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

A lesson in political science

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A lesson in political science

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A lesson in political science

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A lesson in political science

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A lesson in political science

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• 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?

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• 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 25

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

GAME – preliminary results

Where is polyploidy going? | Paul Berkman | Page 28

GAME – preliminary results

Where is polyploidy going? | Paul Berkman | Page 29

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 paul.berkman@csiro.auw www.csiro.au/pi

CSIRO PLANT INDUSTRY