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Between biodiversity and crops: needs from stochastic

models at the ecosystem scale Pat Heslop-Harrison

www.AoBBlog.com phh4@le.ac.ukwww.molcyt.com ID/PW ‘visitor’

Workshop on Stochastic Modelling in EcosystemsGlasgow, June 2012

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RainfallDistribution

mm/yr

5Artist: R . Sphestre?, Le Tadorne, Piney, France. 2012

NASAThe Blue Marble

Apollo 17 7 Dec 1972

Stochastic Modelling in Ecosystems

Living components– Plants and cyanobacteria (primary producers)– Bacteria, fungi, animals

Interacting with abiotic components– Light– Water– Wind, soil, nutrients, toxins, gasses ...

Recognizable homogeneity in one ecosystem 7

Ecosystems anchor slide

Largely– Self-organizing– Self-maintained– Cycling– Defined scope

– cf Household– Aircraft–

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Stochastic Modelling in Ecosystems

Recognizing–Inputs–Outputs–Networks / webs of organisms–Cycles–Scales–Functions

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Inputs– Light– Heat– Water– Gasses– Nutrients

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50% of the world's protein needs are derived from atmospheric nitrogen fixed by the Haber-Bosch process and its successors.

Global consumption of fertilizer (chemically fixed nitrogen) 80 million tonnes

<<200 million tonnes fixed naturally

Outputs– Light– Heat

– Water– Gasses

– Nutrients

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Outputs– Light– Heat

– Water– Gasses

– Nutrients

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Discussion at the meeting: Prof Mathew Williams pointed out that the ‘heat’ input is also an important modified output of an ecosystem. Consider the different temperatures and temperature cycles of the desert and jungle ecosystems in the second slide.

OutputsEcosystem ServicesWater, gasses,nutrients”nature’s services, like flood control, water filtration, waste assimilation”

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Outputs– Light– Heat

– Ecosystem services• Water, gasses, nutrients

– Chemical energy

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Ecosystems: What do we take out?The seven Fs

–Food–Feed–Fuel–Fibre–Flowers–Pharmaceuticals–Fun

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Outputs– Light– Heat

– Ecosystem services• Water, gasses, nutrients

– Chemical energy– Long term storage

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Stores of biologically produced carbon in

LimestonePeatOil and gas

Dynamic processes: turn-over

Outputs– Limestone

–Made by marine organisms, formation and stability affected by pH and

temperature

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Inputs - Biotic– Diseases– New organisms

• Aliens/invasives– New genes and

genotypes of existing organisms

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Outputs– Light– Heat

– Ecosystem services– Chemical energy

– Long term storage

Requiredand valued

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Rio de Janeiro Conference in June 1992Biological diversity as “the variability

among living organisms and the ecological complexes of which they are part”

Conservation of ecosystemsSustainability of human activityAnalysis of human effects and interactions

with the environment 23

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… all suggest modelling … but

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Biotic Inputs– New genes– New species

• Diseases• Alien species

Abiotic inputs– Irrigation– ‘Salt’ (NaCl)– Nitrogen– Phosphorous

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Water hyacinth – Eichornia: an invasive alien plant from South America, fills water courses (a surface habitat not used by any native species) in Asia and Africa

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Argenome mexicana: a goat-proof plant fromMexcio introduced and successful in Africa

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Inputs are random variables– with known or unknown

distributions

Does the mean or the extreme matter?

How does oscillation lead to robustness?

Can routes from input to output be simplified? 30

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RainfallDistribution

mm/yr

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Occasional ‘extreme inputs’:Limiting composition of ecosystemsmore than ‘mean input’ - Robustness

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Anhalt, Barth, HH Euphytica 2009 Theor App Gen

2008

Regulation of oscillations Synchronization without

external regulators

Oscillations: noise and stability

Stochastic fluctuations– preserve stable oscillations– ensure robustness of the oscillations to cell-to-cell

variationsRobustness analysis requires stochastic

simulationJongRae Kim et al. Stochastic noise and synchronisation during Dictyostelium aggregation make cAMP oscillations robust. PLoS Computational Biology 2007

Jeong-Rae Kim, PHH, Kwang-Hyun Cho. J Cell Sci 2010

Coupling of oscillators seen at all scales fromsubcellular to ecosystem

Stable cAMP oscillations in the cells with other molecules/ions

Valeyev et al. Mol Biosyst 2009

Entrainment of a cell by surrounding cells: Individual cells synchronized/oscillate in

phase Regardless of frequency, some effect of

[cAMP]Valeyev et al. Mol Biosyst 2009

No Stronger Coupling

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Eyespot (fungus Pseudocercosporella) resistance from Aegilops ventricosa introduced to wheat by chromosome engineering

Many diseases where all varieties are highly susceptible

Alien variation can be found and used7

Host and non-host resistances

Crop standing

Lodging in cereals

Crop fallen

Ecosystems anchor slide

Largely– Self-organizing– Self-maintained– Cycling– Defined scope

Networks are– Stable– Oscillating– Complex and

maybe modular– Simplification– Models for

modelling 47

Dynamic interactions between calcium, IP3 and G protein-dependent modules

Valeyev et al. Mol Biosyst 2009 5: 612

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Identification of design principles: points of structural fragility in networksDynamic interactions between the different modules generate more stable and robust cAMP oscillations

Int. J. Robust Nonlinear Control 2010; 20:1017–1026. DOI: 10.1002/rnc.1528

Analysis and extension of a biochemical network model using robust control theory J.-S. Kim, Valeyev, Postlethwaite, PHH, Cho, Bates

Robustness comparison including module

interactions

Light in ecosystems

Energy

Photosynthesis

Information

Quantity Quality Direction Periodicity

Control of development

Heat

Simplification of genetic networks while maintaining dynamic properties

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Reduction of Complex Signaling Networks to a Representative Kernel Jeong-Rae Kim, Junil Kim,Yung-Keun Kwon, Hwang-Yeol Lee, PHH. Kwang-Hyun Cho. Science Signaling 4 (175), ra35. [DOI:10.1126/scisignal.2001390]

Network reduction

Kim, HH, Cho et al. 2011 Science Signaling

Circadian Clock regulation

after Leloup & Goldbeter;

Andrew Millarin Arabidopsis

X X

Y

Y

Z

Z

Integrin gene network

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Function and multifunction

How many genes are there?1990s: perhaps 100,0002000: 25,000How does this give the range of

functions and control?

Najl Valeyev

Lolium Biomass production

Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

Anhalt, Barth, HH et al. Segregation distortion in Lolium: evidence for genetic effects. Theoretical & Applied Genetics 2008

Anhalt, Barth, HH Euphytica 2009Theor App Gen 2008

Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F2 population. Euphytica 170: 99-107.

Network structures differ between systems: what about ecosystems?

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Kim TH, Kim J, PHH, Cho KH. 2011. Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. Bioinformatics 27: 245-251. http://dx.doi.org/10.1093/bioinformatics/btq633

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Threats to sustainability:no different for 10,000 years

Habitat destructionClimate change (abiotic

stresses)Diseases (biotic stresses)Changes in what people wantMORE outputs neededMORE stability in outputs from

less stable inputs / poorer environments

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How to exploit modelsIncreased sustainabilityIncreased valueGenetic improvementRobustness (‘food security’)

Benefits to all stakeholders:Breeders, Farmers, Processors,Retailers, Consumers, Citizens

50 years of plant breeding progress

1961 1965 1970 1975 1980 1985 1990 1995 2000 2005 20070

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MaizeRiceWheatHumanArea

Agronomy

Genetics

GM maize

United Nations Millennium Development Goals-MDGs

• Goal 1 – Eradicate extreme poverty and hunger

•Goal 2 – Achieve universal primary education

• Goal 3 – Promote gender equity and empower women

• Goal 4 – Reduce child mortality

• Goal 5 – Improve maternal health

• Goal 6- Combat HIV/AIDS, malaria and other diseases

• Goal 7 - Ensure environmental sustainability

• Goal 8 - Develop a global partnership for development

Conventional Breeding

Superdomestication

Cross the best with the best and hope for something better

Decide what is wanted and then plan how to get it– Variety crosses– Mutations– Hybrids (sexual or cell-fusion)– Genepool– Transformation

Economic growth

Separate into increases in inputs (resources, labour and capital) and technical progress

90% of the growth in US output per worker is attributable to technical progress Robert Solow – Economist

Market Demand “MORE”

Food production volume–No possibility of market collapse

–Only slow market increase–Reduced post-harvest loss–Some crops gain/hit by global trends

Inputs

Better genetically– Harvest more– Stress resistant (Disease = biotic and

environment – abiotic)Higher

– Weed control improving for 8000 yearsLower

– Production loss less than cost decrease– Better agronomy (cropping cycles etc.)

Needs from Stochastic Models of Ecosystems

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Outputs

Ecosystem services

– Chemical energy

– Long term storage

Inputs

– Light– Heat– Water– Gasses– Nutrients

13/04/2023 73

Between biodiversity and crops: needs from stochastic

models at the ecosystem scale Pat Heslop-Harrison

www.AoBBlog.com phh4@le.ac.ukwww.molcyt.com ID/PW ‘visitor’

Workshop on Stochastic Modelling in EcosystemsGlasgow, June 2012