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16th September 2014

Convergence for everyone? Detecting disparate signals of genomic adaptive convergence in several different datasets: Initial results, lessons & perspectives. 16th September 2014. Joe Parker, Queen Mary University London. Adaptive molecular convergence. Definition Methods to detect

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16th September 2014

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  1. Convergence for everyone?Detecting disparate signals of genomic adaptive convergence in several different datasets:Initial results, lessons & perspectives 16th September 2014 Joe Parker, Queen Mary University London

  2. Adaptive molecular convergence • Definition • Methods to detect • Datasets and results • Sampling issues • Interpretational issues • Future

  3. Defining molecular convergence • Surprisingly hard • It isn’t: • Divergence (adaptive or neutral) • Conservation or purifying selection • Retention of ancestral states with secondary changes in outgroups • ‘Neutral’ homoplasy • It ought to be: • ‘Adaptive’ homoplasies • ‘Excess’ homoplasies

  4. Observations • ‘Adaptive convergence’ predicated on assumption adaptive sites ‘count’ more - conditions for detection? • Can parallel changes with dN/dS ~ 1 be ‘convergent’ • ‘Excess’ - a problematic definition without a good null model • Odds-ratio based? • Empirical CDF? • Eyeball…

  5. Methods • Species phylogeny and inputs • Selection detection • Site-based methods • Tree-based methods

  6. Site-based methods • Look at tips • Sample balance?

  7. Site-based methods • Look at tips • Reconstruct ancestral changes

  8. Site-based methods • Look at tips • Reconstruct ancestral changes • Pairwise P(conv) ~ P(div) changes

  9. Site-based methods • Look at tips • Reconstruct ancestral changes • Pairwise P(conv) ~ P(div) changes • BEB posterior probabilities

  10. Tree-based methods • de novo tree search • Inference error • Signal : noise • Multiple phylogenies

  11. Tree-based methods • ∆SSLS (likelhood comparison) • Which hypotheses? • Multiple simultaneous comparisons? • Models insensitive • How extreme

  12. Tree-based methods • Unrestricted / ennumerated phylogeny fitting

  13. Trees and sites methods • dN/dS and ∆SSLS correlation

  14. Trees and sites methods • Random control tree correction

  15. Genomic approaches • Pool information across sites • Are loci comparable • Error rates? • Orthology, paralogy

  16. Sampling • Sampling balance • Within locus • Between loci • Gene selection / ascertainment bias • Networks • Tree selection • a priori phylogenies

  17. Convergence in echolocating mammals • 22 mammals, 2,326 loci • Convergence signals across genome

  18. Convergence in echolocating bats • The • The

  19. Convergence in mole-rats • The • The

  20. Interpretational issues • Relative measure • Strength of evidence • Null model? Sampling? Which phylogenies

  21. Interpretation • Notional convergence detected genomically, or not at all • Selection, incongruence • Which trees?

  22. Which Trees? • Choice of hypothesis, subtly different from usual practice • If we accept tree space distance important… • … Hypotheses are parameters • Ennumerate over trees?

  23. Future directions • Null model • Alternative (convergent) model • Tree space distance

  24. Conclusion • Strong evidence molecular convergence, or something like our best definition of it, is a pervasive force • Very early work; contrast with e.g. early dN/dS tests

  25. Acknowlegements • Colleagues • Institutions • Funding

  26. Further information • Reading • Li, Liu, Castoe, Parker • Resources • SVN, site, j.d.parker@qmul.ac.uk

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