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Lecture 3 Phylogenetic Inference from Darwin’S Notebook in 1837

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Lecture 3 Phylogenetic Inference from Darwin’S Notebook in 1837 Lecture 3 Phylogenetic Inference From Darwin’s notebook in 1837 Phylogenomics of dogs Phylogeny of dog breeds Charles Darwin Willi Hennig From “The Origin” in 1859 Cladistics Phylogenetic inference Willi Hennig, Cladistics Clade, Monophyletic group, Natural group a. All individuals in the clade derived from a single ancestor b. This ancestor’s descendants are all in the clade Monophyletic groups Tetrapods Sarcopterygians Lungfishes Fishes Coelacanths Fishes Phylogenetic inference Definitions: 2. Ancestral v.s. Derived characters A B C D Phylogenetic inference Definitions: apomorphy: derived character synapomorphy: Shared derived character A B C D apomorphy synapomorphy Phylogenetic inference Definitions: 4. Reversal evolution ← ← ← Phylogenetic inference 5. Homoplasy, Convergent evolution Fossa, Madagascar Mongoose Mountain Lion, California, Cat Thylacine, Tasmania Marsupial Phylogenetic inference 6. Parallel evolution Phylogenetic Inference • phylogenetic trees are built from “characters”. Phylogenetic Inference • phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. Phylogenetic Inference • phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about the characters used to build trees: Phylogenetic Inference • phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about the characters used to build trees: 1. they are independent. Phylogenetic Inference • phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about characters used to build trees: 1. they are independent. 2. they are homologous. What is a homologous character? What is a homologous character? • a homologous character is shared by two species because it was inherited from a common ancestor. What is a homologous character? • a homologous character is shared by two species because it was inherited from a common ancestor. • a character possessed by two species but was not present in their recent ancestors, it is said to exhibit “homoplasy”. Types of homoplasy: Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight. Examples of convergent evolution Convergent evolution between placental and marsupial mammals Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight. 2. Parallel evolution Example: lactose tolerance in humans. What is the difference between convergent and parallel evolution? What is the difference between convergent and parallel evolution? Convergent Parallel What is the difference between convergent and parallel evolution? Convergent Parallel Species compared distantly closely related related What is the difference between convergent and parallel evolution? Convergent Parallel Species compared distantly closely related related Trait produced by different genes/ same genes/ developmental developmental pathways pathways Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight. 2. Parallel evolution Example: lactose tolerance in human adults 3. Evolutionary reversals Example: back mutations at the DNA sequence level (C → A → C). Phylogenetic reconstructions 1. Phenetics (Neighbor - Joining) 2. Cladistics (Maximum Parsimony) 3. Statistics (Maximum Likelihood) Phylogenetic reconstructions Phenetics (Distance Methods) A ATGTTGCCA A B C D * A B AAGTTGCCA B 1 ***** C 4 5 C ATCAACCCA D 7 8 4 * ** D CTCAACTTA Phylogenetic reconstructions Phenetics (Distance Methods) (A,B)=1 (A,B)C=(4+5)/2=4.5 (A,B)D=(7+8)/2=7.5 A B C D (A,B,C)D=(7+8+4)/3=6.3 A B 1 C 4 5 A B C D D 7 8 4 0.5 2.25 1.75 3.15 0.9 Phylogenetic reconstructions Cladistics: A B C D G G A A Maximum Parsimony G A Method 1 step G A C B D A D B C G A G A G A G A G A G A 3 steps 3 steps G G Phylogenetic reconstructions Cladistics: Maximum Parsimony Number of possible rooted trees Number of taxa Number of Number of rooted trees unrooted trees 4 15 3 7 10,395 954 10 34,459,425 2,027,025 Independent gain of camera eye requires two changes Evolution and loss of camera eye requires six changes How do distance trees differ from cladograms? Distance trees Cladograms Characters used as many as synapomorphies possible only Monophyly not required absolute requirement Emphasis branch lengths branch-splitting Outgroup not required absolute requirement Phylogenetic reconstructions 3. Statistics (Maximum Likelihood) The only method based on a mutation model ! Phylogenetic reconstructions 3. Maximum Likelihood A α G α α α α pAn = 3α C α T Jukes-Cantor Model Phylogenetic reconstructions 3. Maximum Likelihood A α G A α G α α α α β β β β C α T C α T Jukes-Cantor Kimura - 2 parameter Model Model Phylogenetic reconstructions 3. Maximum Likelihood A α G pAn = α + 2β β β β β C α T Kimura - 2 parameter Model Markov chain Monte Carlo 1. Start at an arbitrary point 2. Make a small random move 3. Calculate height ratio (r) of new state to old state: 1. r > 1 -> new state accepted 2. r < 1 -> new state accepted with probability r. If new state not accepted, stay in the old state 4. Go to step 2 always accept 2a 1 The proportion of time the accept sometimes MCMC procedure samples 2b from a particular parameter region is an estimate of that region’s posterior probability density 20 % 48 % 32 % tree 1 tree 2 tree 3 Markov chain Monte Carlo 1. Start at an arbitrary point 2. Make a small random move 3. Calculate height ratio (r) of new state to old state: 1. r > 1 -> new state accepted 2. r < 1 -> new state accepted with probability r. If new state not accepted, stay in the old state 4. Go to step 2 always accept 2a 1 The proportion of time the accept sometimes MCMC procedure samples 2b from a particular parameter region is an estimate of that region’s posterior probability density 20 % 48 % 32 % tree 1 tree 2 tree 3 Phylogenetic reconstructions 1. Phenetics (Neighbor - Joining) 2. Cladistics (Maximum Parsimony) 3. Statistics (Maximum Likelihood) Phylogenetic Inference Two points to keep in mind: 1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees • a species tree depicts the evolutionary history of a group of species. • a gene tree depicts the evolutionary history of a specific locus. Infer relationships among three species: Outgroup: Conflict between gene trees and species trees Conflict between gene trees and species trees .
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