GAMEModelling a genes-eye view of evolutionPaul Berkman | OCE Postdoctoral Fellow – Sugarcane Genome Bioinformatics22 Marc...
Overview• Sugarcane genomics• A (somewhat) new perspective?• Some fun and GAMEsWhere is polyploidy going? | Paul Berkman |...
Basic BreedingGISH on cultivars              80% S. officinarum                            S. spontaneum   S. officinarum ...
Complex Genome                   S. spontaneumS. officinarum            recombinants                                      ...
Complex Genome                   S. spontaneumS. officinarum            recombinants          sugarcane                   ...
7.7       WGD 10-15Allopolyploid wheat          10-16                                                            (8-9)    ...
Autopolyploid sugarcane       Jannoo, et al., Plant Journal (2007)                                                        ...
A whole lot of copies…                                  S. spontaneum             S. officinarum               recombinant...
What seems to be the problem?• A networks perspective                                                         A           ...
What seems to be the problem?• A networks perspective                                              ?               A   Moo...
What seems to be the problem?• A networks perspective                                          B                          ...
What seems to be the problem?• A networks perspective                                          B                          ...
What seems to be the problem?                                                                  S. spontaneum• A networks p...
What seems to be the problem?• What shall we do with the big black hole?• How might we elucidate some general principles o...
A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 15
A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 16
A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 17
A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 18
A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 19
Game theory• Mathematical study of players, strategy sets, and pay-offs• Economics, politics, anthropology• Assumes ration...
Game theory at the gene level?• The Selfish Gene, Richard Dawkins 1976• Genes as agents operating in evolution• Some criti...
Game theory at the gene level?• Gene token as an agent     • Optimisation theory rationalises the premise     • Functions ...
Game theory at the gene level?“… the gene’s eye view … must ultimately be judged according tohow well it facilitates hypot...
GAME• Gene-Agent Modelling of Evolution     • Python toolkit based on pyabm, open source agent-based modelling• They have ...
GAMEWhere is polyploidy going? | Paul Berkman | Page 25
GAME                  A,A                                 A,A   A,A         A,A                  B,B                      ...
GAME                  A,A                                 A,A’   A,A         A,A                  B,B                     ...
GAME – preliminary resultsWhere is polyploidy going? | Paul Berkman | Page 28
GAME – preliminary resultsWhere is polyploidy going? | Paul Berkman | Page 29
Why GAME?• Gene networks/systems approach     • Lends itself to analysis of competition over evolutionary time• Diploidisa...
Polyploid game theory• Universal framework applying evolutionary game theoryWhere is polyploidy going? | Paul Berkman | Pa...
AcknowledgementsKaren Aitken                                          Adam SkarshewskiNathalie Pipiridis                  ...
Thank youCSIRO Plant IndustryPaul BerkmanOCE Postdoctoral Fellowt +61 7 3214 2361e paul.berkman@csiro.auw www.csiro.au/piC...
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GAME: modelling a gene's-eye view of evolution - Paul Berkman

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It is now nearly half a century since the establishment of game theory as a mechanism for studying evolution. While the primary application of this work has been at the population and species level, the gene's-eye view of evolution was postulated only shortly after evolutionary game theory itself. However, an experimental or empirical approach to the gene's-eye view has not been well developed, primarily due to the challenges associated with measuring how genes act as agents over the course of evolution, with the first mathematical theory describing this perspective only published in 2011. Major advances in our understanding of the core tenets of genetics and biochemistry over the last few decades are providing the data needed to calibrate the gene's-eye approach, and high-throughput sequencing technologies promise to provide even more such data.
In this talk I will present GAME (Gene-Agent Modelling of Evolution), a software package designed for agent-based modelling of evolution from the gene perspective. This model provides a simulation of changes to the value and fitness of individual genes in a population of organisms over time. I will present preliminary results regarding the impacts of mutation and allelic diversity over time, testing the hypothesis that greater allelic diversity at a locus results in greater fitness for that locus.

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GAME: modelling a gene's-eye view of evolution - Paul Berkman

  1. 1. GAMEModelling a genes-eye view of evolutionPaul Berkman | OCE Postdoctoral Fellow – Sugarcane Genome Bioinformatics22 March 2013CSIRO PLANT INDUSTRY
  2. 2. Overview• Sugarcane genomics• A (somewhat) new perspective?• Some fun and GAMEsWhere is polyploidy going? | Paul Berkman | Page 2
  3. 3. Basic BreedingGISH on cultivars 80% S. officinarum S. spontaneum S. officinarum S. spontaneumspontaneum 15% S. S. officinarum recombinants 2n = 80 5% recombinants2n = 40 - 128 modern cultivars Sugarcane cultivarsWhere is polyploidy going? | Paul Berkman | Page 3
  4. 4. Complex Genome S. spontaneumS. officinarum recombinants Arabidopsis 300 Mbp sugarcane sorghum maize rice Wheat cultivar 1600 Mbp 5500 Mbp 800 Mbp 34000 Mbp 10000 Mbp Where is polyploidy going? | Paul Berkman | Page 4
  5. 5. Complex Genome S. spontaneumS. officinarum recombinants sugarcane Human Wheat cultivar 6000 Mbp 34000 Mbp 10000 Mbp Where is polyploidy going? | Paul Berkman | Page 5
  6. 6. 7.7 WGD 10-15Allopolyploid wheat 10-16 (8-9) 10-16 32-39 ~27 7 7 7 7 7 40-54 (7 Gbp) (13 Gbp) (17 Gbp) (4 Gbp) (5 Gbp) T. monococcum T. turgidum T. aes vum A. tauschii H. vulgare 7-10 KYA 45-60 Legend WGD 56-73 0.5-3 9 Basic chromosome number (515 Mbp) Haploid/monoploid genome size S. italica Modern species 10-16 Divergence meframe (MYA) 2-3 Polyploidisa on event 2.5-6 Moore et al. www.jic.ac.uk/Where is polyploidy going? | Paul Berkman | Page 6
  7. 7. Autopolyploid sugarcane Jannoo, et al., Plant Journal (2007) 9 7 10 10 8 10 (515 Mbp) (2.4 Gbp) (730 Mbp) (750 Mbp) (930 Mbp) (2.3 Gbp) S. sponteneum S. italica P. glaucum S. bicolor S. officinarum Z. mays Auto- 1.5-2 polyploidy 7.7 WGD 10-15 (8-9) 10-16 10-16 Wang, et al., BMC Genomics (2010) ~27Where is polyploidy going? | Paul Berkman | Page 7 40
  8. 8. A whole lot of copies… S. spontaneum S. officinarum recombinants sugarcane cultivar 10000 MbpWhere is polyploidy going? | Paul Berkman | Page 8
  9. 9. What seems to be the problem?• A networks perspective A B D C F EWhere is polyploidy going? | Paul Berkman | Page 9
  10. 10. What seems to be the problem?• A networks perspective ? A Moore et al. www.jic.ac.uk/ A B B D C D C F F E EWhere is polyploidy going? | Paul Berkman | Page 10
  11. 11. What seems to be the problem?• A networks perspective B C B B C C Moore et al. www.jic.ac.uk/i=interactions, d=duplications, g=genesPolyploid network = id (+dg)Where is polyploidy going? | Paul Berkman | Page 11
  12. 12. What seems to be the problem?• A networks perspective B C B B C C Moore et al. www.jic.ac.uk/X = lost connections, Y = new connectionsPolyploid network = id (+dg) – X + YWhere is polyploidy going? | Paul Berkman | Page 12
  13. 13. What seems to be the problem? S. spontaneum• A networks perspective S. officinarum recombinantsPolyploid network = id (+dg) – X + Y = big black hole of insanityWhere is polyploidy going? | Paul Berkman | Page 13
  14. 14. What seems to be the problem?• What shall we do with the big black hole?• How might we elucidate some general principles on the impact of polyploidy on biological systems?• An idea…Where is polyploidy going? | Paul Berkman | Page 14
  15. 15. A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 15
  16. 16. A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 16
  17. 17. A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 17
  18. 18. A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 18
  19. 19. A lesson in political scienceWhere is polyploidy going? | Paul Berkman | Page 19
  20. 20. Game theory• Mathematical study of players, strategy sets, and pay-offs• Economics, politics, anthropology• Assumes rationality• Application in evolution • Selective pressure, not rationality • Has been applied at population/ecosystem levelWhere is polyploidy going? | Paul Berkman | Page 20
  21. 21. Game theory at the gene level?• The Selfish Gene, Richard Dawkins 1976• Genes as agents operating in evolution• Some criticisms • Genes aren’t intentional • Genes aren’t always “selfish” • Multi-gene/complex phenotypes • Selection must occur at the population levelWhere is polyploidy going? | Paul Berkman | Page 21
  22. 22. Game theory at the gene level?• Gene token as an agent • Optimisation theory rationalises the premise • Functions for genotype, phenotype, and fitness • An index of genes with associated alleles and phenotypesWhere is polyploidy going? | Paul Berkman | Page 22
  23. 23. Game theory at the gene level?“… the gene’s eye view … must ultimately be judged according tohow well it facilitates hypothesis generation and empirical testingand advancing scientific understanding of the natural world.” Gardner & Welch, p1810Where is polyploidy going? | Paul Berkman | Page 23
  24. 24. GAME• Gene-Agent Modelling of Evolution • Python toolkit based on pyabm, open source agent-based modelling• They have proposed: • Complete model requires: • Fitness function • Set-up function • Genotype function • Reproduce function • assigns genic value to genes • Mutation function • Phenotype function • Death function • pertinent to gene interaction • Allele, Gene, Phenotype, and • Locus, Organism, and Cell ID Interaction IDWhere is polyploidy going? | Paul Berkman | Page 24
  25. 25. GAMEWhere is polyploidy going? | Paul Berkman | Page 25
  26. 26. GAME A,A A,A A,A A,A B,B B,B B,B B,B A,A A,A B,B B,B A,A A,A A,A A,A B,B B,B B,B B,B A,A A,A B,B B,BWhere is polyploidy going? | Paul Berkman | Page 26
  27. 27. GAME A,A A,A’ A,A A,A B,B B,B B,B B,B A,A A,A B,B B,B A,A A,A A,A A,A B,B’ B,B B,B B,B A,A’’ A,A B,B B,BWhere is polyploidy going? | Paul Berkman | Page 27
  28. 28. GAME – preliminary resultsWhere is polyploidy going? | Paul Berkman | Page 28
  29. 29. GAME – preliminary resultsWhere is polyploidy going? | Paul Berkman | Page 29
  30. 30. Why GAME?• Gene networks/systems approach • Lends itself to analysis of competition over evolutionary time• Diploidisation • Evolutionary Stable State? • Specific mechanisms?• Polyploid game theory? • Genes as players in the game, alleles as strategy sets • Pay-offs as conferred selective advantage• How is this useful? • Accounts for gene network interactions • May ultimately provide predictive capacity • Support manipulation of complex systemsWhere is polyploidy going? | Paul Berkman | Page 30
  31. 31. Polyploid game theory• Universal framework applying evolutionary game theoryWhere is polyploidy going? | Paul Berkman | Page 31
  32. 32. AcknowledgementsKaren Aitken Adam SkarshewskiNathalie Pipiridis Mike ImelfortJiri Stiller Steven MaereJen Taylor Yves Van De Peer Mike Freeling Damon LischWhere is polyploidy going? | Paul Berkman | Page 32
  33. 33. Thank youCSIRO Plant IndustryPaul BerkmanOCE Postdoctoral Fellowt +61 7 3214 2361e paul.berkman@csiro.auw www.csiro.au/piCSIRO PLANT INDUSTRY
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