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

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Presentation on theme: "How to estimate phylogenies? On parsimony, likelihood and probability. Duur Aanen."— Presentation transcript:

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

2 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 Overview

3 Basics Phylogeny = evolutionary history of a group Phylogenetic tree: graphical representation (phylogenetic reconstruction ABC

4 A B C Unrooted tree

5 CBA Rooted tree

6 A B C

7 A B C CBA

8 A B C BCA CBA

9 A B C ACB CBA BCA

10 A B C ACB CBA BCA

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 hamster mouse rathamstermouse ratmousehamster mouserat

13 Gorilla ?

14 rat hamster mouse rathamstermouse hamsterrat gorilla hamstermouserat

15 hamster mouse hamsterrat gorilla rathamstermouse ! gorilla hamster mouserat

16 CBA AB: monophyletic group: A and B share a unique common ancestor

17 CBA BC: no monophyletic group: B and C do not share a unique common ancestor

18 Outgroup: Example: evolutionary history of three species: 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 3:G  T 7:A  T

25 111 123456789012 Chimp ATTCGAGTAGCT Human ATTCGAGTAGCT Gorilla ATGCGAGTAGCT Orang-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 (p=0.8) but we don’t know which one Experiment: 10 tosses with 1 of the 10 coins: HHHHHHHHHH Likelihood: Pr [data | hypothesis] Pr [10H | biased] = 0.8 10 = 0.107 Pr [10H | fair] = 0.5 10 = 0.00098 Maximum Likelihood estimate: the coin is biased!

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. sequencesno. possible rooted trees 2 13 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 2113354829308321145237289349456774432829304974 6389294775489579847592843759314562131843276117 4912347721241323233245569964443827487648712865 2143778687234129346123462394984237415736553232 2518798537837558885200938452003255000329843122 001192827437745585983493487551798753932 !!! No. of possible rooted trees

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 (p=0.8) but we don’t 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 = pr[10H|biased]*pr[biased] / [ pr[10H|biased]*pr[biased] + pr[10H|biased]*pr[unbiased] ]  Posterior probability that coin is biased = 0.92 (Remember: Likelihood: Pr [data | hypothesis], Pr [10H | biased] = 0.8 10 = 0.107, Pr [10H | fair] = 0.5 10 = 0.00098)

34 For trees... Pr[tree|data] 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 50 th tree (  30.000 trees) The first 10 trees sampled...

39 Microtermes sp. 103 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 tree 1

40 Microtermes sp. 103 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 tree 2

41 Microtermes sp. 103 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 tree 3

42 Microtermes sp. 103 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 tree 4

43 Microtermes sp. 103 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 tree 5

44 Microtermes sp. 103 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 tree 6

45 Microtermes sp. 103 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 tree 7

46 Microtermes sp. 103 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 tree 8

47 Microtermes sp. 103 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 tree 9

48 Microtermes sp. 103 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 tree 10

49 Not very stable... Does it get more stable? Plot likelihoods against the number of generations...

50

51 Delete first 2.000 trees (100.000 generations), keep the remaining 28.000 (1.400.000 generations)... Let’s look at the first 15 trees in the stable fase...

52 Microtermes sp. 103 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 tree 2001

53 Microtermes sp. 103 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 tree 2002

54 Microtermes sp. 103 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 tree 2003

55 Microtermes sp. 103 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 tree 2004

56 Microtermes sp. 103 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 tree 2005

57 Microtermes sp. 103 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 tree 2006

58 Microtermes sp. 103 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 tree 2007

59 Microtermes sp. 103 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 tree 2008

60 Microtermes sp. 103 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 tree 2009

61 Microtermes sp. 103 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 tree 2010

62 Microtermes sp. 103 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 tree 2011

63 Microtermes sp. 103 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 tree 2012

64 Microtermes sp. 103 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 tree 2013

65 Microtermes sp. 103 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 tree 2014

66 Microtermes sp. 103 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 tree 2015

67 Microtermes sp. 103 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 tree 2016

68

69 Microtermes sp. 103 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 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 169 100 99 82 78 100 52 100 83 97 100 65 100 97 100 92 95 100 95 100 81 100 92 100 60 100 Majority rule consensus tree of trees sampled after the ’burn in’

70 Differences ML and Bayesian methods ML Identical ML estimates, but very different, and far more informative Bayesian estimates! Bayesian 95% posterior probability distribution

71 Example: the evolution of fungus-growing termites and their mutualistic fungal symbionts king

72 Some facts Macrotermitinae one of four subfamilies Termitidae 11 genera, 330 species Obligatory dependent on fungi of the basidiomycete genus Termitomyces

73 ’primary faeces’ Consumption by termites fungus comb digestion

74 Photograph by Birgith Pedersen

75 Photographs by Karen Machielsen

76 Photograph by Karen Machielsen

77

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 Mi. sp.3 Mi. sp.1 Mi. sp.2 An. cavithorax An. crucifer Ma. bellicosus Ma. ahmadi* Ma. malacensis Ma. muelleri Ma. lilljeborgi* Ma. nobilis Ma. subhyalinus Sy. heterodon Ac. acanthothorax Ps. militaris Fo. valens La. butelreepeni origin of fungus growing 100 64 100 58 <50 98 <50 100 88 80 <50 86 <50 100 88 80 <50 100 51 68 97 60 100 66 96 89 66 <50 Lyophyllum semitale Lyophyllum atratum Tephrocybe rancida Pr. minutus 100 Pr. prorepens Od. sp.4 Od. sp.3* Od. latericius ssp.1 Od. sp.2* Od. nilensis Od. latericius ssp.2 Od. minutus Hy. xenotermitis Od. oblongatus* Od. sp.5* Od. javanicus Od. sarawakensis Od. billitoni Od. sp.1 Od. silvicolus 100 93 76 100 93 100 89 91 69 93 51 96 <50 93 <50 100 82 63 <50 100 <50 100 52 79 <50 A D B C An. cavithorax Ma. bellicosus Ac. acanthothorax E 100 Termito- myces symbiont clade 100 97 100 (5 Mi 5 An 2 Sy) medius 100 96 100 99 63 <50 64 58 98 ‘ 68 62 <50 100 86 100 76 100 81 robustus letestui 100 93 66 63 93 61 microcarpus 81 55 53 <50 98 56 100 60 56 100 96 100 90 microcarpus clypeatus 82 <50 52 <50 aurantiacus titanicus 53 <50 100 clypeatus 100


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