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Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71

Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71. Week6: Intro to Phylogenetic Reconstruction & Distance Based Methods. • introduction to phylogenies • distance based methods • phylogeny exercises. Phylogeny Objectives

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Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71

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  1. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Week6: Intro to Phylogenetic Reconstruction & Distance Based Methods • introduction to phylogenies • distance based methods • phylogeny exercises Phylogeny Objectives 1 - understand the essence of phylogenies (definition of terms) 2 - understand distance based methods of phylogenetic reconstruction 3 - should be able to use various software packages to reconstruct and view phylogenies: ClustalX, MEGA, DAMBE, Treeview Lecture #6 Page 1

  2. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Molecular phylogeny study of relationships among organisms (molecular systematics), proteins or genes using molecular biology techniques • Darwin - thesis #1 - organisms descend with modification from common ancestors (CA) • relationships among organisms, proteins, genes are illustrated by a phylogenetic tree internal node - common ancestor (CA) external node - operational taxonomic unit (OTU) order of branches define the relationships (topology) branch length defines the number of changes Lecture #6 Page 2

  3. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 A brief history of molecular phylogeny • phylogenetic inference is old (for Biology) Charles Darwin – Orgin of Species (1859) Illustration of ‘descent with modification’ Ernst Haeckel “Tree of life” (1891) Lecture #6 Page 3

  4. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 A brief history of molecular phylogeny more modern developments … Molecular phylogeny • Nuttall (1904) found that the strength of serological cross reactions was correlated with the level of relatedness between animals - applied to primate phylogeny • starting 1950’s many more sources of molecular information become avaiable: e.g. amino acid sequences, allozyme frequencies, DNA hybridization • these data stimulated the development of quantitative ‘numerical taxonomy’ techniques for phylogenetic analysis Algorithmic approaches • first numerical approach to phylogeny based on phenetic approach – i.e. similarity of morphological characters (Michener and Sokal 1957) • phylogenetic studies of human populations based on blood allele frequencies led to the introduction of distance, parsimony & likelihood methods (Edwards & Cavalli-Sforza 1963, 1964) Lecture #6 Page 4

  5. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 A brief history of molecular phylogeny … emergence of sequence based methods:  accumulation of amino acid sequences stimulates development of sequence based phylogenetic methods  these soon emerge as the most powerful methods (see slide #6 for reasons) Parsimony, Distance & Maximum likelihood methods (see slide # 10)  Eck and Dayhoff (1966) – working of Atlas of Protein Sequence and Structure – publish first method for phylogenetic analysis of sequences based on parsimony  Fitch and Margoliash (1967) publish first distance based method – weighted least squares – for sequence based (cytochrome c) phylogenetic inference  Statistician Neyman (1971) publishes first maximum likelihood method for phylogenetic analysis of sequence data Lecture #6 Page 5

  6. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Benefits of using molecular sequences for phylogenetics 1 - sequences evolve in a much more regular manner than morphological characters 2 - less prone to confusion between homology and analogy, homoplasies 3 - vast abundance of characters to analyze 4 - molecular data more amenable to quantitative treatments 5 - molecular data ubiquitous - can be used for microorganisms 6 - can be used to study relationships at many different evolutionary levels faster evolving genes - mitochondrial DNA - closely related species slower evolving genes - ribosomal RNA genes - distantly related species Some success stories …. • primate evolution - who are humans closest relatives ? • origin of Cetacea mammals (whales, dolphins, porpoises) • revising deep taxonomic classification scheme - 3 domains of life Lecture #6 Page 6

  7. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Unrooted versus rooted phylogenies R time unrooted rooted only specifies relationships not the evolutionary path root (R) is common ancestor of all OTUs path from root to OTUs specifies time knowledge of outgroup required to define root Lecture #6 Page 7

  8. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Different visual representations of trees rectangular cladogram slanted cladogram branch lengths not proportional to distance phylogram branch lengths proportional to distance Lecture #6 Page 8

  9. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Species tree versus gene tree species tree - represents evolutionary relationships among species gene tree - represents evolutionary relationship among genes species trees and genes trees can (and often do!) differ Reasons for this ?? • comparison of orthologous versus paralogous genes • horizontal (later) transfer of genes more on these important concepts later in course the concept of an accurate species tree is notoriously difficult to pin down in this class we will deal almost exclusively with genes trees Lecture #6 Page 9

  10. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Methods of phylogenetic reconstruction Distance based • pairwise evolutionary distances computed for all taxa • tree constructed using algorithm based on relationships between distances Maximum parsimony • nucleotides or amino acids are considered as character states • best phylogeny is chosen as the one that minimizes the number of changes between character states Maximum likelihood • statistical method of phylogeny reconstruction • explicit model for how data set generated - nucleotide or amino acid substitution • find topology that maximizes the probability of the data given the model and the parameter values (estimated from data) Lecture #6 Page 10

  11. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Phylogenetic inference 1 – sequences change as they evolve from a common ancestor over time 2 – a group of related sequences retains information (incomplete) about the evolutionary history that unites them – based on the pattern of changes 3 – phylogeny is estimation, make the best estimate about evolutionary history given the incomplete information in the sequences being analyzed 4 – information about the past is not available, only extant sequences 5 – therefore any evolutionary scenario (i.e. phylogeny) can be postulated to explain the changes in the sequences being analyzed 6 – must have some way to discriminate among the (many!) possible phylogenies Lecture #6 Page 11

  12. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Number of OTUs and number of possible trees n  (2i-5) i=3 n  (2i-5)  (2n-3) i=3 # unrooted trees # rooted trees # OTUs (n) 2 1 1 3 1 3 4 3 15 5 15 105 6 105 954 7 954 10,395 8 10,395 135,135 9 135,135 2,027,025 10 2,027,025 34,459,425 true tree - true evolutionary history is one of many possibilities difficult to infer true tree when # OTUs is large inferred tree - obtained using data and reconstruction method not necessarily the same as the true tree - a hypothesis Lecture #6 Page 12

  13. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Alogrithms & Optimality Criteria Two ways for selecting preferred phylogenies:  Algorithms – sequence of steps that leads to the selection of a phylogeny - combine phylogeny inference and criterion definition into single step - move directly to toward the best tree without evaluating many different trees e.g. UPGMA & Neighbor-joining Optimality criteria – a criteria is defined whereby different phylogenies are - compared to one another to determine which is better - two steps involved: 1 – define criteria (objective function) 2 – use algorithm to compute objective function on different trees - this method is much slower – must evaluate many trees (shorcuts often necessary) - may be more robust because scores are assigned to every phylogeny and then they are ranked – yields information about how well specified the tree is e.g. Least squares & Minimum evolution Compromise – define starting tree with algorithm approach and then search nearby tree-space using optimality criteria approach Lecture #6 Page 13

  14. RS = (dij – eij)2 i<j A B C D A 0 17 21 27 B 17 0 12 18 C 21 12 0 14 D 27 18 14 0 Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Least squares method  First distance based method developed; Cavalli-Sforza & Edwards (1967) Fitch & Margoliash (1967)  Optimality criterion = minimize the residual sum of squares (RS) between the observed distances (dij - based on distance matrix) and the patristic differences (eij – based on the branch lengths of the inferred phylogeny) e.g. dBD = 18 eBD = 6 + 2 + 8 = 16 RS-BD = (18 – 16)2 = 4 Lecture #6 Page 14

  15. RS = [(dij – eij)2 / dij] i<j Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Least squares method …  Statisitcally very sound method since based on Least squares  Logically challenged since it formally estimates branch lengths and not topologies  In principle RS is computed for all possible topologies but in practice this quickly becomes impracticable (see slide #12) – short cuts are available to minimize search space (see lecture week7)  Fitch & Margoliash (1967) introduced weighted least squares that corrects for the bias introduced by long distances  Negative branch length estimates can confound method – constraint of non-negative branch lengths results in substantial improvement Lecture #6 Page 15

  16. T S = bi i  Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Minimum evolution method  Optimality criterion = choose the phylogeny that gives the smallest value of S - the sum of all branch lengths where T = total # branches bi = branch length i estimate S = 35.6 S = 35.0 Lecture #6 Page 16

  17. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Minimum evolution method …  As with least squares, S should ideally be computed for all possible trees but this is impossible with many taxa  One shortcut is to start search with neighbor-joining tree and then evaluate closely related trees to find the best one  Close neighbor interchange (CNI) start with temporary ME tree (e.g. NJ tree for first step) and evaluate all trees that differ by one or two topological changes  This approach may be more robust than using neighbor-joining alone because it can result in an ordered list of trees, if many trees represent the data almost equally well then the best tree may not be so well supported Lecture #6 Page 17

  18. A A B B dAB / 2 C d(AB)C / 2 A B B dAB C dAC dBC Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 UPGMA method (unweighted pair group method with arithmetic mean)  simplest method - uses sequential clustering algorithm  results in ‘ultrameric’ trees – equal distances from root to all tips  based on assumption of strict rate constancy among lineages – this is often violated and so method often gives erroneous trees (not reccomended) step 1 step 2 (AB) C d(AB)C Distance matrix Tree d(AB)C = (dAC + dAB) / 2 Lecture #6 Page 18

  19. A A B B dAB / 2 C d(AB)C / 2 A B B 4 C 57 Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 UPGMA example step 1 step 2 (AB) C6 Distance matrix Tree d(AB)C = (dAC + dAB) / 2 2 2 1 3 2 2 Lecture #6 Page 19

  20. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Neighbor-joining method uses ‘star decomposition’ – identification of neighbors that sequentially minimize the total length of the tree 1 - start with star tree - no topology S = total branch length of tree 2 - separate pair of OTUs from all others S12 = total branch length of tree 3 - choose pair of OTUs that minimizes total branch lengths in the tree 4 - this pair collapsed as single OTU and distance matrix recalculated 5 - next pair of OTUs that gives smallest branch length is chosen 6 - iterate until complete Lecture #6 Page 20

  21. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Neighbor-joining example Lecture #6 Page 21

  22. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Neighbor-joining method …  Extremely fast and efficient method, widely used & found in numerous publications  Tends to perform fairly well in simulation studies  May produce tie trees from data set but this appears to be rare  Algorithm is ‘greedy’ and so can get stuck in local optima Main criticism is that it produces only one tree and does not give any idea of how many other trees are equally well or almost as supported by the data  For this reason, neighbor-joining is often used as a method to find a starting tree that other methods (e.g. minimum evolution) will evaluate to find the best tree Lecture #6 Page 22

  23. Johns Hopkins University - Fall 2003 Phylogenetics & Computational Genomics - 410.640.71 Exercises 1 - choose some alignment to work on 2 - load alignment into Clustal and build neighbor-joining tree 3 - open tree in Treeview and view, manipulate and save tree 4 - load alignment into DAMBE and into MEGA and reconstruct and view trees using all distance methods available – look for differences in results 5 - manually reconstruct UPGMA tree for the distance matrix on slide #14 6 - open the MEGA formatted version of this same distance matrix http://jhunix.hcf.jhu.edu/~kjordan6/distances.meg in MEGA and reconstruct distance based trees using all 3 methods available (check UPGMA result against manually reconstructed UPGMA tree) 7 - calculate RS for all three distance based trees from #6 and pick best tree 8 - calculate S for all three distance based trees from #6 and pick best tree Lecture #6 Page 23

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