simulation of spatial self-organization in a stepping stone environment
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Simulation of Spatial Self-Organization in a Stepping Stone Environment. Presenter: Bilal Gonen. Outline. Definition of Self-Organization Our Beetle-World experiment EvoSimulator Tool Questions & Comments. Self-Organization. - PowerPoint PPT PresentationTRANSCRIPT
Presenter: Bilal Gonen
Simulation of Spatial Self-Organization in a Stepping Stone Environment
Outline
• Definition of Self-Organization• Our Beetle-World experiment• EvoSimulator Tool• Questions & Comments
Self-Organization
Self-organization is the process where a structure or pattern appears in a system without a central authority or external element imposing it through planning.
Schools of fish
Source: Experimental Evidence for Spatial Self-Organization and Its Emergent Effects in Mussel Bed Ecosystems, Johan van de Koppel, Joanna C. Gascoigne, Guy Theraulaz, Max Rietkerk, Wolf M. Mooij and Peter M. J. HermanScience 31 October 2008, Vol. 322 no. 5902 pp. 739-742
Self-Organizing Mussels
Ant Colonies
Source: Vitorino Ramos, Fernando Muge, Pedro Pina, Self-Organized Data and Image Retrieval as a Consequence of Inter-Dynamic Synergistic Relationships in Artificial Ant Colonies, in Javier Ruiz-del-Solar, Ajith Abraham and Mario Köppen (Eds.), Frontiers in Artificial Intelligence and Applications, Soft Computing Systems - Design, Management and Applications, 2nd Int. Conf. on Hybrid Intelligent Systems, IOS Press, Vol. 87, ISBN 1 5860 32976, pp. 500-509, Santiago, Chile, Dec. 2002.
initial state 2 hours later 6 hours later 26 hours later
Outline
• Definition of Self-Organization• Our Beetle-World experiment• EvoSimulator Tool• Questions & Comments
Parameters• Number of stepping stones = 5
EvoSimulation Example
Parameters• Number of stepping stones = 5
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
EvoSimulation Example
We split the stepping stones into subdivisions
based on their FST values
FST (Fixation index) is a measure of population differentiation, genetic distance, based on genetic polymorphism data.
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
EvoSimulation Example
We split the stepping stones into subdivisions
based on their FST values
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Produce offspring and put them into stepping
stones
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Produce offspring and put them into stepping
stones
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Fill Vacancies in the stepping stones
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Fill Vacancies in the stepping stones
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Kill parent individuals
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Kill parent individuals
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Grow up the children
EvoSimulation Example
Parameters• Number of stepping stones = 5• Number of individuals per
stepping stone = 6• Number of alleles = 5• Number of generations = 10
Grow up the children
EvoSimulation Example
EvoSimulation Steps
Creating individuals and initializing stepping stones
Grouping the stepping stones
Creating new generations
• Produce offspring and put them into stepping stones
• Fill Vacancies in the stepping stones• Kill parent individuals
Grouping the stepping stones
ID: 1 ID: 2 ID: 3 ID: 4 ID: 5
Split point
ID: 6 ID: 7 ID: 8 ID: 9
Group-1 Group-2
ID: 1 ID: 2 ID: 3 ID: 4 ID: 5
Split point
ID: 6 ID: 7 ID: 8 ID: 9
Group-1 Group-2
ID: 1 ID: 2 ID: 3 ID: 4 ID: 5
Split point
ID: 6 ID: 7 ID: 8 ID: 9
Group-1 Group-2
ID: 1 ID: 2 ID: 3 ID: 4 ID: 5 ID: 6 ID: 7 ID: 8 ID: 9
Group-1 Group-3
Let’s assume splitting between plate-5 and plate-6 gives the maximum FST. Then the result will be as below.
Group-2
Outline
• Definition of Self-Organization• Our Beetle-World experiment• EvoSimulator Tool• Questions & Comments
These are the default values.
Let’s change this one
Let’s change this one
Let’s change this one
Click this button
8 is the last generation
This is how the beetles are placed
in the plates
This is the FST for this generation if the plates are grouped in this way
Let’s go to another generation to see how the groupings and
FST changes below.
Let’s go to another generation to see how the groupings and
FST changes below.
Let’s change number of groups to see how the groupings and
FST changes below.
FST increased as expected.
Let’s make this 4 and 5.
This graph represents FST-Delta vs. Number of
groups
Change here to see FST vs. Number of groups
Simulator : www.evosimulator.comWeb : www.bilalgonen.comEmail : [email protected]
Outline
• Definition of Self-Organization• Our Beetle-World experiment• EvoSimulator Tool• Questions & Comments
