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Time-dependent rates of molecular evolution Evidence and causes

Time-dependent rates of molecular evolution Evidence and causes. Simon Ho School of Biological Sciences. Acknowledgements. Acknowledgements. Rob Lanfear , Lindell Bromham , Matt Phillips Australian National University Julien Soubrier , Alan Cooper University of Adelaide

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Time-dependent rates of molecular evolution Evidence and causes

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  1. Time-dependent rates of molecular evolution Evidence and causes Simon Ho School of Biological Sciences

  2. Acknowledgements Acknowledgements • Rob Lanfear, LindellBromham, Matt PhillipsAustralian National University • JulienSoubrier, Alan CooperUniversity of Adelaide • Allen RodrigoDuke University & University of Auckland • Jeremy and Barbara

  3. Introduction Morphological rates • Measured in darwins or haldanes • Neontological studies • Palaeontological studies • Differ by several orders of magnitude Gingerich (2001)

  4. Introduction Molecular rates: Pedigrees Howell et al. (2003)

  5. Introduction Molecular rates: Phylogenies 6 Myr Rate = / 6 Myr 0.06 difference =0.01 / Myr

  6. Introduction A B A B Recent splitFast rate Ancient splitSlow rate Estimating rates A B Fossil record Biogeography Sampling times Pedigrees

  7. Introduction Calibration

  8. Evidence Evidence Birds (mtDNA) Primates (mtDNA) Primates (D-loop) Ho et al. (2005)

  9. Evidence Evidence Genneret al. (2007) Burridgeet al. (2008)

  10. Evidence Evidence Hennet al. (2009) Papadopoulouet al. (2009)

  11. Evidence Evidence from ancient DNA

  12. Evidence Evidence from ancient DNA Hay et al. (2008) 12

  13. Implications Implications: Human migration Endicott et al. (2009)

  14. Implications Implications: Human migration Ho & Endicott (2008)

  15. Implications Implications: LPO hypothesis

  16. LPO hypothesis Ho et al. (2008)

  17. Causes Causes • The basic biological framework • The effects of natural selection • The effects of calibration errors • The effect of model misspecification • Artefacts causing time-dependent molecular rates

  18. Biological framework Evidence

  19. Biological framework Evidence

  20. Natural selection Negative selection • Most mutations are deleterious • Time-dependent decline in ratio of nonsynonymous to synonymous mutations • Stronger time-dependence of rates in coding DNA Subramanian (2009)

  21. Natural selection Positive selection • Selection favouring advantageous mutations • Evidence • Adaptive mitochondrial variation in response to climatic factors

  22. Calibration errors Coalescent calibration error • Genetic divergence precedes reproductive isolation Genetic divergence Reproductiveisolation

  23. Calibration errors Fossil calibration error • Fossil appearance is later than genetic divergence 6 Myr

  24. Model misspecification Phylogenetic assumptions • Mitochondrial DNA • No recombination • Maternally inherited • Homoplasmy

  25. Model misspecification Saturation • Mutational hotspots • Under-correction for saturation over longer time periods

  26. Model misspecification Demographic factors • Population structure • Misspecified demographic model Navascues & Emerson (2009)

  27. Artefacts Sequence error • Sequencing error • Post-mortem damage(ancient DNA) • Artificial mutations • Inflate rate estimates • Corrected usingphylogenetic modelsof sequence error

  28. Ancient DNA Ancient DNA • Evidence from ancient DNA is pivotal

  29. Ancient DNA Ancient DNA • Heterochronous tips • Ages up to 500,000 years

  30. Ancient DNA Challenges • Ancient DNA data from populations • Low variation • Small range of sampling times • Lack of control over sampling design • Cost of radiocarbon dating • Post-mortem damage

  31. Concluding remarks Concluding remarks • Difficulties in estimating rates empirically • Paucity of reliable age calibrations • Range of potential biological and methodological causes • We need to disentangle these factors so that we can estimate timescales accurately

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