MPAW Estimation of divergence times Fabia U. Battistuzzi [email_address]
Two dimensions of evolution Lineage Relations Time frame Evolutionary Rate
Molecular clocks – brief overview Time Sequence Change X Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 19...
Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st  prot...
Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st  prot...
Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st  prot...
Molecular clocks – brief overview Kumar, Nature Reviews Genetics (2005) 1962 1968 1972 1976 1984 1989 1997 2006 1 st  prot...
What can we do with molecular clocks? <ul><li>Species divergence </li></ul><ul><li>Phylogeography </li></ul><ul><li>Epidem...
Molecular clock packages available <ul><li>BEAST  – Drummond & Rambaut </li></ul><ul><ul><li>Uncorrelated rates </li></ul>...
Molecular clock packages available <ul><li>BEAST – uncorrelated rates </li></ul><ul><li>MCMCTree – uncorrelated & autocorr...
Calibration priors Minimum only Maximum only Minimum-Maximum time lognormal : 95% probability uniform time exponential tim...
Calibration priors Minimum only Maximum only Minimum-Maximum time : 95% probability time exponential time normal time Hedg...
BEAUTI & BEAST <ul><li>nexus file </li></ul><ul><li>xml file </li></ul>
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....
Strict clock & Relaxed clock Priors
Operators <ul><li>remove “Tree” operator for fixed phylogeny </li></ul>
Generations <ul><li>Convergence & ESS values </li></ul>
Beast running…
A fuzzy caterpillar
MCMCTree seqfile = exampleseqs.phy treefile =  example.tre outfile = exampleseqs_3.out (((((Ssc,Bta),((Cfa,Fca)' B(0.45,0....
MCMCTree seqfile = exampleseqs.phy treefile =  example.tre outfile = exampleseqs_3.out (((((Ssc,Bta),((Cfa,Fca)‘ L(0.35,0....
MCMCTree seqfile = exampleseqs.phy treefile = example.tre outfile = exampleseqs_3.out ndata = 1 usedata = 3  * 0: no data;...
MCMCTree model = 4  * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85 alpha = 0  * alpha for gamma rates at sites ncatG = 5  * No. ca...
TimeTrees 300 250 200 150 100 50 0 Time (millions of years)
TimeTrees Ssc Bta Cfa Fca Eca Rno Mmu Ocu Hsa Ptr Ppy Mml Tvu1 Gga 0 50 100 150 200 Time (millions of years)
TimeTrees Ssc Bta Cfa Fca Eca Rno Mmu Ocu Hsa Ptr Ppy Mml Tvu1 Gga 0 50 100 150 200 Time (millions of years)
BEAST
MCMCTree autocorrelation uncorrelation
MultiDivTime
95% Credibility intervals TT TT Success Failure Model Match Model Violation
Things to remember <ul><li>Check priors for calibrations, substitution rate, rate  </li></ul><ul><li>model, etc. </li></ul...
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Estimation of divergence times

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

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  • Evolution expressed in time units Allows comparisons across trees with different evolutionary scales (e.g., different rates)
  • Basic principle of molecular clocks Global clocks vs. local/relaxed clocks Rate variation models
  • Basic principle of molecular clocks Global clocks vs. local/relaxed clocks Rate variation models
  • Basic principle of molecular clocks Global clocks vs. local/relaxed clocks Rate variation models
  • Basic principle of molecular clocks Global clocks vs. local/relaxed clocks Rate variation models
  • Basic principle of molecular clocks Global clocks vs. local/relaxed clocks Rate variation models
  • Screen shots of Beauti with the various options Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Screen shots of Beauti with the various options Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Screen shots of Beauti with the various options Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Screen shots of Beauti with the various options Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Screen shots of Beauti with the various options Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Show how to fix phylogeny Discuss problem of priors and how to define them discuss calibration distributions Priors only
  • Cauchy distribution for calibrations
  • Cauchy distribution for calibrations
  • Cauchy distribution for calibrations
  • Screen shots of mcmctree ctl files AR vs. RR Cauchy distribution for calibrations
  • Estimation of divergence times

    1. 1. MPAW Estimation of divergence times Fabia U. Battistuzzi [email_address]
    2. 2. Two dimensions of evolution Lineage Relations Time frame Evolutionary Rate
    3. 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. 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. 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. 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. 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
    8. 8. What can we do with molecular clocks? <ul><li>Species divergence </li></ul><ul><li>Phylogeography </li></ul><ul><li>Epidemiology </li></ul><ul><li>Rate estimations </li></ul>Eastern fox squirrel ( Sciurus niger ) lacks phylogeographic structure: recent range expansion and phenotypic differentiation
    9. 9. Molecular clock packages available <ul><li>BEAST – Drummond & Rambaut </li></ul><ul><ul><li>Uncorrelated rates </li></ul></ul><ul><li>MCMCTree – Yang </li></ul><ul><ul><li>Uncorrelated and autocorrelated rates </li></ul></ul><ul><li>MultiDivTime – Thorne & Kishino </li></ul><ul><ul><li>Autocorrelated rates between ancestor-descendant </li></ul></ul><ul><li>Pathd8 – Britton et al. </li></ul><ul><ul><li>Autocorrelation between sister groups </li></ul></ul><ul><li>Phylobayes – Lartillot et al. </li></ul><ul><ul><li>Uncorrelated and autocorrelated rates </li></ul></ul><ul><li>R8s – Sanderson </li></ul><ul><ul><li>Strict, local, relaxed clock </li></ul></ul>
    10. 10. Molecular clock packages available <ul><li>BEAST – uncorrelated rates </li></ul><ul><li>MCMCTree – uncorrelated & autocorrelated rates </li></ul><ul><li>MultiDivTime – autocorrelated rates </li></ul><ul><li>Basic functionality </li></ul><ul><li>1. bayesian methods: based on priors and data, estimate posteriors (divergence times and credibility intervals) </li></ul><ul><li>2. analyze partitioned data (codon positions, genes) </li></ul><ul><li>3. calibration points </li></ul><ul><li>4. estimate phylogeny and/or branch lengths </li></ul>
    11. 11. Calibration priors Minimum only Maximum only Minimum-Maximum time lognormal : 95% probability uniform time exponential time normal time
    12. 12. Calibration priors Minimum only Maximum only Minimum-Maximum time : 95% probability time exponential time normal time Hedges and Kumar, Trends in Genetics (2004)
    13. 13. BEAUTI & BEAST <ul><li>nexus file </li></ul><ul><li>xml file </li></ul>
    14. 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. 15. Strict clock & Relaxed clock Priors
    16. 16. Operators <ul><li>remove “Tree” operator for fixed phylogeny </li></ul>
    17. 17. Generations <ul><li>Convergence & ESS values </li></ul>
    18. 18. Beast running…
    19. 19. A fuzzy caterpillar
    20. 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. 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. 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. 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. 24. TimeTrees 300 250 200 150 100 50 0 Time (millions of years)
    25. 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. 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. 27. BEAST
    28. 28. MCMCTree autocorrelation uncorrelation
    29. 29. MultiDivTime
    30. 30. 95% Credibility intervals TT TT Success Failure Model Match Model Violation
    31. 31. Things to remember <ul><li>Check priors for calibrations, substitution rate, rate </li></ul><ul><li>model, etc. </li></ul><ul><li>Repeat every analyses at least twice to check for </li></ul><ul><li>convergence </li></ul><ul><li>Look for the “fuzzy caterpillar” for all parameters </li></ul><ul><li>Test assumptions’ effects using multiple methods and </li></ul><ul><li>priors (bayes factors) </li></ul><ul><li>Credibility intervals are a conservative estimate of </li></ul><ul><li>divergences </li></ul>Questions ?

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