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The Origin of Gene Subfunctions and Genotypic Complexity by Modular Restructuring

The Origin of Gene Subfunctions and Genotypic Complexity by Modular Restructuring. Allan Force, Bill Cresko, F Bryan Pickett, Chris Amemiya, and Mike Lynch. Subdivision and specialization - a trend in evolution. Evolutionary Time.

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The Origin of Gene Subfunctions and Genotypic Complexity by Modular Restructuring

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  1. The Origin of Gene Subfunctions and Genotypic Complexity by Modular Restructuring Allan Force, Bill Cresko, F Bryan Pickett, Chris Amemiya, and Mike Lynch

  2. Subdivision and specialization - a trend in evolution Evolutionary Time

  3. Is the Increasing Phenotypic Specialization Reflected in Underlying Genetic Circuitry?

  4. What is the default contribution to specialization of body regions at the genotypic level produced by mutation pressure and genetic drift?

  5. . Modular Restructuring Evolution of differential connectivity of the genotypic- phenotypic map via subfunction formation and resolution in developmental genetic networks by nearly neutral processes

  6. . Modular Restructuring Evolution of differential connectivity of the genotypic- phenotypic map via subfunction formation and resolution in developmental genetic networks by nearly neutral processes . Subfunction Formation The processes which lead to origin of new gene subfunctions either by co-option or fission mechanisms

  7. . Modular Restructuring Evolution of differential connectivity of the genotypic- phenotypic map via subfunction formation and resolution in developmental genetic networks by nearly neutral processes . Subfunction Formation The processes which lead to origin of new gene subfunctions either by co-option or fission mechanisms . Subfunction Resolution The processes which lead to the partitioning of existing subfunctions between gene duplicates by DDC mechanisms

  8. Multifunctional gene Subfunction 1 Subfunction 2

  9. Given that many genes are multifunctional, how do new subfunctions evolve?

  10. SubfunctionCo-option

  11. Subfunction Fission

  12. TFA

  13. A TFA A

  14. A TFA TFB A TFA and TFB TFA

  15. A TFA TFB TFC A TFA and TFB TFA and TFC

  16. TFA TFB TFC A A B B TFA and TFB TFA and TFC

  17. TFA TFB TFC A A B C B C TFA and TFB TFA and TFC

  18. TFA TFB TFC B C C B

  19. B TFB TFC C B C

  20. Fission Phase 1: Accretion, Degeneration, and Replacement Abc AbC ABc Time? ABC aBC

  21. abc abC Abc aBc AbC aBC ABc ABC

  22. PXW= (1/2ma + 4Ne)-1 PYX= (1/ma + 4Ne)-1 PZY= (1/md + 4Ne)-1 State X (AbC) or (ABc) State Z (aBC) State W (Abc) State Y (ABC) PWX= (1/md + 4Ne)-1 PXY= (1/2md + 4Ne)-1 PZY= (1/2ma + 4Ne)-1

  23. Time for subfunction fission phase 1 when the addition and deletion rates are equal

  24. When the time to fission for phase 1 is very long in large effective population sizes does this mean the precursor allele (ABC allele) is unavailable?

  25. Infinite population size equilibrium frequencies for the 3 site fission model 1 ABC Abc 0.75 0.5 Equilibrium Frequencies ABc+AbC 0.25 aBC 0 0 5 10 15 20 (ma/ md ) Addition Deletion Rate ratio

  26. The effect of population size on the equilibrium frequencies under the 3 site fission model 0.3 md= ma ABC 0.25 ABc or AbC 0.2 Equilibrium Frequency Abc 0.15 aBC 0.1 103 107 105 101 Effective Population Size

  27. What about multiple TF binding Sites? AABBCC

  28. Effects of additional TF binding sites on the time to fission phase 1 under the 6 site model 1010 Sim3 10-4 108 Sim3 10-5 Generations Sim6 10-4 106 Sim6 10-5 104 101 105 103 Effective Population Size

  29. More complex models have similar behavior to that of the basic 3-site model 1) Increasing the number of TF binding sites in the 6-site model does not significantly change the behavior relative to the 3-site model, but does reduce the time for phase 1 2) Allowing for different rates of mutation of the A site relative to the B and C sites does not significantly change the behavior of 3 site model for reasonable mutation rates

  30. Phase II Enhancer Subfunctionalization

  31. The probability of enhancer subfunctionalization 1.0 Ratio1=.25 0.1 Ratio2=.75 Ratio1 est 1 Pr(Enhancer Subfunctionalization) Ratio1 est 2 Ratio2 est 1 Ratio2 est 2 0.001 101 105 103 Effective Population Size

  32. Modular Restructuring

  33. Summary: Subfunction fission leads to the emergence of new subfunctions from the splitting of old subfunctions and may proceed under the guidance of mutation pressure in small populations (Nm < .1). More generally, small effective population size and mutation may be sufficient to drive the evolution of the complexity of genes, networks, and developmental pathways passively by modular restructuring. Changes in the underlying genetic architecture may not be initially observed at the phenotypic level. However, the long-term cumulative effects of modular restructuring may lead to abrupt and rapid changes at the phenotypic level when organisms find themselves exposed to novel environments.

  34. AMEMIYA LABORATORY Allan Force Tom Miyake Tom Powers Wendy Lippman Alicia Hill - Force Andrew Stuart Deb Tinnemore Josh Danke Michael Schoenborn Garnet Navarro Ayumi Aoki Mary West Chris Amemiya Funding sources: NSF, DOE, NHGRI, NCRR

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