GAME: modelling a gene's-eye view of evolution - Paul Berkman
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Transcript of GAME: modelling a gene's-eye view of evolution - Paul Berkman
GAME
Paul Berkman | OCE Postdoctoral Fellow – Sugarcane Genome Bioinformatics
22 March 2013
CSIRO PLANT INDUSTRY
Modelling a genes-eye view of evolution
• Sugarcane genomics
• A (somewhat) new perspective?
• Some fun and GAMEs
Overview
Where is polyploidy going? | Paul Berkman | Page 2
S. officinarum
2n = 80S. spontaneum
2n = 40 - 128
modern cultivars
Basic BreedingGISH on cultivars
80% S. officinarum
5% recombinants
15% S. spontaneum recombinants
S. spontaneum
S. officinarum
Sugarcane cultivars
Where is polyploidy going? | Paul Berkman | Page 3
Complex Genome
Where is polyploidy going? | Paul Berkman | Page 4
sugarcane
cultivar
10000 Mbp
maize
5500 Mbp
rice
800 Mbp
sorghum
1600 MbpWheat
34000 Mbp
recombinants
S. spontaneum
S. officinarum
Arabidopsis
300 Mbp
Complex Genome
Where is polyploidy going? | Paul Berkman | Page 5
sugarcane
cultivar
10000 Mbp
Wheat
34000 Mbp
recombinants
S. spontaneum
S. officinarum
Human
6000 Mbp
Allopolyploid wheat
Where is polyploidy going? | Paul Berkman | Page 6
Moore et al. www.jic.ac.uk/
WGD56-73
WGD10-15
Auto-polyploidy
S.italica P.glaucum S.bicolor S.officinarumS.sponteneum
Z.mays O.sa va B.distachyon
Tri ceae
T.monococcum T.turgidum T.aes vum H.vulgare
~27
10-1610-16
7.7(8-9)
1.5-2
40-54
45-60
32-39
2.5-6
0.5-3
2-3
7-10KYA
9 7 10 10 8 10 12 5
7 7 7
A.tauschii
7 7
(515Mbp) (2.4Gbp) (730Mbp) (750Mbp) (930Mbp) (2.3Gbp) (430Mbp) (272Mbp)
(7Gbp) (13Gbp) (17Gbp) (4Gbp) (5Gbp)
Legend
9 Basicchromosomenumber
(515Mbp) Haploid/monoploidgenomesize
S.italica Modernspecies
10-16 Divergence meframe(MYA)
Polyploidisa onevent
Autopolyploid sugarcane
Where is polyploidy going? | Paul Berkman | Page 7
WGD56-73
WGD10-15
Auto-polyploidy
S.italica P.glaucum S.bicolor S.officinarumS.sponteneum
Z.mays O.sa va B.distachyon
Tri ceae
T.monococcum T.turgidum T.aes vum H.vulgare
~27
10-1610-16
7.7(8-9)
1.5-2
40-54
45-60
32-39
2.5-6
0.5-3
2-3
7-10KYA
9 7 10 10 8 10 12 5
7 7 7
A.tauschii
7 7
(515Mbp) (2.4Gbp) (730Mbp) (750Mbp) (930Mbp) (2.3Gbp) (430Mbp) (272Mbp)
(7Gbp) (13Gbp) (17Gbp) (4Gbp) (5Gbp)
Legend
9 Basicchromosomenumber
(515Mbp) Haploid/monoploidgenomesize
S.italica Modernspecies
10-16 Divergence meframe(MYA)
Polyploidisa onevent
Jannoo, et al., Plant Journal (2007)
Wang, et al., BMC Genomics (2010)
A whole lot of copies…
Where is polyploidy going? | Paul Berkman | Page 8
sugarcane
cultivar
10000 Mbp
recombinants
S. spontaneum
S. officinarum
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 9
A
F
B
D C
E
• A networks perspective
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 10
A
F
B
D C
E
• A networks perspective
A
F
B
D C
E
?Moore et al. www.jic.ac.uk/
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 11
• A networks perspective
B
C
B
C
B
C
i=interactions, d=duplications, g=genes
Polyploid network = id (+dg)
Moore et al. www.jic.ac.uk/
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 12
• A networks perspective
B
C
B
C
B
C
X = lost connections, Y = new connections
Polyploid network = id (+dg) – X + Y
Moore et al. www.jic.ac.uk/
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 13
• A networks perspective
Polyploid network = id (+dg) – X + Y
= big black hole of insanity
recombinants
S. spontaneum
S. officinarum
• 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…
What seems to be the problem?
Where is polyploidy going? | Paul Berkman | Page 14
• 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 level
Game theory
Where is polyploidy going? | Paul Berkman | Page 20
• 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 level
Game theory at the gene level?
Where is polyploidy going? | Paul Berkman | Page 21
• Gene token as an agent• Optimisation theory rationalises the premise
• Functions for genotype, phenotype, and fitness
• An index of genes with associated alleles and phenotypes
Game theory at the gene level?
Where is polyploidy going? | Paul Berkman | Page 22
“… the gene’s eye view … must ultimately be judged according to how well it facilitates hypothesis generation and empirical testing and advancing scientific understanding of the natural world.”
Gardner & Welch, p1810
Game theory at the gene level?
Where is polyploidy going? | Paul Berkman | Page 23
GAME
Where is polyploidy going? | Paul Berkman | Page 24
• Gene-Agent Modelling of Evolution• Python toolkit based on pyabm, open source agent-based modelling
• They have proposed:
• Fitness function
• Genotype function
• assigns genic value to genes
• Phenotype function
• pertinent to gene interaction
• Allele, Gene, Phenotype, and Interaction ID
• Complete model requires:
• Set-up function
• Reproduce function
• Mutation function
• Death function
• Locus, Organism, and Cell ID
GAME
Where is polyploidy going? | Paul Berkman | Page 26
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
GAME
Where is polyploidy going? | Paul Berkman | Page 27
A,AB,B
A,A’B,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B
A,AB,B’
A,AB,B
A,A’’B,B
Why GAME?
Where is polyploidy going? | Paul Berkman | Page 30
• 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 systems
Where is polyploidy going? | Paul Berkman | Page 31
• Universal framework applying evolutionary game theory
Polyploid game theory
Adam Skarshewski
Mike Imelfort
Steven Maere
Yves Van De Peer
Mike Freeling
Damon Lisch
Acknowledgements
Where is polyploidy going? | Paul Berkman | Page 32
Karen Aitken
Nathalie Pipiridis
Jiri Stiller
Jen Taylor
Thank youCSIRO Plant IndustryPaul BerkmanOCE Postdoctoral Fellow
t +61 7 3214 2361e [email protected] www.csiro.au/pi
CSIRO PLANT INDUSTRY