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Inferring shared demographic changes from genomic data

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Lightning talk for the 2018 Meeting of the Society of Systematic Biologists (SSB) in Columbus, Ohio.

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Inferring shared demographic changes from genomic data

  1. 1. Inferring shared demographic changes from genomic data Jamie R. Oaks Department of Biological Sciences & Museum of Natural History, Auburn University June 3, 2018 Shared demographic changes Jamie Oaks – phyletica.org 1/14
  2. 2. τ1 Recent interest in testing shared demographic changes Several nice ABC approaches1,2,3 It’s a tricky inference problem 1 Y. L. Chan et al. (2014). Molecular Biology and Evolution 31: 2501–2515 2 A. T. Xue et al. (2015). Molecular Ecology 24: 6223–6240 3 X. A. T. et al. (2017). Molecular Ecology Resources 17: e212–e224 Shared demographic changes Jamie Oaks – phyletica.org 2/14
  3. 3. Shared demographic changes Jamie Oaks – phyletica.org 3/14
  4. 4. Given genomic data, can we infer the correct model and the timing of the demographic events? Shared demographic changes Jamie Oaks – phyletica.org 3/14
  5. 5. Ecoevolity: Estimating evolutionary coevality Simulate datasets with 500k characters Use Bayesian model averaging with full likelihood1,2 No model misspecification Time of change ∼ Exponential(mean = 0.01) 1 J. R. Oaks (2018). bioRxiv 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Shared demographic changes Jamie Oaks – phyletica.org 4/14
  6. 6. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population Ecoevolity: Estimating evolutionary coevality Simulate datasets with 500k characters Use Bayesian model averaging with full likelihood1,2 No model misspecification Time of change ∼ Exponential(mean = 0.01) 1 J. R. Oaks (2018). bioRxiv 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Shared demographic changes Jamie Oaks – phyletica.org 4/14
  7. 7. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population Shared demographic changes Jamie Oaks – phyletica.org 5/14
  8. 8. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population 0.00 0.02 0.04 0.06 0.00 0.02 0.04 0.06 Estimatedeventtime(ˆt) p(t ∈ CI) = 0.942 0.00 0.02 0.04 0.06 0.00 0.01 0.02 0.03 0.04 0.05 0.06 p(t ∈ CI) = 0.953 0.00 0.02 0.04 0.06 0.00 0.01 0.02 0.03 0.04 0.05 0.06 p(t ∈ CI) = 0.937 True event time (t) Shared demographic changes Jamie Oaks – phyletica.org 6/14
  9. 9. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population 1 2 3 1 2 3 Estimated#ofevents(ˆk) 64 33 6 65 194 98 0 15 25 p(k ∈ CS) = 0.988 p(ˆk = k) = 0.566 p(k|D) = 0.480 1 2 3 1 2 3 9 8 1 106 246 128 1 0 1 p(k ∈ CS) = 1.000 p(ˆk = k) = 0.512 p(k|D) = 0.458 1 2 3 1 2 3 28 37 5 100 190 104 0 18 18 p(k ∈ CS) = 0.998 p(ˆk = k) = 0.472 p(k|D) = 0.446 True number of events (k) Shared demographic changes Jamie Oaks – phyletica.org 7/14
  10. 10. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population 0.000 0.002 0.004 0.006 0.000 0.001 0.002 0.003 0.004 0.005 0.006 Estimatedsize(ˆNeµ) p(Neµ ∈ CI) = 0.952 0.000 0.002 0.004 0.006 0.000 0.001 0.002 0.003 0.004 0.005 0.006 p(Neµ ∈ CI) = 0.935 0.000 0.002 0.004 0.006 0.000 0.002 0.004 0.006 p(Neµ ∈ CI) = 0.945 True size of descendant population (Neµ) Shared demographic changes Jamie Oaks – phyletica.org 8/14
  11. 11. 0 1 2 3 4 0.0 0.5 1.0 1.5 2.0 2.5 Density Gamma(10, mean = 0.5) 0 1 2 3 4 0.00 0.25 0.50 0.75 1.00 1.25 Gamma(10, mean = 1.0) 0 1 2 3 4 0.0 0.2 0.4 0.6 Gamma(10, mean = 2.0) Relative size of ancestral population 0.000 0.001 0.002 0.003 0.000 0.001 0.002 0.003 Estimatedsize(ˆNeµ) p(Neµ ∈ CI) = 0.943 0.000 0.002 0.004 0.006 0.008 0.000 0.002 0.004 0.006 0.008 p(Neµ ∈ CI) = 0.957 0.000 0.005 0.010 0.015 0.000 0.005 0.010 0.015 p(Neµ ∈ CI) = 0.943 True size of ancestral population (Neµ) Shared demographic changes Jamie Oaks – phyletica.org 9/14
  12. 12. Thoughts Yes, this is a difficult inference problem Next step: Are there regions of parameter space where this works? Shared demographic changes Jamie Oaks – phyletica.org 10/14
  13. 13. 0.00 0.02 0.04 0.06 True divergence time (t) 0.00 0.01 0.02 0.03 0.04 0.05 0.06 Estimateddivergencetime(ˆt) p(t ∈ CI) = 0.946 RMSE = 1.02e-04 1 2 3 True number of events (k) 1 2 3 Estimatednumberofevents(ˆk) 105 5 0 1 266 7 0 2 114 p(ˆk = k) = 0.970 p(k|D) = 0.980 Good news: Inferring shared divergence times does seem to work1 1 J. R. Oaks (2018). bioRxiv Shared demographic changes Jamie Oaks – phyletica.org 11/14
  14. 14. Everything is on GitHub. . . Software: Ecoevolity: http://phyletica.org/ecoevolity Open-Science Notebooks: https://github.com/phyletica/ecoevolity-demog-experiments https://github.com/phyletica/ecoevolity-experiments Shared demographic changes Jamie Oaks – phyletica.org 12/14
  15. 15. Acknowledgments Ideas and feedback: Phyletica Lab Leach´e Lab Minin Lab Mark Holder Computation: Funding: Photo credits: PhyloPic! Shared demographic changes Jamie Oaks – phyletica.org 13/14
  16. 16. Questions? joaks@auburn.edu c 2007 Boris Kulikov boris-kulikov.blogspot.com Shared demographic changes Jamie Oaks – phyletica.org 14/14

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