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Molecular Phylogeny Analysis, Part I. Mehrshid Riahi, Ph.D. Iranian Biological Research Center (IBRC), July 14-15, 2012.

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Presentation on theme: "Molecular Phylogeny Analysis, Part I. Mehrshid Riahi, Ph.D. Iranian Biological Research Center (IBRC), July 14-15, 2012."— Presentation transcript:

1 Molecular Phylogeny Analysis, Part I. Mehrshid Riahi, Ph.D. Iranian Biological Research Center (IBRC), July 14-15, 2012

2 Topics Introduction Four steps in Phylogenetic Inference Reading Phylogenetic Tree Tree interpretation in practice Reconstructing Evolutionary Trees Molecular Phylogeny Analysis2

3 Introduction Taxonomy = the naming & grouping of creatures by characteristics Classification = the process of grouping things based on their similarities. * Biologists use it to organize living things into groups for easier study. Molecular Phylogeny Analysis3

4 Man’s Early Systems of Classification: * Aristole (Greek in 4th centrury B.C.) Three groups (Fly, Swim, Walk) * Linnaeus (1750’s) used a two-part naming system from Latin. (Dog = Canis familiaris) - Binomial Nomenclature = a two-part name 1. Genus = first part of the name (Capitalized) (Groups similar, related organisms) 2. Species = second part of the name. (Lowercase) (“species identifier”) (Groups similar organisms that can mate and produce fertile offspring) Molecular Phylogeny Analysis4

5 Seven (7) Levels of Classification: ** For plants the phylum level is called “Division”. Kingdom – Phylum – Class – Order – Family – Genus – Species – “Kingdom” is the biggest and broadest. Each kingdom contains phyla – each phyla contains classes, etc. The more levels that two organisms share, the more characteristics they have in common. Molecular Phylogeny Analysis5

6 Phylogeny and classification Hierarchy All taxonomic classifications are hierarchical – how does phylogeny differ? Class Order Family Genus Species 1 Species 2 Species 3 Species 4 Species 1 Species 2 Species 3 Genus Species 1 Species 2 Order Family Genus Species 1 Species 2 Species 3 Species 4 Species 5 Species 6 Species 7 Species 8 Species 9 Genus Species 1 Species 2 Species 1 Genus Species 1 Species 2 Species 3 Genus 6Molecular Phylogeny Analysis

7 How can you identify an organism you find? Field Guide = book with pictures and descriptions of organisms and characteristics Taxonomic Key = series of paired statements describing characteristics of organisms Molecular Phylogeny Analysis7

8 8

9 Modern Phylogenetic Taxonomy Systematics is the modern method of organizing “creatures” in the context of evolution. Phylogeny = the supposed evolutionary history of an organism Phylogenetics is the science of the pattern of evolution * Evolutionary theory now dominates the classification system, and assumes that similar organisms in a group evolved from a common ancestor. Phylogenetic Trees are family trees supposedly showing evolutionary relationships “thought to exist among groups of organisms”, “shows possible relationships”. Molecular Phylogeny Analysis9

10 Phylogenetic tree of Kingdom Plantae Molecular Phylogeny Analysis10

11 Molecular Phylogeny Analysis Linnaeus “Lawn” His ‘lawn’ concept hypothesized that: Each Genesis “kind” was unrelated to others Each “kind” stayed the same without variation Today’s species = the original “kinds” He was right about unrelated “kinds”. He was wrong about NO variation and species. 11

12 Molecular Phylogeny Analysis Evolutionary “Tree” This evolutionary ‘tree’ claims that: - all modern species are descended from a common ancestor 12

13 Phylogenetics The central problem of phylogenetics: how do we determine the relationships between taxa? in phylogenetic studies, the most convenient way of presenting evolutionary relationships among a group of organisms is the phylogenetic tree Molecular Phylogeny Analysis13

14 Phylogenetic Taxonomy Systematic taxonomists use several lines of evidence to construct a phylogenetic tree.” Fossil Record – “Billions of dead things buried in rock layers, laid down by water, all over the earth” (Ken Ham) Morphology – similar shape or form (homologous features) among different animals. Embryological Patterns of Development – (Ontogeny) Chromosomes and Macromolecules – Genetic similarities Molecular Phylogeny Analysis14

15 What is molecular phylogeny? Molecular Phylogeny Analysis15 phylon = Greek for “stem” genesis = Greek for “origin” molecular phylogeny = studying relationships among organisms using molecular markers (e.g. DNA or protein sequences) dissimilarities among sequences = genetic divergence caused by mutations during the course of time

16 Four steps in Phylogenetic Inference  Character (data) selection (not too fast, not too slow) 2. Alignment of Data (hypotheses of primary homology) 3. Analysis selection (choose the best model / method(s)) 4. Conduct analysis Molecular Phylogeny Analysis16

17 aim: group of organisms or gene family Choice of molecular marker(s) and Taxon sampling Extraction/Amplification/Sequencing Alignment Choice of evolutionary model Phylogenetic analyses Tree(s) Results Work- Flow User- defined trees And topology testing Improvement of 17Molecular Phylogeny Analysis

18 Types of Markers Marker is a piece of DNA molecule that is associated with a certain trait of a organism Morphological: Characters are selected based on appearance Disadvantage: lack of polymorphism Biochemical: Characters are selected based on biochemical properties Disadvantage: Age dependent, Influenced by environment It covers less than 10% of genome Chromosomal: Characters are selected based on Structural and Numerical Variations (Structural- Deletions, Insertions etc. Numerical- Trisomy, Monosomy, Nullysomy) Disadvantage: low polymorphism Genetic: Molecular Phylogeny Analysis18

19 Molecular Marker Revealing variation at a DNA level Characteristics: Co-dominant expression Nondestructive assay Early onset of phenotypic expression High polymorphism Random distribution throughout the genome Assay can be automated Molecular Phylogeny Analysis19

20 Methodological Advantages I. DNA isolated from any tissue eg. Blood, hair etc. II. DNA isolated at any stage even during foetal life III. DNA has longer shelf-life readily exchangeable b/w labs IV. Analysis of DNA carried out at early age/ even at the embryonic V. Stage irrespective of sex Molecular Phylogeny Analysis20

21 Molecular Phylogeny Analysis21 Molecular Markers Single locus marker Multi-locus marker RFLP Microsatellite STS DNA Fingerprinting AFLP RAPD

22 Selection of characters Morphologists typically choose: 1. Characters that are not constant 2. Characters that are not too variable Molecular systematists use the same criteria to select which gene(s) to sequence Genes that are virtually constant don’t have enough information Genes that are hypervariable have too much misinformation Molecular Phylogeny Analysis22

23 Selection of Molecular characters Character / discrete data: nucleotide or amino acid sequences (can be converted to distances) “fast & slow” genes: - there is variation in the rate of change among regions of the genome e.g. rRNA (e.g. 18S) evolves slowly enough to hold information that is over 250 million years old - whereas mtDNA (e.g. COII) evolves much faster and most information over million yrs of age is probably gone (starts to go at my) Molecular Phylogeny Analysis23

24 Selection of Molecular characters Higher-level phylogenetics: (families & above) use slower, conserved genes, nuclear genes - evolve slowly due to functional constraints: e.g. some proteins “still work” with many potential amino acids others won’t, e.g. histones are strongly conserved - faster evolving regions, e.g. mtDNA, -information is overwritten - back mutations - yield nonsense phylogenies for deep splits Molecular Phylogeny Analysis24

25 Selection of Molecular characters Lower-level phylogenetics: (subfamilies & below) use faster, less-conserved genes, mtDNA - because slower genes would be identical across your species - must select genes most appropriate for your study taxa Molecular Phylogeny Analysis25

26 Typical structure of a eukaryotic gene Molecular Phylogeny Analysis26 TATA box Transcription initiation Initiation codon Stop codon AATAA Poly (A) addition site Exon 1 Exon 2 Exon 3 Flanking region 5' 3' Intron I Intron II

27 Selection of Molecular characters Three types of genes tRNA - transfer RNA (short) rRNA - ribosomal RNA (long, conserved) mRNA - messenger RNA - protein coding (exon) Also introns - non coding sequence sometimes inside a protein coding gene Can be Nuclear Typically slower evolving than mitochondrial better for deeper (older) divergences Can be Mitochondrial Better for shallow (recent) divergences Molecular Phylogeny Analysis27

28 Molecular Phylogeny Analysis28 DNA Amplification

29 PHYLOGENETIC DATA ANALYSIS: THE FOUR STEPS A straightforward phylogenetic analysis consists of four steps: 1. Alignment (both building the data model and extracting a phylogenetic dataset) 2. Determining the substitution model 3. Tree building 4. Tree evaluation Molecular Phylogeny Analysis29

30 READING PHYLOGENETIC TREE Molecular Phylogeny Analysis30

31 Assumptions Evolution produces dichotomous branching Evolution is simple – the best explanation assumes least mutations If we assume: 1. Our characters are independent 2. Our character states are homologous (& genes orthologous) 3. Evolution has happened We can infer the evolutionary relationships among organisms Molecular Phylogeny Analysis31

32 Reading phylogenetic trees: A quick review (Adapted from evolution.berkeley.edu) A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon) that are believed to have a common ancestor. 32Molecular Phylogeny Analysis

33 Tips, Internal Nodes, Edges The tips of the phylogenetic tree represent groups of descendent taxa (often species) The internal nodes of the tree represent the common ancestors of those descendents. The tips are the present and the internal nodes are the past. The edge lengths in some trees correspond to time estimates – evolutionary time. 33Molecular Phylogeny Analysis

34 Parts of a phylogenetic tree Internal Nodes or Divergence Points (represent hypothetical ancestors of the taxa) Branch, Lineages : defines the relationship between the taxa in terms of descent and ancestry Topology: the branching patterns of the tree Branch length (scaled trees only): represents the number of changes that have occurred in the branch Root: the common ancestor of all taxa Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains Molecular Phylogeny Analysis34 Root Branch Clade Node

35 Sister Groups and a common ancestor Two descendents that split from the same node are called sister groups. In the trees above, species A & B are sister groups — they are each other's closest relatives; which means that: i) they have a lot of evolutionary history in common and very little evolutionary history that is unique to either one of the two sister species and ii) that they have a common ancestor that is unique to them. 35Molecular Phylogeny Analysis

36 Equivalent trees For any speciation event on a phylogeny, the choice of which lineage goes to the right and which one goes to the left is arbitrary. These three phylogenies are therefore equivalent. 36Molecular Phylogeny Analysis

37 Phylogenetic trees There are many ways of drawing a tree Molecular Phylogeny Analysis37 == ECD B A

38 Phylogenetic trees There are many ways of drawing a tree Molecular Phylogeny Analysis38

39 Phylogenetic trees There are many ways of drawing a tree Molecular Phylogeny Analysis39 == no meaning

40 Outgroup Many phylogenies also include an outgroup — a taxon outside the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees. 40Molecular Phylogeny Analysis

41 Branches and clades Evolutionary trees depict clades. A clade is a group of organisms that are all descendent from a common ancestor; thus a clade includes an ancestor and all descendents of that ancestor. You can think of a clade as a branch on the tree of life. Some examples of clades and non-clades in a phylogenetic tree are shown here 41Molecular Phylogeny Analysis

42 More on clades. Nested clades Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few. Some examples of clades at different levels are marked on the phylogenies above. Notice how clades can be nested within larger clades. 42Molecular Phylogeny Analysis

43 Types of trees: unrooted vs rooted A rooted phylogenetic tree is a tree with a unique root node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves (aka tips) of the tree. A rooted tree is a binary tree.imputed Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about common ancestry. An unrooted tree has a node with three edges; the rest of the nodes have up to two edges. 43Molecular Phylogeny Analysis

44 Rooting the Tree In an unrooted tree the direction of evolution is unknown The root is the hypothesized ancestor of the sequences in the tree The root can either be placed on a branch or at a node You should start by viewing an unrooted tree 44Molecular Phylogeny Analysis

45 45 Positioning Roots in Unrooted Trees We can estimate the position of the root by introducing an outgroup: AardvarkBisonChimpDogElephant Falcon Proposed root Molecular Phylogeny Analysis

46 Rooting Using an Outgroup 1. The outgroup should be a sequence (or set of sequences) known to be less closely related to the rest of the sequences than they are to each other 2. It should ideally be as closely related as possible to the rest of the sequences while still satisfying condition 1 The root must be somewhere between the outgroup and the rest (either on the node or in a branch) 46Molecular Phylogeny Analysis

47 Dendrogram, cladogram, phylogram Dendrogram is the ‘generic’ term applied to any type of diagrammatic representation of phylogenetic trees. All four trees depicted here are dendrograms. Cladogram (to some biologists) is a tree in which branch lengths DO NOT represent evolutionary time; clades just represent a hypothesis about actual evolutionary history TREE1 and TREE2 are cladograms and TREE1 = TREE2 Phylogram (to some biologists) is a tree in which branch lengths DO represent evolutionary time; clades represent true evolutionary history (amount of character change) TREE3 and TREE4 are phylograms and TREE3 ≠ TREE4 47Molecular Phylogeny Analysis

48 Phylogenetic trees Molecular Phylogeny Analysis48

49 Phylogenetic Trees and classification Phylogenetic trees classify organisms into clades. By contrast, the Linnaean system of classification assigns every organism a kingdom, phylum, class, order, family, genus, and species. The phylogenetic tree depicted here identifies four cladesLinnaean system of classification To build a phylogenetic tree biologists collect data about the characters of each organism they are interested in. Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits.characters Some molecular biologists (like C. Woese) build phylogenetic trees from genetic sequences alone. 49Molecular Phylogeny Analysis

50 Phylogenetic trees Bifurcation versus Multifurcation (e.g. Trifurcation)  Multifurcation (also called polytomy): a node in a tree that connects more than three branches. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation ) Molecular Phylogeny Analysis50 Bifurcation Trifurcation = /

51 Completely unresolved or "star" phylogeny Partially resolved phylogeny Fully resolved, bifurcating phylogeny AAA B BB C C C E E E D DD Polytomy or multifurcationA bifurcation The goal of phylogeny inference is to resolve the branching orders of lineages in evolutionary trees: 51Molecular Phylogeny Analysis

52 Phylogenetic trees Trees can be scaled or unscaled (with or without branch lengths) Molecular Phylogeny Analysis52

53 TREE INTERPRETATION IN PRACTICE Molecular Phylogeny Analysis53

54 1) By reference to the tree above, which of the following is an accurate statement of relationships? a) A green alga is more closely related to a red alga than to a moss b) A green alga is more closely related to a moss than to a red alga c) A green alga is equally related to a red alga and a moss d) A green alga is related to a red alga, but is not related to a moss 54Molecular Phylogeny Analysis

55 1) By reference to the tree above, which of the following is an accurate statement of relationships? a) A green alga is more closely related to a red alga than to a moss b) A green alga is more closely related to a moss than to a red alga c) A green alga is equally related to a red alga and a moss d) A green alga is related to a red alga, but is not related to a moss 55Molecular Phylogeny Analysis

56 2) By reference to the tree above, which of the following is an accurate statement of relationships? a) A crocodile is more closely related to a lizard than to a bird b) A crocodile is more closely related to a bird than to a lizard c) A crocodile is equally related to a lizard and a bird d) A crocodile is related to a lizard, but is not related to a bird 56Molecular Phylogeny Analysis

57 2) By reference to the tree above, which of the following is an accurate statement of relationships? a) A crocodile is more closely related to a lizard than to a bird b) A crocodile is more closely related to a bird than to a lizard c) A crocodile is equally related to a lizard and a bird d) A crocodile is related to a lizard, but is not related to a bird 57Molecular Phylogeny Analysis

58 3) By reference to the tree above, which of the following is an accurate statement of relationships? a) A seal is more closely related to a horse than to a whale b) A seal is more closely related to a whale than to a horse c) A seal is equally related to a horse and a whale d) A seal is related to a whale, but is not related to a horse 58Molecular Phylogeny Analysis

59 3) By reference to the tree above, which of the following is an accurate statement of relationships? a) A seal is more closely related to a horse than to a whale b) A seal is more closely related to a whale than to a horse c) A seal is equally related to a horse and a whale d) A seal is related to a whale, but is not related to a horse 59Molecular Phylogeny Analysis

60 4) Which of the five marks in the tree above corresponds to the most recent common ancestor of a mushroom and a sponge? 60Molecular Phylogeny Analysis

61 4) Which of the five marks in the tree above corresponds to the most recent common ancestor of a mushroom and a sponge? 61Molecular Phylogeny Analysis

62 5) If you were to add a trout to the phylogeny shown above, where would its lineage attach to the rest of the tree? 62Molecular Phylogeny Analysis

63 5) If you were to add a trout to the phylogeny shown above, where would its lineage attach to the rest of the tree? 63Molecular Phylogeny Analysis

64 6) Which of trees below is false given the larger phylogeny above? 64Molecular Phylogeny Analysis

65 6) Which of trees below is false given the larger phylogeny above? 65Molecular Phylogeny Analysis

66 7) Which of the four trees above depicts a different pattern of relationships than the others? 66Molecular Phylogeny Analysis

67 7) Which of the four trees above depicts a different pattern of relationships than the others? 67Molecular Phylogeny Analysis

68 8) Which of the four trees above depicts a different pattern of relationships than the others? 68Molecular Phylogeny Analysis

69 8) Which of the four trees above depicts a different pattern of relationships than the others? 69Molecular Phylogeny Analysis

70 9) In the above tree, assume that the ancestor had a long tail, ear flaps, external testes, and fixed claws. Based on the tree and assuming that all evolutionary changes in these traits are shown, what traits does a sea lion have? a) long tail, ear flaps, external testes, and fixed claws b) short tail, no ear flaps, external testes, and fixed claws c) short tail, no ear flaps, abdominal testes, and fixed claws d) short tail, ear flaps, abdominal testes, and fixed claws e) long tail, ear flaps, abdominal testes, and retractable claws 70Molecular Phylogeny Analysis

71 9) In the above tree, assume that the ancestor had a long tail, ear flaps, external testes, and fixed claws. Based on the tree and assuming that all evolutionary changes in these traits are shown, what traits does a sea lion have? a) long tail, ear flaps, external testes, and fixed claws b) short tail, no ear flaps, external testes, and fixed claws c) short tail, no ear flaps, abdominal testes, and fixed claws d) short tail, ear flaps, abdominal testes, and fixed claws e) long tail, ear flaps, abdominal testes, and retractable claws 71Molecular Phylogeny Analysis

72 10) In the above tree, assume that the ancestor was a herb (not a tree) without leaves or seeds. Based on the tree and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit and lacks true leaves? a) Lepidodendron b) Clubmoss c) Oak d) Psilotum e) Fern 72Molecular Phylogeny Analysis

73 10) In the above tree, assume that the ancestor was a herb (not a tree) without leaves or seeds. Based on the tree and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit and lacks true leaves? a) Lepidodendron b) Clubmoss c) Oak d) Psilotum e) Fern 73Molecular Phylogeny Analysis

74 Tree structure I.A tree can be also presented in a text format: (A(B(C,D))) II.The graphic structure can be difficult to interpret (2-dimentional) Molecular Phylogeny Analysis74

75 Visualising trees  Treeview  You can change the graphic presentation of a tree (cladogram, rectangular cladogram, radial tree, phylogram), but not change the structure of a tree Molecular Phylogeny Analysis75

76 RECONSTRUCTING EVOLUTIONARY TREES Molecular Phylogeny Analysis76

77 Recall The phylogeny of a group of taxa (species, etc.) is its evolutionary history A phylogenetic tree is a graphical summary of this history — indicating the sequence in which lineages appeared and how the lineages are related to one another Because we do not have direct knowledge of evolutionary history, every phylogenetic tree is an hypothesis about relationships Of course, some hypotheses are well supported by data, others are not Molecular Phylogeny Analysis77

78 Questions How do we make phylogenetic trees? Cladistic methodology Similarity (phenetics) What kinds of data do we use? Morphology Physiology Behavior Molecules How do we decide among competing alternative trees? Molecular Phylogeny Analysis78

79 Similarity The basic idea of phylogenetic reconstruction is simple: Taxa that are closely related (descended from a relatively recent common ancestor) should be more similar to each other than taxa that are more distantly related — so, all we need to do is build trees that put similar taxa on nearby branches — this is the phenetic approach to tree building Consider, as a trivial example, leopards, lions, wolves and coyotes: all are mammals, all are carnivores, but no one would have any difficulty recognizing the basic similarity between leopards and lions, on the one hand, and between wolves and coyotes, on the other, and producing this tree; which, it would probably be universally agreed, reflects the true relationships of these 4 taxa leopardlionwolfcoyote Molecular Phylogeny Analysis79

80 Causes of similarity Things are seldom as simple as in the preceding example We need to consider the concept of biological similarity, and the way in which similarity conveys phylogenetic information, in greater depth: Homology Homoplasy Molecular Phylogeny Analysis80

81 Homology A character is similar (or present) in two taxa because their common ancestor had that character: In this diagram, wings are homologous characters in hawks and doves because both inherited wings from their common winged ancestor cathawkdove wings Molecular Phylogeny Analysis81

82 Homoplasy A character is similar (or present) in two taxa because of independent evolutionary origin (i.e., the similarity does not derive from common ancestry): In this diagram, wings are a homoplasy in hawks and bats because their common ancestor was an un-winged tetrapod reptile. Bird wings and bat wings evolved independently. hawkbatcat wings Molecular Phylogeny Analysis82

83 Types of homoplasy Convergence Independent evolution of similar traits in distantly related taxa — streamlined shape, dorsal fins, etc. in sharks and dolphins Parallelism Independent evolution of similar traits in closely related taxa — evolution of blindness in different cave populations of the same fish species Reversal A character in one taxon reverts to an earlier state (not present in its immediate ancestor) Molecular Phylogeny Analysis83

84 Reversal A character is similar (or present) in two taxa because a reversal to an earlier state occurred in the lineage leading to one of the taxa: In this diagram, hawks and cats share the ancestral nucleotide sequence ACCT, but this is due to a reversal on the lineage leading to cats hawkbatcat ACTT ACCT Molecular Phylogeny Analysis84

85 Cladograms Within a tree a clade is defined as a group that includes an ancestral species and all of its descendants. Cladistics is the science of how species may be grouped into clades. Molecular Phylogeny Analysis85

86 Cladistics By definition, homology indicates evolutionary relationship — when we see a shared homologous character in two species, we know that they share a common ancestor Build phylogenetic trees by analyzing shared homologous characters Of course, we still have the problem of deciding which shared similarities are homologies and which are homoplasies (to which we shall return) Molecular Phylogeny Analysis86

87 Two kinds of homology – 1 Shared ancestral homology — a trait found in all members of a group for which we are making a phylogenetic tree (and which was present in their common ancestor) — symplesiomorphy For example: a backbone is a shared ancestral homology for dogs, humans, and lizards Symplesiomorphies DO NOT provide phylogenetic information about relationships within the group being studied Molecular Phylogeny Analysis87

88 Two kinds of homology – 2 Shared derived homology — a trait found in some members of a group for which we are making a phylogenetic tree (and which was NOT present in the common ancestor of the entire group) — synapomorphy For example: hair is (potentially) a shared derived homology in the group [dogs, humans, lizards] Synapomorphies DO provide phylogenetic information about relationships within the group being studied In this particular case, if hair is a synapomorphy in dogs and humans, then dogs and humans share a common ancestor that is not shared with lizards, and the common dog-human ancestor must have lived more recently than the common ancestor of all three taxa Molecular Phylogeny Analysis88

89 A tree for [dogs, humans, lizards] – 1 lizardhumandog hair backbone The TWO major assumptions that we are making when we build this tree are: 1)hair is homologous in humans and dogs 2)hair is a derived trait within tetrapods Molecular Phylogeny Analysis89

90 A tree for [dogs, humans, lizards] – 2 lizardhumandog hair backbone In the absence of other information, the assumption of homology of hair in humans and dogs is justified by parsimony (fewest number of evolutionary steps is most likely = simplest explanation) Also we can check to see that hair is formed in the same way by the same kinds of cells, etc. Molecular Phylogeny Analysis90

91 A tree for [dogs, humans, lizards] – 3 These trees (in which hair is considered a homoplasy in dogs and humans) are less parsimonious than the one on the previous slide, because they require two independent evolutionary origins of hair humanlizarddog hair backbone hair doglizardhuman hair backbone hair Molecular Phylogeny Analysis91

92 Character Polarity What’s the basis for our second major assumption – that hair is a derived trait within this group (and that absence of hair is primitive)? Fossil record Outgroup analysis Molecular Phylogeny Analysis92

93 Outgroups – 1 An outgroup is a taxon that is related to, but not part of the set of taxa for which we are constructing the tree (the “in group”) Selection of an outgroup requires that we already have a phylogenetic hypothesis A character state that is present in both the outgroup and the in group is taken to be primitive by the principle of parsimony (present in the common ancestor of both the outgroup and the in group and, therefore, homologous) Molecular Phylogeny Analysis93

94 Outgroups – 2 In the present example, [dog, human, lizard] are all amniote tetrapods. The anamniote tetrapods (amphibia) make a reasonable outgroup for this problem No amphibia have hair, therefore absence of hair [amphibia, lizards] is primitive (plesiomorphic) and presence of hair [dogs, humans] is derived (apomorphic) So, presence of hair is a shared derived character (synapomorphy), and dogs and humans are more closely related to each other than either is to lizards Molecular Phylogeny Analysis94

95 A tree for [dogs, humans, lizards] – 4 The presence of hair is apomorphic (derived) because no amphibians have hair lizardhumandog hair backbone Amphibia amniotic egg Molecular Phylogeny Analysis95

96 Theories of taxonomy There are two current major theories of taxonomy: Traditional Evolutionary Taxonomy Phylogenetic Systematics (Cladistics) Both based on evolutionary principles, but differ in the application of those principles to formulate taxonomic groups. Molecular Phylogeny Analysis96

97 Theories of taxonomy There are three different ways a taxon may be related to a phylogentic tree. The taxon may be a monophyletic, paraphyletic or polyphyletic grouping Molecular Phylogeny Analysis97

98 Monophyletic Group A monophyletic taxon includes the most recent common ancestor of a group and all of its descendents. Molecular Phylogeny Analysis98

99 Molecular Phylogeny Analysis99

100 Paraphyletic group A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all of its descendents. Molecular Phylogeny Analysis100

101 Molecular Phylogeny Analysis101

102 Polyphyletic grouping A taxon is polyphyletic if it does not contain the most recent common ancestor of all members of the group. This situation requires the group to have had independent evolutionary origin of some diagnostic feature. E.g. If you grouped birds and bats into a group you called “WingedThings” it would be a polyphyletic group because birds and bats evolved wings separately. Molecular Phylogeny Analysis102

103 Molecular Phylogeny Analysis103

104 Theories of taxonomy Both traditional evolutionary taxonomy and cladistics reject polyphyletic groups. They both accept monophyletic groups, but differ in their treatment of paraphyletic groupings. Molecular Phylogeny Analysis104

105 Phylogeny and classification Monophyly Each of the colored lineages in this echinoderm phylogeny is a good monophyletic group Asteroidea Ophiuroidea Echinoidea Holothuroidea Crinoidea Each group shares a common ancestor that is not shared by any members of another group 105Molecular Phylogeny Analysis

106 Lindblad-Toh et al. (2005) Nature 438: Paraphyletic groups Paraphyly “Foxes” are paraphyletic with respect to dogs, wolves, jackals, coyotes, etc. This is a trivial example because “fox” and “dog” are not formal taxonomic units, but it does show that a dog or a wolf is just a derived fox in the phylogenetic sense Foxes 106Molecular Phylogeny Analysis

107 Paraphyletic groups Fry et al. (2006) Nature 439: Paraphyly “Lizards” (Sauria) are paraphyletic with respect to snakes (Serpentes) Serpentes is a monophyletic clade within lizards Squamata (lizards + snakes) is a monophyletic clade sister to sphenodontida Snakes are just derived, limbless lizards Lizards 107Molecular Phylogeny Analysis

108 Traditional Evolutionary Taxonomy TET uses two principles for designating taxa. Common descent Amount of adaptive evolutionary change The second criterion leads to the idea that groups may be designated as higher level taxa because they represent a distinct “adaptive zone” (Simpson) because they have undergone adaptive change that fits them to a unique role (e.g. penguins, humans). Molecular Phylogeny Analysis108


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