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How to estimate phylogenies? On parsimony, likelihood and probability.

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Title: How to estimate phylogenies? On parsimony, likelihood and probability.


1
How to estimate phylogenies?On parsimony,
likelihood and probability.
  • Duur Aanen

2
Overview
  • Basics
  • What is a phylogenetic tree
  • Rooted, unrooted, monophyletic group
  • Distance methods
  • Maximum parsimony
  • Likelihood methods
  • Maximum likelihood
  • Bayesian analysis
  • Differences
  • Example the evolution of fungus-growing termites
    and their mutualistic fungal symbionts

3
Basics
  • Phylogeny evolutionary history of a group
  • Phylogenetic tree graphical representation
  • (phylogenetic reconstruction

4
Unrooted tree
A
C
B
5
Rooted tree
6
A
C
B
7
A
C
B
8
A
C
B
A
C
B
9
A
C
B
A
C
B
B
C
A
10
A
C
B
A
C
B
B
C
A
11
How do we know where the root is?
  • Usually by including an outgroup in the analysis
  • a species that falls outside the group you study
    (the ingroup)
  • Examples
  • ingroup birds, outgroup crocodile
  • ingroup rodents, outgroup gorilla

12
rat
mouse
hamster
13
Gorilla ?
14
rat
mouse
hamster
rat
mouse
hamster
rat
hamster
mouse
15
rat
mouse
hamster
rat
mouse
hamster
rat
hamster
mouse
16
C
B
A
AB monophyletic group A and B share a unique
common ancestor
17
C
B
A
BC no monophyletic group B and C do not share
a unique common ancestor
18
Example evolutionary history of three species
Outgroup
slide after Fredrik Ronquist
19
Three possible trees
A
C
B
slide after Fredrik Ronquist
20
How to decide?
  • Not known
  • Estimate!
  • Use (some kind of) similarity to estimate
  • Similarity based on characters
  • Morphology
  • DNA!
  • Method to come from character to tree

21
DNA characters
  • 111
  • 123456789012
  • Chimp ATTCGAGTAGCT
  • Human ATTCGAGTAGCT
  • Gorilla ATGCGAGTAGCT
  • Orang-utan ATGCGAGAAGCT

22
Methods to estimate tree from data
  • Maximum parsimony
  • Distance based methods
  • Likelihood based methods
  • Maximum likelihood
  • Bayesian inference

23
  • 111
  • 123456789012
  • Chimp ATTCGAGTAGCT
  • Human ATTCGAGTAGCT
  • Gorilla ATGCGAGTAGCT
  • Orang-utan ATGCGAGAAGCT

24
Most parsimonious solution 2 steps
3G?T
7A?T
25
111 123456789012 Chimp ATTCGAGTA
GCT Human ATTCGAGTAGCT Gorilla ATGCGAGTAGCT Ora
ng-utan ATGCGAGAAGCT
26
Distance based
0 0 1 2 0 1 2 0 1
0
27
Maximum likelihood
  • The tree that maximizes the likelihood of
    observing the data from that tree is the best
    tree
  • Requires evolutionary model of sequence evolution
  • Calculation takes lot of computer time

28
Example (coin tossing)
  • 10 coins, 1 is biased (p0.8) but we dont know
    which one
  • Experiment 10 tosses with 1 of the 10 coins
  • HHHHHHHHHH
  • Likelihood Pr data hypothesis
  • Pr 10H biased 0.810 0.107
  • Pr 10H fair 0.510 0.00098

29
The best tree?
  • How can we know for sure?
  • Unlikely that we can decide for sure which tree
  • Often unlikely that we can find it

30
No. of possible rooted trees
no. sequences no. possible rooted
trees 2 1 3 3 4 15 5 105 6 945 7
10.395 8 135.135 9 2.027.025 10 34.469
.425 . . . 20. 8.200.794.532.637.891.559.000
. . . 135 21133548293083211452372893494567744328
29304974 63892947754895798475928437593145621318
43276117 49123477212413232332455699644438274876
48712865 21437786872341293461234623949842374157
36553232 25187985378375588852009384520032550003
29843122 00119282743774558598349348755179875393
2 !!!
31
Phylogeny as a statistical problem...
  • Many possible trees, with different likelihoods
  • Estimate the probability distribution of trees

32
Bayesian methods...
  • Bayes theorem
  • Posterior probability probability of a
    hypothesis given the data
  • For trees probability of a tree given the DNA
    sequences and model of sequence evolution
  • (likelihood is probability of data given a
    hypothesis, or of the DNA sequences given the
    tree)

33
Example (coin tossing)
  • 10 coins, 1 is biased (p0.8) but we dont know
    which one
  • Prior probability biased coin 0.1
  • Experiment 10 tosses with one of the 10 coins
  • HHHHHHHHHH
  • Bayes theorem
  • Posterior probability of biased coin given 10H
  • pr10Hbiasedprbiased /
  • pr10Hbiasedprbiased pr10Hbiasedpru
    nbiased
  • ? Posterior probability that coin is biased
    0.92
  • (Remember Likelihood Pr data hypothesis,
  • Pr 10H biased 0.810 0.107, Pr 10H
    fair 0.510 0.00098)

34
For trees...
  • Prtreedata
  • Impossible to calculate
  • Tree
  • Branch lengths
  • Evolutionary model with many parameters...
  • ? estimation using Markow Chain Monte Carlo
    (MCMC) simulation
  • Start with a random tree
  • Propose new tree by changing current tree
  • Accept or reject with some criterion (likelihood
    and chance implemented in criterion)
  • Many generations
  • Save sample of trees

35
slide after François Lutzoni
36
  • Different starting tree...

37
slide after François Lutzoni
38
  • Example 40 termite species, 937 nucleotides
  • Analysed with MrBayes (GTR SSR)
  • 1.500.000 generations, sampled every 50th tree (?
    30.000 trees)
  • The first 10 trees sampled...

39
Microtermes sp. 103
tree 1
Macrotermes subhyalinus 64
Microtermes sp. 3
Odontotermes lateritius 39
Odontotermes billitori 168
Odontotermes sp. 303
Ancistrotermes cavitorax 46
Macrotermes bellicosus 19
Acanthotermes acanthotorax Pauls
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes sp.4 110
Odontotermes nilensis 93
Odontotermes sp.3 126
Odontotermes minutus 161
Odontotermes sarawakensis 167
Odontotermes javanicus 165
Macrotermes lilljeborgi 143
Macrotermes muelleri Corinnes
Macrotermes nobilis 569
Pseudacanthotermes militaris 134
Macrotermes subhyalinus 5
Macrotermes bellicosus 8
Acanthotermes acanthotorax 136
Hypotermes xenotermitis 166
Macrotermes malacensis 160
Odontotermes silvicolus 6
Microtermes sp. 146
Synacanthotermes heterodon 118
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sp.1 130
Macrotermes ahmadi pe5
Ancistrotermes sp. 140
Protermes minutus 129
Ancistrotermes cavitorax 34
Labritermes butelreepeni 169
Microtermes sp. 38
Microtermes sp. 107
Foraminitermes sp. 159
40
Microtermes sp. 103
tree 2
Microtermes sp. 107
Protermes minutus 567
Odontotermes nilensis 93
Pseudacanthotermes militaris 134
Ancistrotermes cavitorax 46
Synacanthotermes heterodon 118
Labritermes butelreepeni 169
Odontotermes minutus 161
Macrotermes nobilis 569
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Odontotermes silvicolus 6
Odontotermes sp.1 130
Ancistrotermes sp. 140
Macrotermes malacensis 160
Odontotermes lateritius 39
Microtermes sp. 3
Microtermes sp. 146
Odontotermes sp.4 110
Macrotermes subhyalinus 64
Odontotermes sp. 303
Macrotermes bellicosus 19
Acanthotermes acanthotorax 136
Macrotermes muelleri Corinnes
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 34
Protermes minutus 129
Odontotermes javanicus 165
Odontotermes oblongatus 162
Macrotermes subhyalinus 5
Hypotermes xenotermitis 166
Macrotermes bellicosus 8
Macrotermes ahmadi pe5
Microtermes sp. 38
Odontotermes billitori 168
Odontotermes lateritius 81
Odontotermes sp.3 126
Ancistro Odonto sp. 164
Foraminitermes sp. 159
41
Microtermes sp. 103
tree 3
Microtermes sp. 107
Protermes minutus 567
Odontotermes nilensis 93
Pseudacanthotermes militaris 134
Ancistrotermes cavitorax 46
Synacanthotermes heterodon 118
Labritermes butelreepeni 169
Macrotermes nobilis 569
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Odontotermes silvicolus 6
Odontotermes sp.1 130
Odontotermes lateritius 39
Macrotermes malacensis 160
Ancistrotermes sp. 140
Microtermes sp. 3
Microtermes sp. 146
Odontotermes minutus 161
Odontotermes sp.4 110
Macrotermes subhyalinus 64
Odontotermes sp. 303
Macrotermes bellicosus 19
Acanthotermes acanthotorax 136
Macrotermes muelleri Corinnes
Microtermes sp. 38
Odontotermes billitori 168
Macrotermes bellicosus 8
Macrotermes ahmadi pe5
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 34
Odontotermes javanicus 165
Protermes minutus 129
Odontotermes oblongatus 162
Hypotermes xenotermitis 166
Macrotermes subhyalinus 5
Odontotermes lateritius 81
Odontotermes sp.3 126
Ancistro Odonto sp. 164
Foraminitermes sp. 159
42
Microtermes sp. 103
tree 4
Pseudacanthotermes militaris 134
Protermes minutus 567
Odontotermes minutus 161
Odontotermes sp.1 130
Macrotermes lilljeborgi 143
Macrotermes bellicosus 19
Microtermes sp. 38
Ancistrotermes sp. 140
Macrotermes subhyalinus 64
Odontotermes silvicolus 6
Acanthotermes acanthotorax Pauls
Odontotermes sp.4 110
Odontotermes sp. 303
Odontotermes oblongatus 162
Odontotermes sarawakensis 167
Macrotermes bellicosus 8
Odontotermes billitori 168
Macrotermes malacensis 160
Macrotermes nobilis 569
Microtermes sp. 107
Macrotermes muelleri Corinnes
Microtermes sp. 3
Macrotermes ahmadi pe5
Macrotermes subhyalinus 5
Protermes minutus 129
Ancistrotermes cavitorax 34
Synacanthotermes heterodon 118
Labritermes butelreepeni 169
Odontotermes javanicus 165
Microtermes sp. 146
Odontotermes nilensis 93
Odontotermes lateritius 39
Ancistrotermes cavitorax 46
Odontotermes lateritius 81
Acanthotermes acanthotorax 136
Hypotermes xenotermitis 166
Ancistro Odonto sp. 164
Odontotermes sp.3 126
Foraminitermes sp. 159
43
Microtermes sp. 103
tree 5
Macrotermes subhyalinus 64
Microtermes sp. 3
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes sp.4 110
Odontotermes nilensis 93
Odontotermes sp.3 126
Macrotermes bellicosus 19
Odontotermes minutus 161
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Hypotermes xenotermitis 166
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Odontotermes silvicolus 6
Microtermes sp. 146
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Synacanthotermes heterodon 118
Odontotermes sp.1 130
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Ancistrotermes cavitorax 34
Labritermes butelreepeni 169
Microtermes sp. 38
Microtermes sp. 107
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
44
Microtermes sp. 103
tree 6
Macrotermes subhyalinus 64
Microtermes sp. 3
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes sp.4 110
Odontotermes nilensis 93
Odontotermes sp.3 126
Macrotermes bellicosus 19
Odontotermes minutus 161
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Hypotermes xenotermitis 166
Synacanthotermes heterodon 118
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Odontotermes silvicolus 6
Microtermes sp. 146
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sp.1 130
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Ancistrotermes cavitorax 34
Labritermes butelreepeni 169
Microtermes sp. 38
Microtermes sp. 107
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
45
Microtermes sp. 103
tree 7
Macrotermes subhyalinus 64
Microtermes sp. 3
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Macrotermes bellicosus 19
Odontotermes minutus 161
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes sp.4 110
Odontotermes nilensis 93
Odontotermes sp.3 126
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Hypotermes xenotermitis 166
Odontotermes silvicolus 6
Microtermes sp. 146
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sp.1 130
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Labritermes butelreepeni 169
Ancistrotermes cavitorax 34
Microtermes sp. 38
Microtermes sp. 107
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
46
Microtermes sp. 103
tree 8
Macrotermes subhyalinus 64
Macrotermes bellicosus 19
Odontotermes minutus 161
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes nilensis 93
Odontotermes sp.4 110
Odontotermes sp.3 126
Microtermes sp. 3
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Hypotermes xenotermitis 166
Synacanthotermes heterodon 118
Odontotermes silvicolus 6
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Microtermes sp. 146
Odontotermes sp.1 130
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Labritermes butelreepeni 169
Ancistrotermes cavitorax 34
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Microtermes sp. 38
Microtermes sp. 107
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
47
Microtermes sp. 103
tree 9
Macrotermes subhyalinus 64
Macrotermes bellicosus 19
Odontotermes minutus 161
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes nilensis 93
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Microtermes sp. 3
Microtermes sp. 107
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Hypotermes xenotermitis 166
Synacanthotermes heterodon 118
Odontotermes silvicolus 6
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sp.1 130
Microtermes sp. 146
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Labritermes butelreepeni 169
Ancistrotermes cavitorax 34
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Microtermes sp. 38
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
48
Microtermes sp. 103
tree 10
Macrotermes subhyalinus 64
Macrotermes bellicosus 19
Odontotermes minutus 161
Protermes minutus 567
Odontotermes lateritius 81
Odontotermes nilensis 93
Odontotermes sp.4 110
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes billitori 168
Odontotermes sp.3 126
Microtermes sp. 3
Microtermes sp. 107
Macrotermes muelleri Corinnes
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Odontotermes silvicolus 6
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sp.1 130
Microtermes sp. 146
Hypotermes xenotermitis 166
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Pseudacanthotermes militaris 134
Acanthotermes acanthotorax 136
Macrotermes bellicosus 8
Labritermes butelreepeni 169
Ancistrotermes cavitorax 34
Protermes minutus 129
Ancistrotermes sp. 140
Macrotermes ahmadi pe5
Microtermes sp. 38
Acanthotermes acanthotorax Pauls
Ancistrotermes cavitorax 46
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Macrotermes lilljeborgi 143
Foraminitermes sp. 159
49
  • Not very stable...
  • Does it get more stable?
  • Plot likelihoods against the number of
    generations...

50
(No Transcript)
51
  • Delete first 2.000 trees (100.000 generations),
    keep the remaining 28.000 (1.400.000
    generations)...
  • Lets look at the first 15 trees in the stable
    fase...

52
Microtermes sp. 103
tree 2001
Microtermes sp. 146
Microtermes sp. 107
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
53
Microtermes sp. 103
tree 2002
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes javanicus 165
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
54
Microtermes sp. 103
tree 2003
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes javanicus 165
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
55
Microtermes sp. 103
tree 2004
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes javanicus 165
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
56
Microtermes sp. 103
tree 2005
Microtermes sp. 146
Microtermes sp. 107
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
57
Microtermes sp. 103
tree 2006
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
58
Microtermes sp. 103
tree 2007
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
59
Microtermes sp. 103
tree 2008
Microtermes sp. 146
Microtermes sp. 107
Microtermes sp. 38
Microtermes sp. 3
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes minutus 161
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Hypotermes xenotermitis 166
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
60
Microtermes sp. 103
tree 2009
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
61
Microtermes sp. 103
tree 2010
Microtermes sp. 146
Microtermes sp. 107
Microtermes sp. 3
Microtermes sp. 38
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
62
Microtermes sp. 103
tree 2011
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes billitori 168
Odontotermes sarawakensis 167
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
63
Microtermes sp. 103
tree 2012
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
64
Microtermes sp. 103
tree 2013
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
65
Microtermes sp. 103
tree 2014
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
66
Microtermes sp. 103
tree 2015
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes sarawakensis 167
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
67
Microtermes sp. 103
tree 2016
Microtermes sp. 107
Microtermes sp. 146
Microtermes sp. 3
Microtermes sp. 38
Macrotermes bellicosus 19
Macrotermes bellicosus 8
Macrotermes muelleri Corinnes
Macrotermes lilljeborgi 143
Macrotermes nobilis 569
Macrotermes subhyalinus 5
Macrotermes subhyalinus 64
Macrotermes ahmadi pe5
Macrotermes malacensis 160
Ancistrotermes cavitorax 34
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Synacanthotermes heterodon 118
Protermes minutus 567
Protermes minutus 129
Odontotermes silvicolus 6
Odontotermes sp.4 110
Odontotermes sp.3 126
Odontotermes lateritius 39
Odontotermes sp. 303
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
Hypotermes xenotermitis 166
Odontotermes oblongatus 162
Ancistro Odonto sp. 164
Odontotermes javanicus 165
Odontotermes billitori 168
Odontotermes sarawakensis 167
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
68
(No Transcript)
69
Microtermes sp. 103
52
100
Microtermes sp. 107
Microtermes sp. 146
Majority rule consensus tree of trees sampled
after the burn in
100
Microtermes sp. 3
Microtermes sp. 38
78
Ancistrotermes cavitorax 34
100
100
Ancistrotermes cavitorax 46
Ancistrotermes sp. 140
Macrotermes bellicosus 19
100
Macrotermes bellicosus 8
82
Macrotermes muelleri Corinnes
97
100
Macrotermes lilljeborgi 143
97
Macrotermes nobilis 569
65
Macrotermes subhyalinus 5
100
Macrotermes subhyalinus 64
83
Macrotermes ahmadi pe5
100
Macrotermes malacensis 160
99
Synacanthotermes heterodon 118
Protermes minutus 567
100
Protermes minutus 129
Odontotermes silvicolus 6
95
Odontotermes sp.4 110
100
Odontotermes sp.3 126
Odontotermes lateritius 39
100
100
Odontotermes sp. 303
100
95
100
Odontotermes nilensis 93
Odontotermes lateritius 81
Odontotermes minutus 161
92
95
Hypotermes xenotermitis 166
100
Odontotermes oblongatus 162
92
100
81
Ancistro Odonto sp. 164
100
Odontotermes javanicus 165
Odontotermes sarawakensis 167
60
100
Odontotermes billitori 168
Odontotermes sp.1 130
Acanthotermes acanthotorax Pauls
100
60
Acanthotermes acanthotorax 136
Pseudacanthotermes militaris 134
Foraminitermes sp. 159
Labritermes butelreepeni 169
70
Differences ML and Bayesian methods
Identical ML estimates, but very different, and
far more informative Bayesian estimates!
71
Example the evolution of fungus-growing termites
and their mutualistic fungal symbionts
72
Some facts
  • Macrotermitinae one of four subfamilies
    Termitidae
  • 11 genera, 330 species
  • Obligatory dependent on fungi of the
    basidiomycete genus Termitomyces

73
fungus comb
digestion
74
Photograph by Birgith Pedersen
75
Photographs by Karen Machielsen
76
Photograph by Karen Machielsen
77
(No Transcript)
78
(Fungus growing Fungus growing ants)
termites
79
The actual work...
80
Phylogenies
  • Termites COI (mitochondrial)
  • Fungi two ribosomal genes (nuclear and
    mitochondrial) Specific fungal primers
    developed use of termite guts as source for
    fungal DNA
  • Analysis of DNA sequences with Bayesian techniques

81
51 68
Mi. sp.3
100 100
Mi. sp.3
100 96
100 88
Mi. sp.3
A
100 99
Mi. sp.1
medius
80 lt50
Mi. sp.2
63 lt50
(5 Mi 5 An 2 Sy)
100 100
An. cavithorax
100 100
An. cavithorax
An. crucifer
80 lt50
Sy. heterodon
100 100
Ma. bellicosus
64 58
86 lt50
98 68
Ma. bellicosus
100 66
Ma. ahmadi
B
Termito- myces symbiont clade
Ma. malacensis
97 60
62 lt50
96 89
100 100
Ma. muelleri
100 100
Ma. lilljeborgi
100 86
66 lt50
Ma. nobilis
100 76
100 100
Ma. subhyalinus
98 lt50
53 lt50
Ma. subhyalinus
aurantiacus
Od. sp.1
100 81
origin of fungus growing
63 lt50
Od. billitoni
titanicus
100 97
Od. sarawakensis
100 82
66 63
100 93
Od. javanicus
79 lt50
93 61
100 lt50
Od. sp.5
91 69
robustus
100 52
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