1 Dan Graur Molecular Phylogenetics

2 Objectives of molecular phylogenetics Reconstruct the correct evolutionary relationships among biological entities Estimate the time of divergence between biological entities Chronicle the sequence of events along evolutionary lineages

3 Evolutionary relationships are illustrated by means of a phylogenetic tree or a dendogram.

4 Ernst Heinrich Haeckel

5 July 1837 July 2007

6 November 1859

7 The routes of inheritance represent the passage of genes from parents to offspring, and the branching pattern depicts a gene tree.

8 Different genes, however, may have different evolutionary histories, i.e., different routes of inheritance.

9 The routes of inheritance are confined by reproductive barriers, i.e., gene flow occurs only within a species. A species tree is a representation of splitting of species lineages.

10 Terminology

11 A phylogenetic tree or dendrogram is a graph composed of nodes and branches, in which only one branch connects any two adjacent nodes.

12 Internal External or Peripheral Branch

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14 Assumptions: Bifurcation = Real speciation event Multifurcation = Lack of resolution

15 Binary tree

16 Rooted and unrooted trees

17 How many unrooted topologies are here? a b c d e a e c d b a b c e d b a c d e 43 21

18 central branch In an unrooted tree with four external nodes, the internal branch is referred to as the central branch.

19 Cladograms & Phylograms (collectively Dendograms) Bacterium 1 Bacterium 3 Bacterium 2 Eukaryote 1 Eukaryote 4 Eukaryote 3 Eukaryote 2 Bacterium 1 Bacterium 3 Bacterium 2 Eukaryote 1 Eukaryote 4 Eukaryote 3 Eukaryote 2 Phylograms show branch order and branch lengths Cladograms show branching order - branch lengths are meaningless

20 Unscaled phylogram Scaled phylogram

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23 The Newick format In computer programs, trees are represented in a linear form by a string of nested parentheses, enclosing taxon names (and possibly also branch lengths and bootstrap values), and separated by commas. This type of representation is called the Newick format. The originator of this format in mathematics was Arthur Cayley.

24 The Newick format The Newick format for phylogenetic trees was adopted on June 26, 1986 at an informal meeting at Newick's Lobster House in Dover, New Hampshire. The Newick format currently serves as the de facto standard for representing phylogenetic tree and is employed by almost all phylogenetic software tools. Unfortunately, it has never been described in a formal publication; the first time it is mentioned in a publication is in 1992.

25 The Newick format In the Newick format, the pattern of the parentheses indicates the topology of the tree by having each pair of parentheses enclose all members of a monophyletic group. A phylogenetic tree in the Newick format always ends in a semicolon (;). ;

26 The Newick format One can use the Newick format to write down rooted trees, unrooted trees, multifurcations, branch lengths, and bootstrap values.

27 3 OTUs 1 unrooted tree = 3 rooted trees

28 4 OTUs 3 unrooted trees = 15 rooted trees

29 The number of possible bifurcating rooted trees (N R ) for n  2  OTUs The number of possible bifurcating unrooted trees (N U ) for n  3  OTUs

30  Number of OTUs Number of possible rooted tree  , ,135 92,027, ,459, ,458,046,676, ,200,794,532,637,891,559,375 

31 Evolution is an historical process. Only one historical narrative is true. From 8,200,794,532,637,891,559,375 possibilities, 1 possibility is true and 8,200,794,532,637,891,559,374 are false. Truth is one, falsehoods are many.

32 8,200,794,532,637,891,559,375 How do we know which of the 8,200,794,532,637,891,559,375 trees is true?

33 We don’t, we infer by using decision criteria.

34 True and inferred trees The sequence of speciation events that has led to the formation of a group of OTUs is historically unique. A tree representing the true evolutionary history is called the true tree. A tree that is obtained by using a certain set of data and a certain method of tree reconstruction is called an inferred tree. An inferred tree may or may NOT be the true tree.

35 ancestor descendant 1descendant 2 Cladogenesis Cladogenesis = the splitting of an evolutionary lineage into two genetically independent lineages.

36 ancestor descendant 1descendant 2 Anagenesis Anagenesis = changes occurring along an evolutionary lineage.

37 In molecular phylogenetics, we assume that species are only created by cladogenesis.

38 A gene tree may differ from a species tree

39 Gene trees and species trees It is often assumed that gene trees always equal species trees. This may be not be true. a b c A B D Gene tree Species tree

40 Orthologs and paralogs a A* b* cBC* Ancestral gene Duplication yields 2 copies (paralogs) on the same genome orthologous paralogous A*C*b* A mixture of orthologs and paralogs is sampled

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42 Homo sapiensLepidoptera herbs A taxon is a species or a group of species that has been given a name, e.g., Homo sapiens (modern humans), or Lepidoptera (butterflies), or herbs. There are codes of biological nomenclature which seek to ensure that every taxon has a single and stable name, and that every name is used for only one taxon. Taxon (singular); Taxa (plural)

43 Strictly: A clade is a group of all the taxa that have been derived from a common ancestor plus the common ancestor itself. In molecular phylogenetics: A clade is a group of taxa under study that share a common ancestor, which is not shared by any other species outside the group. Clades* *also: monophyletic groups, natural clades

44 A taxon whose common ancestor is shared by any other taxon is called a paraphyletic taxon or an invalid taxon. Paraphyletic Taxa Reptiles are paraphyletic. 44

45 A named taxon that lacks phylogenetic validity, but is nonetheless used, is called a convenience taxon. “a convenience fish” Fish (Pisces)

46 If a clade is composed of two taxa, these are referred to as sister taxa. Sister Taxa Birds and crocodiles are sister taxa.

47 Phenotypic distance = clades

48 Which of the following groups are not monophyletic? E. coli rat mouse baboon chimp human a. human, chimpanzee, baboon b. mouse, chimpanzee, baboon c. rat, mouse d. human, chimpanzee, baboon, rat, mouse e. E. coli, human, chimpanzee, baboon, rat, mouse

49 Which of the following groups are not monophyletic? E. coli rat mouse baboon chimp human a. human, chimpanzee, baboon b. mouse, chimpanzee, baboon c. rat, mouse d. human, chimpanzee, baboon, rat, mouse e. E. coli, human, chimpanzee, baboon, rat, mouse

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51 A character provides information about an individual OTU. A distance represents a quantitative statement concerning the dissimilarity between two OTUs.

52 A character is a well-defined feature that in a taxonomic unit can assume one out of two or more mutually exclusive character states. Mutually exclusive: If David is tall, David cannot be short.

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55 ContinuousDiscrete BinaryMultistate Unordered UnpolarPolar UnpolarPolar Character Ordered

56 A character is unordered if a change from one character state to any other character state can occur in one step.

57 A character is ordered if there exists a unique symmetrical path of change from one character state to another.

58 Polar A character is polar if there exists a unique asymmetrical (irreversible) path of change from one character state to another.

59 In partially ordered characters the number of steps varies for the different pairwise combinations of character states, but no definite relationship exists between the number of steps and the character-state. Amino-acid sites are partially ordered characters. An amino acid cannot change into all other amino acids in a singe step, as sometimes 2 or 3 steps are required. For example, a tyrosine may only change into a leucine through an intermediate state, i.e., phenylalanine or histidine.

60 The number of steps in partially ordered characters is specified by a step matrix, the elements of which indicate the number of steps required between any two character states

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62 Assumptions about character evolution Methods of phylogenetic reconstruction require that we make explicit assumptions about: (1) the number of discrete steps required for one character state to change into another. (2) the probability with which such a change may occur.

63 Temporal Polarity of Character States Character states may be ranked by relative antiquity into: (1) primitive or ancestral (plesiomorphy) (2) derived or novel (apomorphy)

64 Taxonomic Distribution of Character States A primitive state that is shared by several taxa is a symplesiomorphy. A derived state that is shared by several taxa is a synapomorphy. A derived character state unique to a particular taxon is an autapomorphy. A character state that is shared by several taxa due to convergence, parallelism and reversals, rather than due to common descent, is a homoplasy. sympathy synapse syllable system

65 CC C A A A BAA A B plesiomorphy apomorphy (autapomorphy ) synapomorphy symplesiomorphy homoplasy A D

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67 Distance Data

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69 Most molecular data yield character states that are subsequently converted into distances.

70 Some molecular data can only be expressed as distances.

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