAAGCACAAGUCUCACCGCCUCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGUUACAAAGUAAGCGCAAGUCUCACCGCCUCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGUUACAAAGUAAGCGCAAGUCUCACCACCUCUUGCU----CAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUCucACC cuCUuGCu cAgccUaUAUACCGCCAUCuuCAGCAAACcCu A G aAAGUaAGC AA

: 78 : 78 : 79 : 76 : 76 : 75 : 75 : 75 : 75 : 75 : 75 : 75

From alignment construct pairwise distances.

Species 1: AAGTCTTAGCGCGATSpecies 2: ACGTCGTATCGCGAT

* * * D = 3/15 = 0.2

D = fraction of differences between sequences

BUT - D is not an additive distance,

D does not increase linearly with time.

G

CA

2 substitutions happened - only 1 is visible

G

AA

2 substitutions happened - nothing visible

Models of Sequence Evolution

Pij(t) = probability of being in state j at time t

given that ancestor was in state i at time 0.

States label bases A,C,G & Ti

t

jkjk

ikij rP

dt

dP

rij is the rate of substitution from state i to state j

Jukes - Cantor Model

All substitution rates =

All base frequencies are 1/4

)4exp(4

3

4

1)( ttPii )4exp(

4

1

4

1)( ttPij

))8exp(1(4

3)2(1 ttPD ii

t = 2t

td 6Mean number of substitutions per site:

)3

41ln(

4

3Dd

d increases linearly with time

d = D

D = 3/4

D

d

The HKY model has a more general substitution rate matrix

*

*

*

*

CGA

TGA

TCA

TCG

T

C

G

A

TCGA

to

from

The frequencies of the four bases are

is the transition-transversion rate parameter

* means minus the sum of elements on the row

.,,, TCGA

Baboon Gibbon Orang Gorilla PygmyCh. Chimp Human

Baboon 0.00000 0.18463 0.19997 0.18485 0.17872 0.18213 0.17651

Gibbon 0.18463 0.00000 0.13232 0.11614 0.11901 0.11368 0.11478

Orang 0.19997 0.13232 0.00000 0.09647 0.09767 0.09974 0.09615

Gorilla 0.18485 0.11614 0.09647 0.00000 0.04124 0.04669 0.04111

PygmyChimp 0.17872 0.11901 0.09767 0.04124 0.00000 0.01703 0.03226

Chimp 0.18213 0.11368 0.09974 0.04669 0.01703 0.00000 0.03545

Human 0.17651 0.11478 0.09615 0.04111 0.03226 0.03545 0.00000

Part of the Jukes-Cantor Distance Matrix for the Primates example

Use as input to clustering methods

Mouse-Primates ~ 0.3

Distance Matrix Methods

Follow a clustering procedure on the distance matrix:

1. Join closest 2 clusters

2. Recalculate distances between all the clusters

3. Repeat 1 and 2 until all species are connected in a single cluster.

 

Initially each species is a cluster on its own. The clusters get bigger during the process, until they are all connected to a single tree.

Neighbour Joining method is commonly used clustering method

Neighbour-Joining method

Take two neighbouring nodes i and j and replace by a single new node n.

din + dnk = dik ; djn + dnk = djk ; din + djn = dij ;

therefore dnk = (dik + djk - dij)/2 ; applies for every k

define

k

iki dN

r2

1

kjkj d

Nr

2

1

k

i

j

n n

Let din = (dij + ri - rj)/2 ; djn = (dij + rj - ri)/2 .

Rule: choose i and j for which Dij is smallest, where Dij = dij - ri - rj .

but ...

NJ method produces an Unrooted, Additive Tree

Additive means distance between species = distance summed along internal branches

0.1

Baboon

Mouse

LemurTarsier

SakiMonkey

Marmoset

Gibbon

OrangutanGorilla PygmyChimp

Chimp

Human

0.1

Mouse

Lemur

Tarsier47

SakiMonkey

Marmoset100

Baboon

Gibbon

Orang

Gorilla

Human

PygmyChimp

Chimp100

84

100

99

100

100

100

The tree has been rooted using the Mouse as outgroup

The Maximum Likelihood Criterion

Calculate the likelihood of observing the data on a given the tree.

Choose tree for which the likelihood is the highest.

x

A G

t2t1

)()()( 21 tPtPxL xGxA

x

y z

t2t1

y z

xzxy tPzLtPyLxL )()()()()( 21

Can calculate total likelihood for the site recursively.

Likelihood is a function of tree topology, branch lengths, and parameters in the substitution rate matrix. All of these can be optimized.

Tree log L difference S.E. Significantly worse

1 -5783.03 0.39 7.33 no NJ tree

2 -5782.64 0.00 <-------------best tree (Human,(Gorilla,(Chimp,PygmyCh)))

3 -5787.99 5.35 5.74 no ((Human,Gorilla),(Chimp,PygmyCh))

4 -5783.80 1.16 9.68 no (Lemur,(Tarsier,Other Primates))

5 -5784.76 2.12 9.75 no (Tarsier,(Lemur,Other Primates))

????????????????????????????????????????????????????????????????????

6 -5812.96 30.32 15.22 yes (Gorilla,(Chimp,(Human,PygmyCh)))

7 -5805.21 22.56 13.08 no Orang and Gorilla form clade

8 -5804.98 22.34 13.15 no Gorilla branches earlier than Orang

9 -5812.97 30.33 14.17 yes Gibbon and Baboon form a clade

Using ML to rank the alternative trees for the primates example

0.1

MouseLemur

Tarsier47

SakiMonkeyMarmoset

100

BaboonGibbon

OrangGorilla

HumanPygmyChimpChimp

10084

10099

100100

100

The NJ Tree has:

(Gorilla,(Human,(Chimp,PygmyCh)))

((Lemur,Tarsier),Other Primates))

The Parsimony Criterion

Try to explain the data in the simplest possible way with the fewest arbitrary assumptions

Used initially with morphological characters.

Suppose C and D possess a character (1) that is absent in A and B (0)

A(0) B(0) C(1) D(1)

+

1 2

A(0) C(1) B(0) D(1)

+

*

3

A(0) C(1) B(0) D(1)+ +

In 1, the character evolves only once (+)

In 2, the character evolves once (+) and is lost once (*)

In 3, the character evolves twice independently

The first is the simplest explanation, therefore tree 1 is to be preferred by the parsimony criterion.

Parsimony with molecular data

A(T)

B(T)C(T)

D(G)

E(G)

*

A(T)

B(T)

C(T)

D(G)E(G)

* *

1. Requires one mutation 2. Requires two mutations

By parsimony, 1 is to be preferred to 2.

A(T)

B(T)C(T)

D(T)

E(G)

*A(T)

B(T)

C(T)

D(T)E(G)

*

This site is non-informative. Whatever the arrangement of species, only one mutation is required. To be informative, a site must have at least two bases present at least twice.

The best tree is the one that minimizes the overall number of mutations at all sites.

Searching Tree Space

Require a way of generating trees to be tested by Maximum Likelihood, or Parsimony.

Nearest neighbour interchange

Subtree pruning and regrafting

No. of distinct tree topologies

N Unrooted (UN) Rooted (RN)

3 1 3

4 3 15

5 15 105

6 105 945

7 945 10395

UN = (2N-5)UN-1 RN = (2N-3)RN-1

 Conclusion: there are huge numbers of trees, even for relatively small numbers of species. Therefore you cannot look at them all.

Group III - Supraprimates

Dating from phylogeniesThe molecular clock

must be approx 50 m.y.

must be approx 150 m.y.

known to be 100 m.y.

Can lead to controversies because the clock does not always go at a constant rate

Mammalian orders (primates, rodents, carnivores, bats ....)Molecular dates tend to be earlier (100 m.y.) than those coming from the fossil record (65 m.y.)

Animal phyla - Molecular phylogenies are resolving the relationships between phyla that were not understood from morphology.Still uncertainty about dates - Molecular dates suggest about 1 b.y. Earliest fossil evidence is 560 m.y.

Old morphological phylogeny New molecular phylogeny

Puts LUCA just prior to 4, and origin of eukaryotes at 2.7.

Origin of cyanobacteria is at 2.5, whereas they are claimed to be present in the fossil record at 3.5.

Molecular dating of key events in early evolution