Dr. Battistuzzi's presentation during the 2011 CEMI MPA Workshop.

1. MPAW Estimation of divergence times Fabia U. Battistuzzi [email_address]

2. Two dimensions of evolution Lineage Relations Time frame Evolutionary Rate

3. Molecular clocks – brief overview Time Sequence Change X Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st protein clock

4. Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st protein clock Neutral theory Rate tests

5. Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st protein clock Neutral theory Deut.-Prot. divergence Rate tests Rate Autocorrelation Ancestor Descendant slower faster

6. Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st protein clock Neutral theory Deut.-Prot. divergence Rate tests Rate Autocorrelation Local rates slower faster

7. Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st protein clock Neutral theory Deut.-Prot. divergence Rate tests Rate Autocorrelation Local rates Autocorrelated clocks Uncorrelated clocks

11. Calibration priors Minimum only Maximum only Minimum-Maximum time lognormal : 95% probability uniform time exponential time normal time

12. Calibration priors Minimum only Maximum only Minimum-Maximum time : 95% probability time exponential time normal time Hedges and Kumar, Trends in Genetics (2004)

14. Phylogeny specification <newick id=&quot;startingTree&quot;> (((((Ssc:0.65,Bta:0.65):0.16,((Cfa:0.46,Fca:0.46):0.28,Eca:0.74):0.07):0.11,(((Rno:0.20,Mmu:0.20):0.65,Ocu:0.85):0.05,(((Hsa:0.05,Ptr:0.05):0.05,Ppy:0.10):0.13,Mml:0.23):0.67):0.02):0.81,Tvu1:1.73):1.37,Gga:3.10); </newick>

15. Strict clock & Relaxed clock Priors

18. Beast running…

19. A fuzzy caterpillar

20. MCMCTree seqfile = exampleseqs.phy treefile = example.tre outfile = exampleseqs_3.out (((((Ssc,Bta),((Cfa,Fca)' B(0.45,0.47) ',Eca)),(((Rno,Mmu),Ocu),(((Hsa,Ptr),Ppy)' B(0.09,0.11) ',Mml))),Tvu1),Gga);

21. MCMCTree seqfile = exampleseqs.phy treefile = example.tre outfile = exampleseqs_3.out (((((Ssc,Bta),((Cfa,Fca)‘ L(0.35,0.1,0.5,0.025) ',Eca)),(((Rno,Mmu),Ocu),(((Hsa,Ptr),Ppy),Mml))),Tvu1),Gga); p L p L t L p c

22. MCMCTree seqfile = exampleseqs.phy treefile = example.tre outfile = exampleseqs_3.out ndata = 1 usedata = 3 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates RootAge = < 3.0 * safe constraint on root age, used if no fossil for root. Ancestor Descendant slower faster slower faster Ancestor Descendant uncorrelated autocorrelated

23. MCMCTree model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85 alpha = 0 * alpha for gamma rates at sites ncatG = 5 * No. categories in discrete gamma cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? BDparas = 2 2 0.1 * birth, death, sampling kappa_gamma = 6 2 * gamma prior for kappa alpha_gamma = 1 1 * gamma prior for alpha rgene_gamma = 1 7.13 * gamma prior for overall rates for genes sigma2_gamma = 1 1.15 * gamma prior for sigma^2 (for clock=2 or 3) rgene : prior on rate parameter; Sigma2 : prior on rate heterogeneity;

24. TimeTrees 300 250 200 150 100 50 0 Time (millions of years)

25. TimeTrees Ssc Bta Cfa Fca Eca Rno Mmu Ocu Hsa Ptr Ppy Mml Tvu1 Gga 0 50 100 150 200 Time (millions of years)

26. TimeTrees Ssc Bta Cfa Fca Eca Rno Mmu Ocu Hsa Ptr Ppy Mml Tvu1 Gga 0 50 100 150 200 Time (millions of years)

27. BEAST

28. MCMCTree autocorrelation uncorrelation

29. MultiDivTime

30. 95% Credibility intervals TT TT Success Failure Model Match Model Violation