# Substitution = Mutation followed. by Fixation. Common Ancestor ACGATC 1:A G 2:C A GAGATC 3:G A 6:C T 5:T C 4:A C GAAATT 1:G A

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1 GAGATC 3:G A 6:C T Common Ancestor ACGATC 1:A G 2:C A Substitution = Mutation followed 5:T C by Fixation GAAATT 4:A C 1:G A AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon

2 AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon

3 Likelihood (Prob. of data given model & parameter values) = AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon Likelihood for Site 1 X AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon Likelihood for Site 2 X AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon... X... X... X Likelihood for Site 6 AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon

4 A G G AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon

5 Prob. of A at end of branch given A at beginning Jukes-Cantor Transition Probabilities Expected number of changes per site (branch length)

6 Jukes-Cantor Transition Probabilities Prob. of G at end of branch given A at beginning Expected number of changes per site (branch length)

7 Probabilistic models of nucleotide change (independently and identically evolving sites) Let q ij be the instantaneous rate of change at a site from nucleotide type i to j Q is matrix of instantaneous rates (Q will have 4 rows and 4 columns because i and j can each by any of 4 nucleotide types) For nucleotide starting as type i at time 0, probability nucleotide is type j at time t is denoted p ij (t). p ij (t) is referred to as a transition probability.

8 Consider a very very small amount of evolutionary time t. When i j, p ij ( t). = q ij t p ii ( t). = 1 q ij t j,j i where p ii ( t). = 1 + q ii t q ii = j,j i q ij (in preceding equations, =. can be replaced by = when the limit as t approaches 0 is taken)

9 Jukes-Cantor model is simplest model of nucleotide substitution. It assumes sequence positions evolve independently and it assumes that all possible changes at a position are equally likely. Let π j be probability a residue is type j. π j is called the equilibrium probability of type j. p ij ( ) = π j For Jukes-Cantor model, π j = 1/4 for all 4 nucleotide types j.

10 General Time Reversible Model 3 subst. types (transitions, 2 transversion classes) Tamura-Nei HKY85 Felsenstein 84 Felsenstein 81 Equal Base Frequencies 2 subst. types (transitions vs. transversions) Single Substitution Type 3 subst. types (transitions, 2 transversion classes ) SYM 2 subst. types (transitions vs. transversions) K3ST Kimura 2 Param. Jukes-Cantor Equal Base Frequencies Single Substitution Type based on Figure 11 from Swofford et al. Chapter in Molecular Systematics (Sinauer, 2nd ed. 1996)

11 Rate Matrix for Jukes-Cantor Model F R To O M A C G T A 3µ µ µ µ C µ 3µ µ µ G µ µ 3µ µ T µ µ µ 3µ Note 1: Diagonal matrix elements multiplied by 1 are rate away from nucleotide type of that row. Note 2: In later slide on Jukes-Cantor model, we write s/3 rather than µ.

12 Rate Matrix for Kimura 2-Parameter Model F R To O M A C G T A α 2β β α β C β α 2β β α G α β α 2β β T β α β α 2β Changes involving only purines (i.e., A and G) or only pyrimidines (i.e., C and T) are transitions. Changes involving one purine and one pyrimidine are transversions.

13 Rate Matrix for Felsenstein 1981 Model F R To O M A C G T A µ(π C + π G + π T ) µπ C µπ G µπ T C µπ A µ(π A + π G + π T ) µπ G µπ T G µπ A µπ C µ(π A + π C + π T ) µπ T T µπ A µπ C µπ G µ(π A + π C + π G )

14 Rate Matrix for Hasegawa-Kishino-Yano (a.k.a. HKY or HKY85) Model F R To O M A C G T A µ(π C + κπ G + π T ) µπ C µκπ G µπ T C µπ A µ(π A + π G + κπ T ) µπ G µκπ T G µκπ A µπ C µ(κπ A + π C + π T ) µπ T T µπ A µκπ C µπ G µ(π A + κπ C + π G )

15 Rate Matrix for General Time Reversible Model F R To O M A C G T A µ(aπ C + bπ G + cπ T ) µaπ C µbπ G µcπ T C µaπ A µ(aπ A + dπ G + eπ T ) µdπ G µeπ T G µbπ A µdπ C µ(bπ A + dπ C + fπ T ) µfπ T T µcπ A µeπ C µfπ G µ(cπ A + eπ C + fπ G )

16 Time Reversibility is a common property of models of sequence evolution. Time reversibility means that π i p ij (t) = π j p ji (t) for all i, j, and t. π i q ij = π j q ji for all i and j. For phylogeny reconstruction, time reversibility means that we cannot (on the basis of sequence data alone) hope to distinguish which of two sequence is ancestral and which is the descendant.

17 The practical implication of time reversibility for phylogeny reconstruction is that maximum likelihood cannot infer the position of the root of the tree unless additional information information exists (e.g., which taxa are the outgroups) or additional assumptions are made (e.g., a molecular clock).

18 Q will represent matrix of instantaneous rates of change. For general time reversible model, entries of Q are: To From A C G T A (aπ C + bπ G + cπ T ) aπ c bπ G cπ T C aπ A (aπ A + dπ G + eπ T ) dπ G eπ T G bπ A dπ C (bπ A + dπ C + fπ T ) fπ T T cπ A eπ C fπ G (cπ A + eπ C + fπ G ) In above matrix: a, b, c, d, e, and f cannot be negative. With any rate matrix (including above), the transition probabilities P (t) can be determined from the rate matrix Q and the amount of evolution t via P (t) = e Qt = I + (Qt) 1! + (Qt)2 2! + (Qt)3 3! +..., where I is the identity matrix.

19 Computing p ij (t) for the Jukes-Cantor model The Jukes Cantor model assumes that this is how nucleotide substitution occurs: 0. π A = π G = π C = π T = For each site in the sequence, an event will occur with probability 4 3s per unit evolutionary time. 2. If no event occurs, the residue at the site does not change. 3. If an event occurs, the probability that a residue is type i after the event is π i.

20 What is the probability that no event occurs in t units of evolutionary time? (1 4 3 s) (1 4 3 s) (1 4 3 s)... (1 4 3 s) = (1 4 3 s)t. When 3 4 s is close to 0, s. = e 4 3 s.

21 Pr (no event) = (1 4 3 s)t. = e 4 3 st. When s is redefined as an instantaneous rate per unit evolutionary time, the approximation becomes an equality: Pr (no event) = e 4 3 st. Pr (at least one event) = 1 Pr (no event) = 1 e 4 3 st.

22 If there have been no events, then the residue cannot possibly have changed after an amount of evolution t. If there has been at least one event, then the residue is type j with probability π j. p ii (t) = Pr (no events) + Pr (at least one event)π j = e 4 3 st + (1 e 4 3 st )π j.

23 For i j, p ij (t) = Pr (at least one event)π j = (1 e 4 3 st )π j. Notice that 4 3 s and t appear only as a product. 4 3 s and t cannot be separately estimated. Only their product can be estimated. Note: A generalization of the Jukes Cantor model, the Felsenstein 1981 model does not require π A = π G = π C = π T = 1 4.

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