A (short) introduction to phylogenetics

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "A (short) introduction to phylogenetics"

Transcription

1 A (short) introduction to phylogenetics Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR Statistics, Millport Field Station 16 Aug /39

2 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 2/39

3 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 3/39

4 Phylogenetics: from the origins... From the first growth of the tree, many a limb and branch has decayed and dropped off; and these fallen branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only in a fossil state. C. Darwin, Notebook, /39

5 Phylogenetics:...to the present phylogenetic trees are part of the standard toolbox of genetic data analysis represent the evolutionary history of a set of (sampled) taxa Bininda-Emonds et al., 2007, Nature. 5/39

6 And the main difference is... Current trees look better! (and some other minor differences) 6/39

7 And the main difference is... Current trees look better! (and some other minor differences) 6/39

8 And the main difference is... Current trees look better! (and some other minor differences) 6/39

9 About the minor differences... DNA sequencing revolution huge data banks freely available (e.g. GenBank) easier, cheaper, faster to obtain DNA sequences increasing number of full genomes available Different ways to exploit this information. 7/39

10 About the minor differences... DNA sequencing revolution huge data banks freely available (e.g. GenBank) easier, cheaper, faster to obtain DNA sequences increasing number of full genomes available Different ways to exploit this information. 7/39

11 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 8/39

12 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... 9/39

13 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... 9/39

14 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... 9/39

15 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... 9/39

16 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... 9/39

17 Genetic changes (substitution) accumulate over time Substitution: replacement of a nucleotide (e.g. a t)...attgtacgtaggatctagg......attgaacgtaggatctagg......attgtacgtaccatctagg... Time...attgaacgtagttgctagg......atcgtacgtaccatctggg... Substitution patterns reflect the evolutionary history 9/39

18 Using substitution patterns to reconstruct the evolutionary history...attaaacgtaggatctagg......attaaacgtaggatctagg......attcatacgtaggatcagg......attgtacgtaggatctttt......attgtacgtaggatctttt......attgcatgtaggatctttt... Reconstructed phylogeny 10/39

19 Using substitution patterns to reconstruct the evolutionary history...attaaacgtaggatctagg......attaaacgtaggatctagg......attcatacgtaggatcagg......attgtacgtaggatctttt......attgtacgtaggatctttt......attgcatgtaggatctttt... Reconstructed phylogeny 10/39

20 Using substitution patterns to reconstruct the evolutionary history...attaaacgtaggatctagg......attaaacgtaggatctagg......attcatacgtaggatcagg......attgtacgtaggatctttt......attgtacgtaggatctttt......attgcatgtaggatctttt... Reconstructed phylogeny Phylogenetics aim to reconstruct evolutionary trees (phylogenies) from genetic sequence data. 10/39

21 Using trees to represent the evolutionary history 11/39

22 Using trees to represent the evolutionary history - "taxa" - "tips" - "leaves" - "Operational Taxonomic Units (OTUs)" 11/39

23 Using trees to represent the evolutionary history Most Recent Common Ancestors (MRCA) - "nodes" - "Hypothetical Taxonomic Units (HTUs)" 11/39

24 Using trees to represent the evolutionary history branch - "edge" - length = amount of evolution (not time, as a rule) - length is optional 11/39

25 Using trees to represent the evolutionary history distances between tips - "patristic" distance: sum of branch lengths - other measures of distance/dissimilarity - vertical axis meaningless 11/39

26 Using trees to represent the evolutionary history Root - oldest part of the tree - defined using an outgroup - optional 11/39

27 Using trees to represent the evolutionary history Root - oldest part of the tree - defined using an outgroup - optional How to we build them? 11/39

28 Workflow Prepare data align sequences: alignment software + manual refinement Build the tree distance-based methods maximum parsimony likelihood-based methods (ML, Bayesian) Analyse the tree assess uncertainty test phylogenetic signal model trait evolution... 12/39

29 Workflow Prepare data align sequences: alignment software + manual refinement Build the tree distance-based methods maximum parsimony likelihood-based methods (ML, Bayesian) Analyse the tree assess uncertainty test phylogenetic signal model trait evolution... 12/39

30 Workflow Prepare data align sequences: alignment software + manual refinement Build the tree distance-based methods maximum parsimony likelihood-based methods (ML, Bayesian) Analyse the tree assess uncertainty test phylogenetic signal model trait evolution... 12/39

31 Workflow Prepare data align sequences: alignment software + manual refinement Build the tree distance-based methods maximum parsimony likelihood-based methods (ML, Bayesian) Analyse the tree assess uncertainty test phylogenetic signal model trait evolution... 12/39

32 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 13/39

33 Distance-based phylogenetic reconstruction Approaches relying on agglomerative clustering algorithms (e.g. Single linkage, UPGMA, Neighbor-Joining) Rationale 1. compute pairwise genetic distances D 2. group closest sequences 3. update D 4. go back to 2) until all sequences are grouped 14/39

34 Distance-based phylogenetic reconstruction 15/39

35 Distance-based phylogenetic reconstruction 15/39

36 Distance-based phylogenetic reconstruction 15/39

37 Distance-based phylogenetic reconstruction 15/39

38 Distance-based phylogenetic reconstruction 15/39

39 Distance-based phylogenetic reconstruction 15/39

40 What is the distance between a node and tips? Hierarchical clustering: k D =... k,g single linkage: D k,g = min(d k,i, D k,j ) complete linkage: D k,g = max(d k,i, D k,j ) g i D i,j j UPGMA: D k,g = D k,i+d k,j 2 Neighbor joining: Transforms original distances to account for heterogeneous rates of evolution. 16/39

41 What is the distance between a node and tips? Hierarchical clustering: k D =... k,g single linkage: D k,g = min(d k,i, D k,j ) complete linkage: D k,g = max(d k,i, D k,j ) g i D i,j j UPGMA: D k,g = D k,i+d k,j 2 Neighbor joining: Transforms original distances to account for heterogeneous rates of evolution. 16/39

42 What is the distance between a node and tips? Hierarchical clustering: k D =... k,g single linkage: D k,g = min(d k,i, D k,j ) complete linkage: D k,g = max(d k,i, D k,j ) g i D i,j j UPGMA: D k,g = D k,i+d k,j 2 Neighbor joining: Transforms original distances to account for heterogeneous rates of evolution. 16/39

43 What is the distance between a node and tips? Hierarchical clustering: k D =... k,g single linkage: D k,g = min(d k,i, D k,j ) complete linkage: D k,g = max(d k,i, D k,j ) g i D i,j j UPGMA: D k,g = D k,i+d k,j 2 Neighbor joining: Transforms original distances to account for heterogeneous rates of evolution. 16/39

44 What is the distance between a node and tips? Hierarchical clustering: k D =... k,g single linkage: D k,g = min(d k,i, D k,j ) complete linkage: D k,g = max(d k,i, D k,j ) g i D i,j j UPGMA: D k,g = D k,i+d k,j 2 Neighbor joining: Transforms original distances to account for heterogeneous rates of evolution. 16/39

45 Distance-based phylogenetic reconstruction Advantages simple flexible (many distances and clustering algorithms) fast and scalable (applicable to large datasets) Limitations sensitive to distance/clustering chosen evolutionary rates are not estimated no measure of uncertainty for the tree obtained 17/39

46 Distance-based phylogenetic reconstruction Advantages simple flexible (many distances and clustering algorithms) fast and scalable (applicable to large datasets) Limitations sensitive to distance/clustering chosen evolutionary rates are not estimated no measure of uncertainty for the tree obtained 17/39

47 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 18/39

48 Maximum parsimony phylogenies Approaches relying on finding the tree with the smallest number of character changes (substitutions) Rationale 1. start from a pre-defined tree 2. compute initial parsimony score 3. permute branches and compute parsimony score 4. accept new tree if the parsimony score is improved 5. go back to 3) until convergence 19/39

49 Maximum parsimony phylogenies score: 8 score: 6 Initial tree score: 5 20/39

50 Maximum parsimony phylogenies score: 8 score: 6 Initial tree score: 5 20/39

51 Maximum parsimony phylogenies score: 8 score: 6 Initial tree score: 5 20/39

52 Maximum parsimony phylogenies score: 8 score: 6 Initial tree score: 5 20/39

53 Maximum parsimony phylogenies score: 8 score: 6 Initial tree score: 5 20/39

54 Maximum parsimony phylogenies Advantages applicable to any discontinuous characters (not just DNA) intuitive explanation: simplest evolutionary scenario Limitations evolutionary rates are not estimated no measure of uncertainty for the tree obtained computer-intensive different types of substitutions ignored evolution not necessarily parsimonious sensitive to heterogeneous rates of evolution (long branch attraction) 21/39

55 Maximum parsimony phylogenies Advantages applicable to any discontinuous characters (not just DNA) intuitive explanation: simplest evolutionary scenario Limitations evolutionary rates are not estimated no measure of uncertainty for the tree obtained computer-intensive different types of substitutions ignored evolution not necessarily parsimonious sensitive to heterogeneous rates of evolution (long branch attraction) 21/39

56 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 22/39

57 Likelihood-based phylogenies (ML / Bayesian) Approaches relying on a model of sequence evolution: ML: find tree and evolutionary rates with highest likelihood Bayesian: find tree and evolutionary rates to posterior probability Rationale 1. start from a pre-defined tree 2. compute initial likelihood/posterior 3. permute branches, sample new parameters and compute likelihood/posterior 4. accept new tree and parameters based on likelihood/posterior improvement 5. go back to 3) until convergence 23/39

58 Likelihood-based phylogenies (ML / Bayesian) Approaches relying on a model of sequence evolution: ML: find tree and evolutionary rates with highest likelihood Bayesian: find tree and evolutionary rates to posterior probability Rationale 1. start from a pre-defined tree 2. compute initial likelihood/posterior 3. permute branches, sample new parameters and compute likelihood/posterior 4. accept new tree and parameters based on likelihood/posterior improvement 5. go back to 3) until convergence 23/39

59 Likelihood-based phylogenies (ML / Bayesian) Likelihood / Posterior Density 24/39

60 Likelihood-based phylogenies (ML / Bayesian) Advantages very flexible consistent with a model of evolution statistically consistent (model comparison) parameter estimation (Bayesian) several trees measure of uncertainty Limitations computer-intensive choice of the model of evolution (ML) no measure of uncertainty for the tree obtained (Bayesian) need to find a consensus tree 25/39

61 Likelihood-based phylogenies (ML / Bayesian) Advantages very flexible consistent with a model of evolution statistically consistent (model comparison) parameter estimation (Bayesian) several trees measure of uncertainty Limitations computer-intensive choice of the model of evolution (ML) no measure of uncertainty for the tree obtained (Bayesian) need to find a consensus tree 25/39

62 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 26/39

63 How do we know the tree is robust? Main issue: assess the uncertainty of the tree topology / individual nodes Approaches ML: model selection to compare trees (whole tree) Bayesian methods: between-samples variability (individual nodes) any method: bootstrap (individual nodes) 27/39

64 How do we know the tree is robust? Main issue: assess the uncertainty of the tree topology / individual nodes Approaches ML: model selection to compare trees (whole tree) Bayesian methods: between-samples variability (individual nodes) any method: bootstrap (individual nodes) 27/39

65 How do we know the tree is robust? Main issue: assess the uncertainty of the tree topology / individual nodes Approaches ML: model selection to compare trees (whole tree) Bayesian methods: between-samples variability (individual nodes) any method: bootstrap (individual nodes) 27/39

66 How do we know the tree is robust? Main issue: assess the uncertainty of the tree topology / individual nodes Approaches ML: model selection to compare trees (whole tree) Bayesian methods: between-samples variability (individual nodes) any method: bootstrap (individual nodes) 27/39

67 How do we know the tree is robust? Main issue: assess the uncertainty of the tree topology / individual nodes Approaches ML: model selection to compare trees (whole tree) Bayesian methods: between-samples variability (individual nodes) any method: bootstrap (individual nodes) 27/39

68 Bootstrapping phylogenies assess variability due to sampling the genome and conflicting signals relies on analysing resampled datasets Rationale 1. obtain a reference tree 2. resample the sites with replacement 3. obtain a tree for the resampled dataset 4. go back to 2) until the desired number of bootstrapped trees is attained 5. compute the frequency of each bifurcation of the reference tree occuring in bootstrapped trees 28/39

69 Bootstrapping phylogenies assess variability due to sampling the genome and conflicting signals relies on analysing resampled datasets Rationale 1. obtain a reference tree 2. resample the sites with replacement 3. obtain a tree for the resampled dataset 4. go back to 2) until the desired number of bootstrapped trees is attained 5. compute the frequency of each bifurcation of the reference tree occuring in bootstrapped trees 28/39

70 Bootstrapping phylogenies...attaaacgtaggatctagg......attaaacgtaggatctagg......attcatacgtaggatcagg......attgtacgtaggatctttt......attgtacgtaggatctttt......attgcatgtaggatctttt... Reconstructed phylogeny sampling sites with replacement compare topologies...ttttaaaccatggatctagg......ttttaaaccatggatctagg......ttttaaaccatggatctagg......ttttaaaccatggatctagg......ttttaaaccatggatctagg......atttcatacgtaggatcagg......ttttaaaccatggatctagg......atttcatacgtaggatcagg......ttttaaaccatggatctagg......atttcatacgtaggatcagg......aaatgtaccatggatcttgt......atttcatacgtaggatcagg......aaatgtaccatggatcttgt......atttcatacgtaggatcagg......aaatgtaccatggatcttgt......aaatgtaccatggatcttgt......aaatgtaccatggatcttgt......aaatgcatcatggatcttgt......aaatgtaccatggatcttgt......aaatgcatcatggatcttgt......aaatgtaccatggatcttgt......aaatgcatcatggatcttgt......aaatgcatcatggatcttgt......aaatgcatcatggatcttgt... Reconstructed phylogeny Reconstructed phylogeny Reconstructed phylogeny Reconstructed phylogeny Reconstructed phylogeny 29/39

71 Bootstrapping phylogenies Advantages standard simple to implement Limitations possibly computer-intensive assumes that the genome has been sampled randomly (often wrong) 30/39

72 Bootstrapping phylogenies Advantages standard simple to implement Limitations possibly computer-intensive assumes that the genome has been sampled randomly (often wrong) 30/39

73 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 31/39

74 Plotting trees as rooted Never plot an unrooted tree as rooted /39

75 Plotting trees as rooted Never plot an unrooted tree as rooted /39

76 Interpreting distances 33/39

77 Interpreting distances 33/39

78 Interpreting distances meaningless meaningful distance = sum of branch lengths 33/39

79 The paradox of divergent clusters MRCA and genetic distances may give different information. 34/39

80 The paradox of divergent clusters D(red, red)>d(red,blue) MRCA and genetic distances may give different information. 34/39

81 The paradox of divergent clusters D(red, red)>d(red,blue) MRCA and genetic distances may give different information. 34/39

82 Taking uncertainty into account 193 HIV 1 sequences from DRC (Strimmer & Pybus 2001) At best, the tree is an estimate of the likely evolutionary history of the taxa studied. 35/39

83 Taking uncertainty into account 193 HIV 1 sequences from DRC (Strimmer & Pybus 2001) Collapsed tree (threshold length 0.01) At best, the tree is an estimate of the likely evolutionary history of the taxa studied. 35/39

84 Taking uncertainty into account 193 HIV 1 sequences from DRC (Strimmer & Pybus 2001) Collapsed tree (threshold length 0.01) At best, the tree is an estimate of the likely evolutionary history of the taxa studied. 35/39

85 (Over, Mis)Interpreting temporal trends t6 t62 t4 t48 t72 t29t14 t83 t39 t69 t96 t63 t44 t24 t51 t95 t85 t68 t92 t87 t31 t81 t99 t73 t30t25 t64 t46 t33 t54 t10 t26 t76 t59 t16 t32 t100 t91 t77 t42 t36 t58 t98 t56 t74 t65t79 t37 t80 t12t93 t78 t90 t18 t11 t94 t5 t45 t60t67 t53 t88 t52 t22 t27 t23 t38 t40 t3 t15 t13 t61 t55 t35 t89 t75 t86 t70 t66 t34 t2 t17 t28 t47 t19 t43 t41 t82 t49 t1 t84 t20 t97 t21 t7 t71 t50 t Time trees only make sense under a near-perfect molecular clock. 36/39

86 (Over, Mis)Interpreting temporal trends t6 t62 t4 t48 t72 t29t14 t83 t39 t69 t96 t63 t44 t24 t51 t95 t85 t68 t92 t87 t31 t81 t99 t73 t30t25 t64 t46 t33 t54 t10 t26 t76 t59 t16 t32 t100 t91 t77 t42 t36 t58 t98 t56 t74 t65t79 t37 t80 t12t93 t78 t90 t18 t11 t94 t5 t45 t60t67 t53 t88 t52 t22 t27 t23 t38 t40 t3 t15 t13 t61 t55 t35 t89 t75 t86 t70 t66 t34 t2 t17 t28 t47 t19 t43 t41 t82 t49 t1 t84 t20 t97 t21 t7 t71 t50 t57 Mutations to the root > anova(lm(d.root~-1+t.root)) anova(lm(d.root~-1+t.root)) Analysis of Variance Table Response: d.root Df Sum Sq Mean Sq F value Pr(>F) t.root < 2.2e-16 *** Residuals Time to the root Time trees only make sense under a near-perfect molecular clock. 36/39

87 (Over, Mis)Interpreting temporal trends t6 t62 t4 t48 t72 t29t14 t83 t39 t69 t96 t63 t44 t24 t51 t95 t85 t68 t92 t87 t31 t81 t99 t73 t30t25 t64 t46 t33 t54 t10 t26 t76 t59 t16 t32 t100 t91 t77 t42 t36 t58 t98 t56 t74 t65t79 t37 t80 t12t93 t78 t90 t18 t11 t94 t5 t45 t60t67 t53 t88 t52 t22 t27 t23 t38 t40 t3 t15 t13 t61 t55 t35 t89 t75 t86 t70 t66 t34 t2 t17 t28 t47 t19 t43 t41 t82 t49 t1 t84 t20 t97 t21 t7 t71 t50 t57 Mutations to the root > anova(lm(d.root~-1+t.root)) anova(lm(d.root~-1+t.root)) Analysis of Variance Table Response: d.root Df Sum Sq Mean Sq F value Pr(>F) t.root < 2.2e-16 *** Residuals Time to the root Time trees only make sense under a near-perfect molecular clock. 36/39

88 Context Phylogenies... Distance trees Parsimony Likelihood/Bayesian Uncertainty Pitfalls & best practices And more... Outline 37/39

89 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

90 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

91 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

92 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

93 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

94 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

95 This is only the beginning Many things can be done with trees estimate divergence time model trait evolution (phylogenetic comparative method) reconstruct ancestral states measure diversity infer past demographics/effective population size (coalescence)... and also, other approaches than phylogenetics to analyse genetic data 38/39

96 Time to get your hands dirty! The pdf of the practical is online: or Google adegenet documents GDAR August /39

Multivariate analysis of genetic data exploring group diversity

Multivariate analysis of genetic data exploring group diversity Multivariate analysis of genetic data exploring group diversity Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR

More information

Constructing Evolutionary/Phylogenetic Trees

Constructing Evolutionary/Phylogenetic Trees Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood

More information

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the

More information

Constructing Evolutionary/Phylogenetic Trees

Constructing Evolutionary/Phylogenetic Trees Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood

More information

Dr. Amira A. AL-Hosary

Dr. Amira A. AL-Hosary Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological

More information

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological

More information

Algorithms in Bioinformatics

Algorithms in Bioinformatics Algorithms in Bioinformatics Sami Khuri Department of Computer Science San José State University San José, California, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri Distance Methods Character Methods

More information

Phylogenetic Tree Reconstruction

Phylogenetic Tree Reconstruction I519 Introduction to Bioinformatics, 2011 Phylogenetic Tree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Evolution theory Speciation Evolution of new organisms is driven

More information

BINF6201/8201. Molecular phylogenetic methods

BINF6201/8201. Molecular phylogenetic methods BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics

More information

Phylogenetic inference

Phylogenetic inference Phylogenetic inference Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, March 7 th 016 After this lecture, you can discuss (dis-) advantages of different information types

More information

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying

More information

"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky

Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally

More information

Phylogenetic Analysis. Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center

Phylogenetic Analysis. Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center Phylogenetic Analysis Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center Outline Basic Concepts Tree Construction Methods Distance-based methods

More information

Phylogenetic Trees. Phylogenetic Trees Five. Phylogeny: Inference Tool. Phylogeny Terminology. Picture of Last Quagga. Importance of Phylogeny 5.

Phylogenetic Trees. Phylogenetic Trees Five. Phylogeny: Inference Tool. Phylogeny Terminology. Picture of Last Quagga. Importance of Phylogeny 5. Five Sami Khuri Department of Computer Science San José State University San José, California, USA sami.khuri@sjsu.edu v Distance Methods v Character Methods v Molecular Clock v UPGMA v Maximum Parsimony

More information

How to read and make phylogenetic trees Zuzana Starostová

How to read and make phylogenetic trees Zuzana Starostová How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation

More information

Phylogenetic analyses. Kirsi Kostamo

Phylogenetic analyses. Kirsi Kostamo Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,

More information

EVOLUTIONARY DISTANCES

EVOLUTIONARY DISTANCES EVOLUTIONARY DISTANCES FROM STRINGS TO TREES Luca Bortolussi 1 1 Dipartimento di Matematica ed Informatica Università degli studi di Trieste luca@dmi.units.it Trieste, 14 th November 2007 OUTLINE 1 STRINGS:

More information

Theory of Evolution Charles Darwin

Theory of Evolution Charles Darwin Theory of Evolution Charles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (83-36) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties

More information

Bioinformatics tools for phylogeny and visualization. Yanbin Yin

Bioinformatics tools for phylogeny and visualization. Yanbin Yin Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and

More information

Multivariate analysis of genetic data: exploring groups diversity

Multivariate analysis of genetic data: exploring groups diversity Multivariate analysis of genetic data: exploring groups diversity T. Jombart Imperial College London Bogota 01-12-2010 1/42 Outline Introduction Clustering algorithms Hierarchical clustering K-means Multivariate

More information

Evolutionary Tree Analysis. Overview

Evolutionary Tree Analysis. Overview CSI/BINF 5330 Evolutionary Tree Analysis Young-Rae Cho Associate Professor Department of Computer Science Baylor University Overview Backgrounds Distance-Based Evolutionary Tree Reconstruction Character-Based

More information

How should we organize the diversity of animal life?

How should we organize the diversity of animal life? How should we organize the diversity of animal life? The difference between Taxonomy Linneaus, and Cladistics Darwin What are phylogenies? How do we read them? How do we estimate them? Classification (Taxonomy)

More information

What is Phylogenetics

What is Phylogenetics What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)

More information

Michael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D

Michael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D 7.91 Lecture #5 Database Searching & Molecular Phylogenetics Michael Yaffe B C D B C D (((,B)C)D) Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood

More information

Phylogene)cs. IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, Joyce Nzioki

Phylogene)cs. IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, Joyce Nzioki Phylogene)cs IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, 2016 Joyce Nzioki Phylogenetics The study of evolutionary relatedness of organisms. Derived from two Greek words:» Phle/Phylon: Tribe/Race» Genetikos:

More information

C3020 Molecular Evolution. Exercises #3: Phylogenetics

C3020 Molecular Evolution. Exercises #3: Phylogenetics C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from

More information

Phylogeny: building the tree of life

Phylogeny: building the tree of life Phylogeny: building the tree of life Dr. Fayyaz ul Amir Afsar Minhas Department of Computer and Information Sciences Pakistan Institute of Engineering & Applied Sciences PO Nilore, Islamabad, Pakistan

More information

Phylogenetic Trees. What They Are Why We Do It & How To Do It. Presented by Amy Harris Dr Brad Morantz

Phylogenetic Trees. What They Are Why We Do It & How To Do It. Presented by Amy Harris Dr Brad Morantz Phylogenetic Trees What They Are Why We Do It & How To Do It Presented by Amy Harris Dr Brad Morantz Overview What is a phylogenetic tree Why do we do it How do we do it Methods and programs Parallels

More information

Biology 559R: Introduction to Phylogenetic Comparative Methods Topics for this week (Jan 27 & 29):

Biology 559R: Introduction to Phylogenetic Comparative Methods Topics for this week (Jan 27 & 29): Biology 559R: Introduction to Phylogenetic Comparative Methods Topics for this week (Jan 27 & 29): Statistical estimation of models of sequence evolution Phylogenetic inference using maximum likelihood:

More information

Phylogenetic inference: from sequences to trees

Phylogenetic inference: from sequences to trees W ESTFÄLISCHE W ESTFÄLISCHE W ILHELMS -U NIVERSITÄT NIVERSITÄT WILHELMS-U ÜNSTER MM ÜNSTER VOLUTIONARY FUNCTIONAL UNCTIONAL GENOMICS ENOMICS EVOLUTIONARY Bioinformatics 1 Phylogenetic inference: from sequences

More information

Multiple Sequence Alignment. Sequences

Multiple Sequence Alignment. Sequences Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe

More information

Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?

Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them? Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them? Carolus Linneaus:Systema Naturae (1735) Swedish botanist &

More information

Tree of Life iological Sequence nalysis Chapter http://tolweb.org/tree/ Phylogenetic Prediction ll organisms on Earth have a common ancestor. ll species are related. The relationship is called a phylogeny

More information

9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)

9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree) I9 Introduction to Bioinformatics, 0 Phylogenetic ree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & omputing, IUB Evolution theory Speciation Evolution of new organisms is driven by

More information

Phylogenetics. BIOL 7711 Computational Bioscience

Phylogenetics. BIOL 7711 Computational Bioscience Consortium for Comparative Genomics! University of Colorado School of Medicine Phylogenetics BIOL 7711 Computational Bioscience Biochemistry and Molecular Genetics Computational Bioscience Program Consortium

More information

Lecture 6 Phylogenetic Inference

Lecture 6 Phylogenetic Inference Lecture 6 Phylogenetic Inference From Darwin s notebook in 1837 Charles Darwin Willi Hennig From The Origin in 1859 Cladistics Phylogenetic inference Willi Hennig, Cladistics 1. Clade, Monophyletic group,

More information

Phylogeny. November 7, 2017

Phylogeny. November 7, 2017 Phylogeny November 7, 2017 Phylogenetics Phylon = tribe/race, genetikos = relative to birth Phylogenetics: study of evolutionary relationships among organisms, sequences, or anything in between Related

More information

Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies

Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies 1 What is phylogeny? Essay written for the course in Markov Chains 2004 Torbjörn Karfunkel Phylogeny is the evolutionary development

More information

Consistency Index (CI)

Consistency Index (CI) Consistency Index (CI) minimum number of changes divided by the number required on the tree. CI=1 if there is no homoplasy negatively correlated with the number of species sampled Retention Index (RI)

More information

Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley

Integrative Biology 200 PRINCIPLES OF PHYLOGENETICS Spring 2018 University of California, Berkeley Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;

More information

THEORY. Based on sequence Length According to the length of sequence being compared it is of following two types

THEORY. Based on sequence Length According to the length of sequence being compared it is of following two types Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between

More information

Phylogeny: traditional and Bayesian approaches

Phylogeny: traditional and Bayesian approaches Phylogeny: traditional and Bayesian approaches 5-Feb-2014 DEKM book Notes from Dr. B. John Holder and Lewis, Nature Reviews Genetics 4, 275-284, 2003 1 Phylogeny A graph depicting the ancestor-descendent

More information

C.DARWIN ( )

C.DARWIN ( ) C.DARWIN (1809-1882) LAMARCK Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation DARWIN All organisms are historically interconnected. Their relationships

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT Inferring phylogeny Constructing phylogenetic trees Tõnu Margus Contents What is phylogeny? How/why it is possible to infer it? Representing evolutionary relationships on trees What type questions questions

More information

Intraspecific gene genealogies: trees grafting into networks

Intraspecific gene genealogies: trees grafting into networks Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation

More information

Phylogenetic trees 07/10/13

Phylogenetic trees 07/10/13 Phylogenetic trees 07/10/13 A tree is the only figure to occur in On the Origin of Species by Charles Darwin. It is a graphical representation of the evolutionary relationships among entities that share

More information

Multivariate analysis of genetic data an introduction

Multivariate analysis of genetic data an introduction Multivariate analysis of genetic data an introduction Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Imperial College London Population genomics in Lausanne 23 Aug 2016 1/25 Outline Multivariate

More information

Classification and Phylogeny

Classification and Phylogeny Classification and Phylogeny The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme

More information

Phylogenetics: Building Phylogenetic Trees

Phylogenetics: Building Phylogenetic Trees 1 Phylogenetics: Building Phylogenetic Trees COMP 571 Luay Nakhleh, Rice University 2 Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary model should

More information

Molecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço

Molecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço Molecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço jcarrico@fm.ul.pt Charles Darwin (1809-1882) Charles Darwin s tree of life in Notebook B, 1837-1838 Ernst Haeckel (1934-1919)

More information

Evolutionary Models. Evolutionary Models

Evolutionary Models. Evolutionary Models Edit Operators In standard pairwise alignment, what are the allowed edit operators that transform one sequence into the other? Describe how each of these edit operations are represented on a sequence alignment

More information

Systematics - Bio 615

Systematics - Bio 615 Bayesian Phylogenetic Inference 1. Introduction, history 2. Advantages over ML 3. Bayes Rule 4. The Priors 5. Marginal vs Joint estimation 6. MCMC Derek S. Sikes University of Alaska 7. Posteriors vs Bootstrap

More information

Classification and Phylogeny

Classification and Phylogeny Classification and Phylogeny The diversity it of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme

More information

CHAPTERS 24-25: Evidence for Evolution and Phylogeny

CHAPTERS 24-25: Evidence for Evolution and Phylogeny CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology

More information

Phylogenetics: Building Phylogenetic Trees. COMP Fall 2010 Luay Nakhleh, Rice University

Phylogenetics: Building Phylogenetic Trees. COMP Fall 2010 Luay Nakhleh, Rice University Phylogenetics: Building Phylogenetic Trees COMP 571 - Fall 2010 Luay Nakhleh, Rice University Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary

More information

Concepts and Methods in Molecular Divergence Time Estimation

Concepts and Methods in Molecular Divergence Time Estimation Concepts and Methods in Molecular Divergence Time Estimation 26 November 2012 Prashant P. Sharma American Museum of Natural History Overview 1. Why do we date trees? 2. The molecular clock 3. Local clocks

More information

Anatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses

Anatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses Anatomy of a tree outgroup: an early branching relative of the interest groups sister taxa: taxa derived from the same recent ancestor polytomy: >2 taxa emerge from a node Anatomy of a tree clade is group

More information

Page 1. Evolutionary Trees. Why build evolutionary tree? Outline

Page 1. Evolutionary Trees. Why build evolutionary tree? Outline Page Evolutionary Trees Russ. ltman MI S 7 Outline. Why build evolutionary trees?. istance-based vs. character-based methods. istance-based: Ultrametric Trees dditive Trees. haracter-based: Perfect phylogeny

More information

Introduction to characters and parsimony analysis

Introduction to characters and parsimony analysis Introduction to characters and parsimony analysis Genetic Relationships Genetic relationships exist between individuals within populations These include ancestordescendent relationships and more indirect

More information

Homework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics:

Homework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics: Homework Assignment, Evolutionary Systems Biology, Spring 2009. Homework Part I: Phylogenetics: Introduction. The objective of this assignment is to understand the basics of phylogenetic relationships

More information

Bioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony

Bioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony ioinformatics -- lecture 9 Phylogenetic trees istance-based tree building Parsimony (,(,(,))) rees can be represented in "parenthesis notation". Each set of parentheses represents a branch-point (bifurcation),

More information

Phylogenetics: Bayesian Phylogenetic Analysis. COMP Spring 2015 Luay Nakhleh, Rice University

Phylogenetics: Bayesian Phylogenetic Analysis. COMP Spring 2015 Luay Nakhleh, Rice University Phylogenetics: Bayesian Phylogenetic Analysis COMP 571 - Spring 2015 Luay Nakhleh, Rice University Bayes Rule P(X = x Y = y) = P(X = x, Y = y) P(Y = y) = P(X = x)p(y = y X = x) P x P(X = x 0 )P(Y = y X

More information

Molecular Evolution, course # Final Exam, May 3, 2006

Molecular Evolution, course # Final Exam, May 3, 2006 Molecular Evolution, course #27615 Final Exam, May 3, 2006 This exam includes a total of 12 problems on 7 pages (including this cover page). The maximum number of points obtainable is 150, and at least

More information

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species

More information

Estimating Phylogenies (Evolutionary Trees) II. Biol4230 Thurs, March 2, 2017 Bill Pearson Jordan 6-057

Estimating Phylogenies (Evolutionary Trees) II. Biol4230 Thurs, March 2, 2017 Bill Pearson Jordan 6-057 Estimating Phylogenies (Evolutionary Trees) II Biol4230 Thurs, March 2, 2017 Bill Pearson wrp@virginia.edu 4-2818 Jordan 6-057 Tree estimation strategies: Parsimony?no model, simply count minimum number

More information

molecular evolution and phylogenetics

molecular evolution and phylogenetics molecular evolution and phylogenetics Charlotte Darby Computational Genomics: Applied Comparative Genomics 2.13.18 https://www.thinglink.com/scene/762084640000311296 Internal node Root TIME Branch Leaves

More information

Inferring phylogeny. Today s topics. Milestones of molecular evolution studies Contributions to molecular evolution

Inferring phylogeny. Today s topics. Milestones of molecular evolution studies Contributions to molecular evolution Today s topics Inferring phylogeny Introduction! Distance methods! Parsimony method!"#$%&'(!)* +,-.'/01!23454(6!7!2845*0&4'9#6!:&454(6 ;?@AB=C?DEF Overview of phylogenetic inferences Methodology Methods

More information

A Phylogenetic Network Construction due to Constrained Recombination

A Phylogenetic Network Construction due to Constrained Recombination A Phylogenetic Network Construction due to Constrained Recombination Mohd. Abdul Hai Zahid Research Scholar Research Supervisors: Dr. R.C. Joshi Dr. Ankush Mittal Department of Electronics and Computer

More information

Molecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016

Molecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016 Molecular phylogeny - Using molecular sequences to infer evolutionary relationships Tore Samuelsson Feb 2016 Molecular phylogeny is being used in the identification and characterization of new pathogens,

More information

Today's project. Test input data Six alignments (from six independent markers) of Curcuma species

Today's project. Test input data Six alignments (from six independent markers) of Curcuma species DNA sequences II Analyses of multiple sequence data datasets, incongruence tests, gene trees vs. species tree reconstruction, networks, detection of hybrid species DNA sequences II Test of congruence of

More information

An Adaptive Association Test for Microbiome Data

An Adaptive Association Test for Microbiome Data An Adaptive Association Test for Microbiome Data Chong Wu 1, Jun Chen 2, Junghi 1 Kim and Wei Pan 1 1 Division of Biostatistics, School of Public Health, University of Minnesota; 2 Division of Biomedical

More information

Phylogeny and Evolution. Gina Cannarozzi ETH Zurich Institute of Computational Science

Phylogeny and Evolution. Gina Cannarozzi ETH Zurich Institute of Computational Science Phylogeny and Evolution Gina Cannarozzi ETH Zurich Institute of Computational Science History Aristotle (384-322 BC) classified animals. He found that dolphins do not belong to the fish but to the mammals.

More information

Is the equal branch length model a parsimony model?

Is the equal branch length model a parsimony model? Table 1: n approximation of the probability of data patterns on the tree shown in figure?? made by dropping terms that do not have the minimal exponent for p. Terms that were dropped are shown in red;

More information

Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley. Parsimony & Likelihood [draft]

Integrative Biology 200 PRINCIPLES OF PHYLOGENETICS Spring 2016 University of California, Berkeley. Parsimony & Likelihood [draft] Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley K.W. Will Parsimony & Likelihood [draft] 1. Hennig and Parsimony: Hennig was not concerned with parsimony

More information

Phylogeny Tree Algorithms

Phylogeny Tree Algorithms Phylogeny Tree lgorithms Jianlin heng, PhD School of Electrical Engineering and omputer Science University of entral Florida 2006 Free for academic use. opyright @ Jianlin heng & original sources for some

More information

"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley

PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION Integrative Biology 200B Spring 2009 University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley B.D. Mishler Jan. 22, 2009. Trees I. Summary of previous lecture: Hennigian

More information

Bootstrap confidence levels for phylogenetic trees B. Efron, E. Halloran, and S. Holmes, 1996

Bootstrap confidence levels for phylogenetic trees B. Efron, E. Halloran, and S. Holmes, 1996 Bootstrap confidence levels for phylogenetic trees B. Efron, E. Halloran, and S. Holmes, 1996 Following Confidence limits on phylogenies: an approach using the bootstrap, J. Felsenstein, 1985 1 I. Short

More information

Lecture 11 Friday, October 21, 2011

Lecture 11 Friday, October 21, 2011 Lecture 11 Friday, October 21, 2011 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system

More information

Consensus Methods. * You are only responsible for the first two

Consensus Methods. * You are only responsible for the first two Consensus Trees * consensus trees reconcile clades from different trees * consensus is a conservative estimate of phylogeny that emphasizes points of agreement * philosophy: agreement among data sets is

More information

8/23/2014. Phylogeny and the Tree of Life

8/23/2014. Phylogeny and the Tree of Life Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

Chapter 16: Reconstructing and Using Phylogenies

Chapter 16: Reconstructing and Using Phylogenies Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/

More information

Estimating Evolutionary Trees. Phylogenetic Methods

Estimating Evolutionary Trees. Phylogenetic Methods Estimating Evolutionary Trees v if the data are consistent with infinite sites then all methods should yield the same tree v it gets more complicated when there is homoplasy, i.e., parallel or convergent

More information

Theory of Evolution. Charles Darwin

Theory of Evolution. Charles Darwin Theory of Evolution harles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (8-6) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties

More information

Algorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004,

Algorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004, Tracing the Evolution of Numerical Phylogenetics: History, Philosophy, and Significance Adam W. Ferguson Phylogenetic Systematics 26 January 2009 Inferring Phylogenies Historical endeavor Darwin- 1837

More information

Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!

Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Paul has many great tools for teaching phylogenetics at his web site: http://hydrodictyon.eeb.uconn.edu/people/plewis

More information

Chapter 19: Taxonomy, Systematics, and Phylogeny

Chapter 19: Taxonomy, Systematics, and Phylogeny Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand

More information

(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise

(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise Bot 421/521 PHYLOGENETIC ANALYSIS I. Origins A. Hennig 1950 (German edition) Phylogenetic Systematics 1966 B. Zimmerman (Germany, 1930 s) C. Wagner (Michigan, 1920-2000) II. Characters and character states

More information

Phylogenetics: Distance Methods. COMP Spring 2015 Luay Nakhleh, Rice University

Phylogenetics: Distance Methods. COMP Spring 2015 Luay Nakhleh, Rice University Phylogenetics: Distance Methods COMP 571 - Spring 2015 Luay Nakhleh, Rice University Outline Evolutionary models and distance corrections Distance-based methods Evolutionary Models and Distance Correction

More information

Thanks to Paul Lewis and Joe Felsenstein for the use of slides

Thanks to Paul Lewis and Joe Felsenstein for the use of slides Thanks to Paul Lewis and Joe Felsenstein for the use of slides Review Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPGMA infers a tree from a distance

More information

Modern Evolutionary Classification. Section 18-2 pgs

Modern Evolutionary Classification. Section 18-2 pgs Modern Evolutionary Classification Section 18-2 pgs 451-455 Modern Evolutionary Classification In a sense, organisms determine who belongs to their species by choosing with whom they will mate. Taxonomic

More information

Lecture 27. Phylogeny methods, part 7 (Bootstraps, etc.) p.1/30

Lecture 27. Phylogeny methods, part 7 (Bootstraps, etc.) p.1/30 Lecture 27. Phylogeny methods, part 7 (Bootstraps, etc.) Joe Felsenstein Department of Genome Sciences and Department of Biology Lecture 27. Phylogeny methods, part 7 (Bootstraps, etc.) p.1/30 A non-phylogeny

More information

Reconstructing Evolutionary Trees. Chapter 14

Reconstructing Evolutionary Trees. Chapter 14 Reconstructing Evolutionary Trees Chapter 14 Phylogenetic trees The evolutionary history of a group of species = phylogeny The problem: Evolutionary histories can never truly be known. Once again, we are

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

Rapid evolution of the cerebellum in humans and other great apes

Rapid evolution of the cerebellum in humans and other great apes Rapid evolution of the cerebellum in humans and other great apes Article Accepted Version Barton, R. A. and Venditti, C. (2014) Rapid evolution of the cerebellum in humans and other great apes. Current

More information

Multivariate analysis of genetic data: an introduction

Multivariate analysis of genetic data: an introduction Multivariate analysis of genetic data: an introduction Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Imperial College London XXIV Simposio Internacional De Estadística Bogotá, 25th July

More information

Reconstruire le passé biologique modèles, méthodes, performances, limites

Reconstruire le passé biologique modèles, méthodes, performances, limites Reconstruire le passé biologique modèles, méthodes, performances, limites Olivier Gascuel Centre de Bioinformatique, Biostatistique et Biologie Intégrative C3BI USR 3756 Institut Pasteur & CNRS Reconstruire

More information