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Phylogenetic Reconstruction: Parsimony. Anders Gorm Pedersen [email protected] Trees: terminology. Trees: terminology. Trees: terminology. “Reptilia” is a non-monophyletic group. Trees: representations. Three different representations of the same tree-topology. Trees: rooted vs. unrooted.

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trees terminology4
Trees: terminology

“Reptilia” is a non-monophyletic group

trees representations
Trees: representations

Three different representations of the same tree-topology

trees rooted vs unrooted
Trees: rooted vs. unrooted
  • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
  • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
  • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)

Early

Late

trees rooted vs unrooted7
Trees: rooted vs. unrooted
  • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
  • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
  • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)

Early

Late

trees rooted vs unrooted8
Trees: rooted vs. unrooted
  • A rooted tree has a single node (the root) that represents a point in time that is earlier than any other node in the tree.
  • A rooted tree has directionality (nodes can be ordered in terms of “earlier” or “later”).
  • In the rooted tree, distance between two nodes is represented along the time-axis only (the second axis just helps spread out the leafs)

Early

Late

trees rooted vs unrooted9
Trees: rooted vs. unrooted
  • In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node
  • Distance along branches directly represents node distance
trees rooted vs unrooted10
Trees: rooted vs. unrooted
  • In unrooted trees there is no directionality: we do not know if a node is earlier or later than another node
  • Distance along branches directly represents node distance
homology limb structure
Homology: limb structure

Homology: any similarity between characters that is due to their shared ancestry

homology vs homoplasy
Homology vs. Homoplasy

X

X

X

X

Homology: similar traits inherited from a common ancestor

Homoplasy: similar traits are

not directly caused by common ancestry (convergent evolution).

molecular phylogeny
A A G C G T T G G G C A A

B A G C G T T T G G C A A

C A G C T T T G T G C A A

D A G C T T T T T G C A A

1 2 3

DNA and protein sequences

Homologous characters inferred from alignment.

Other molecular data: absence/presence of restriction sites, DNA hybridization data, antibody cross-reactivity, etc. (but losing importance due to cheap, efficient sequencing).

Molecular phylogeny
morphology vs molecular data
Morphology vs. molecular data

African white-backed vulture

(old world vulture)

Andean condor

(new world vulture)

New and old world vultures seem to be closely related based on morphology.

Molecular data indicates that old world vultures are related to birds of prey (falcons, hawks, etc.) while new world vultures are more closely related to storks

Similar features presumably the result of convergent evolution

parsimonious reconstruction22
Parsimonious reconstruction

A

G..

B

G..

C

T..

D

T..

G..

T..

T..

parsimonious reconstruction23
Parsimonious reconstruction

A

G..

B

G..

C

T..

D

T..

G..

T..

T..

alternative tree homoplasy
Alternative tree: homoplasy

A

G..

B

G..

C

T..

D

T..

G..

T..

T..

A

G..

C

T..

D

T..

B

G..

alternative tree homoplasy25
Alternative tree: homoplasy

A

G..

B

G..

C

T..

D

T..

G..

T..

T..

A

G..

C

T..

D

T..

B

G..

T..

T..

T..

alternative tree homoplasy26
Alternative tree: homoplasy

A

G..

B

G..

C

T..

D

T..

G..

T..

T..

A

G..

D

T..

C

T..

B

G..

T..

T..

T..

one character assumption of no homoplasy is equivalent to finding shortest tree
One character: Assumption of no homoplasy is equivalent to finding shortest tree

A

G...

B

G...

C

T...

D

T...

G..

T..

T..

A

G..

C

T..

D

T..

B

G..

T..

T..

T..

phylogenetic reconstruction28
Phylogenetic reconstruction

A

..G

B

..G

C

..T

D

..T

..G

..T

..T

phylogenetic reconstruction29
Phylogenetic reconstruction

A

G.G

B

G.G

C

T.T

D

T.T

G.G

T.T

T.T

phylogenetic reconstruction conflicts
Phylogenetic reconstruction: conflicts

A

B

C

D

A

.G.

C

.G.

B

.T.

D

.T.

.G.

.T.

.T.

phylogenetic reconstruction conflicts31
Phylogenetic reconstruction: conflicts

A

.G.

B

.T.

C

.G.

D

.T.

.T.

.T.

.T.

A

C

B

D

phylogenetic reconstruction conflicts32
Phylogenetic reconstruction: conflicts

A

B

C

D

A

G.G

C

T.T

B

G.G

D

T.T

T.T

T.T

T.T

several characters choose shortest tree equivalent to fewer assumptions of homoplasy
Several characters: choose shortest tree(equivalent to fewer assumptions of homoplasy)

A

GGG

B

GTG

C

TGT

D

TTT

GTG

Total length of tree: 4

Total length of tree: 5

TTT

TTT

A

GGG

C

TGT

B

GTG

D

TTT

TGT

TTT

TTT

maximum parsimony
Maximum Parsimony
  • Maximum parsimony: the best tree is the shortest tree (the tree requiring the smallest number of mutational events)
  • This corresponds to the tree that implies the least amount of homoplasy (convergent evolution, reversals)
  • How do we find the best tree for a given data set?
maximum parsimony first approach
Maximum Parsimony: first approach
  • Construct list of all possible trees for data set
  • For each tree: determine length, add to list of lengths
  • When finished: select shortest tree from list
  • If several trees have the same length, then they are equally good (equally parsimonious)
maximum parsimony problems
Maximum Parsimony: problems
  • We need algorithm for constructing list of all possible trees
  • We need algorithm for determining length of given tree
  • Should all mutational events have same cost?
constructing list of all possible unrooted trees
Constructing list of all possible unrooted trees
  • Construct unrooted tree from first three taxa. There is only one way of doing this
  • Starting from (1), construct the three possible derived trees by adding taxon 4 to each internal branch
  • From each of the trees constructed in step (2), construct the five possible derived trees by adding taxon 5 to each internal branch.
  • Continue until all taxa have been added in all possible locations
maximum parsimony problems38
Maximum Parsimony: problems
  • We need algorithm for constructing list of all possible trees 
  • We need algorithm for determining length of given tree
  • Should all mutational events have same cost?
algorithm for determining length of given tree fitch
Algorithm for determining length of given tree: Fitch

C

A

A

G

C

What is the length of this tree? (How many mutational steps are required?)

algorithm for determining length of given tree fitch40
Algorithm for determining length of given tree: Fitch
  • Root the tree at an arbitrary internal node (or internal branch)
  • Visit an internal node x for which no state set has been defined, but where the state sets of x’s immediate descendants (y,z) have been defined.
  • If the state sets of y,z have common states, then assign these to x.

If there are no common states, then assign the union of y,z to x, and increase tree length by one.

  • Repeat until all internal nodes have been visited. Note length of current tree.
algorithm for determining length of given tree fitch48
Algorithm for determining length of given tree: Fitch

C

A

C

A

G

{A, G}

{A, C}

{A, C, G}

Length so far = 3

algorithm for determining length of given tree fitch49
Algorithm for determining length of given tree: Fitch

C

A

C

A

G

{A, G}

{A, C}

{A, C, G}

Length so far = 3

{A, C}

algorithm for determining length of given tree fitch50
Algorithm for determining length of given tree: Fitch

C

A

C

A

G

{A, G}

{A, C}

{A, C, G}

Length of tree = 3

{A, C}

algorithm for determining length of given tree fitch51
Algorithm for determining length of given tree: Fitch

C

A

C

A

G

A

A

A

Length of tree = 3

A

One possible reconstruction (several others exist)

maximum parsimony problems52
Maximum Parsimony: problems
  • We need algorithm for constructing list of all possible trees 
  • We need algorithm for determining length of given tree 
  • Should all mutational events have same cost?
mutational events need not have the same cost
Mutational events need not have the same cost

C

A

C

A

G

A C G T

A 0 3 1 3

C 3 0 3 1

G 1 3 0 3

T 3 1 3 0

Sankoff algorithm

maximum parsimony problems54
Maximum Parsimony: problems
  • We need algorithm for constructing list of all possible trees 
  • We need algorithm for determining length of given tree 
  • Should all mutational events have same cost? 
how many branches are there on an unrooted tree with x tips
How many branches are there on an unrooted tree with x tips?
  • There is only one way of con-structing the first tree. This tree has 3 tips and 3 branches
  • Each time an extra taxon is added, two branches are created.
  • A tree with x tips will therefore have the following number of branches:

nbranches = 3+(x-3)*2

= 3+2x-6

= 2x-3

A

B

C

A

B

D

C

how many unrooted trees are there
How many unrooted trees are there?
  • A tree with x tips has 2x-3 branches
  • For each tree with x=n-1 tips, we can therefore construct 2(n-1)-3 derived trees (with n tips).
  • The number of unrooted trees with n tips is therefore:

(2i-3) = 1 x 3 x 5 x 7 x ...

n-1

i=2

branch and bound shortcut to perfection step 1 construction of initial tree by sequential addition
Branch and bound: shortcut to perfection Step 1: Construction of initial tree by sequential addition
branch and bound shortcut to perfection step 2 search treespace discard suboptimal parts
Branch and bound: shortcut to perfectionStep 2: search treespace, discard suboptimal parts
heuristic search
Heuristic search
  • Construct initial tree (e.g., sequential addition); determine length
  • Construct set of “neighboring trees” by making small rearrangements of initial tree; determine lengths
  • If any of the neighboring trees are better than the initial tree, then select it/them and use as starting point for new round of rearrangements. (Possibly several neighbors are equally good)
  • Repeat steps 2+3 until you have found a tree that is better than all of its neighbors.
  • This tree is a “local optimum” (not necessarily a global optimum!)
types of rearrangement i nearest neighbor interchange nni
Types of rearrangement I: nearest neighbor interchange (NNI)

Original tree

Two neighbors per internal branch:

tree with n tips has 2(n-3) neighbors

(For example, a tree with 20 tips has 34 neighbbors)

sankoff minimal length of possible subtrees having nucleotide a at internal node
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

A

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

costAA = 0, costAC = costAG = costAT = 1

sankoff minimal length of possible subtrees having nucleotide a at internal node75
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

0

SA = mini[costAi+ Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node76
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

0

SA = mini[costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node77
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

0

SA = mini[costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node78
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

1

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node79
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

1

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node80
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

1

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node81
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

1

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node82
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

A

0

SA = 1 + minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node83
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

A

1

SA = 1 + minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node84
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

A

1

SA = 1 + minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node85
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

A

1

SA = 1 + minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node86
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

A

0

SA = 1 + minj [costAj + Sright, j]

sankoff minimal length of possible subtrees having nucleotide a at internal node87
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

A

0

1

SA = mini [costAi + Sleft, i] +

minj [costAj + Sright, j]

SA = 1 + 0 = 1

sankoff minimal length of possible subtrees having nucleotide a at internal node88
Sankoff: minimal length of possible subtrees having nucleotide “A” at internal node

C

A

C

A

G

sankoff minimal length of possible subtrees having nucleotide c at internal node
Sankoff: minimal length of possible subtrees having nucleotide “C” at internal node

C

A

1

0

SC = 0 + 1 = 1

sankoff minimal length of possible subtrees having nucleotide g at internal node
Sankoff: minimal length of possible subtrees having nucleotide “G” at internal node

C

A

1

1

SG = 1 + 1 = 2

sankoff minimal length of possible subtrees having nucleotide t at internal node
Sankoff: minimal length of possible subtrees having nucleotide “T” at internal node

C

A

1

1

ST = 1 + 1 = 2

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