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Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
Estimation of divergence times
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Estimation of divergence times

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

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
  • Transcript

    • 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
    • 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. Molecular clock packages available <ul><li>BEAST – Drummond &amp; 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 &amp; 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. Molecular clock packages available <ul><li>BEAST – uncorrelated rates </li></ul><ul><li>MCMCTree – uncorrelated &amp; 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. 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)
    • 13. BEAUTI &amp; BEAST <ul><li>nexus file </li></ul><ul><li>xml file </li></ul>
    • 14. Phylogeny specification &lt;newick id=&amp;quot;startingTree&amp;quot;&gt; (((((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); &lt;/newick&gt;
    • 15. Strict clock &amp; Relaxed clock Priors
    • 16. Operators <ul><li>remove “Tree” operator for fixed phylogeny </li></ul>
    • 17. Generations <ul><li>Convergence &amp; ESS values </li></ul>
    • 18. Beast running…
    • 19. A fuzzy caterpillar
    • 20. MCMCTree seqfile = exampleseqs.phy treefile = example.tre outfile = exampleseqs_3.out (((((Ssc,Bta),((Cfa,Fca)&apos; B(0.45,0.47) &apos;,Eca)),(((Rno,Mmu),Ocu),(((Hsa,Ptr),Ppy)&apos; B(0.09,0.11) &apos;,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) &apos;,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 = &lt; 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
    • 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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