Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure...
-
date post
21-Dec-2015 -
Category
Documents
-
view
213 -
download
0
Transcript of Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure...
![Page 1: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/1.jpg)
Application of DEB theory to a particular organism
in (hopefully somewhat) practical terms
Laure PecquerieUniversity of California
Santa Barbara
![Page 2: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/2.jpg)
How do I apply DEB theory to my research question,
and to the organism I’m studying?
How can I start?
![Page 3: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/3.jpg)
When I started…
Now we have…
Artwork: Yoan Eynaud
But I would have liked another yellow book!!
![Page 4: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/4.jpg)
Imaginary / Abstract world
Real world
Modeling art
Core theory DataParameter
values
![Page 5: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/5.jpg)
maturity
1-maturity
maintenance
development
food faecesassimilation
reserve
structurestructure
somaticmaintenance
growth
reproductionbuffer
reproduction
maturity
1-maturity
maintenance
development
maturitymaturity
1-maturity
maintenance
development
1-maturity
maintenance
development
food faecesassimilation
food faecesassimilation
reserve
structurestructure
somaticmaintenance
growth
reproductionbuffer
reproduction
reproductionbuffer
reproduction
Model simulations
INPUTS DEB MODEL
Food density
Temperature
Flow
Weight
Fecundity / egg size
OUTPUTS
Length
![Page 6: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/6.jpg)
Imaginary / Abstract world
Real world
Modeling art
Core theory Data
Auxiliary theory (Protective belt)
You are the expert
Parameter values
1
2
3
![Page 7: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/7.jpg)
Outline (today and Thursday)
• Core theory:– Standard DEB scheme– (Types of) predictions of a standard DEB model– How do we generate these predictions?
• Auxiliary theory (applied to fish!):– Length, Weight– Reproduction– Stage transitions (first-feeding, metamorphosis)– Products (respiration rate, otolith formation)– Food conditions
![Page 8: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/8.jpg)
maturity
1-maturity
maintenance
development
food faecesassimilation
reserve
structurestructure
somaticmaintenance
growth
Life events in a standard DEB model
reproduction
buffer
reproduction
![Page 9: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/9.jpg)
Predictions of a standard DEB model
• E = f(t)• V = f(t)
• EH = f(t)
• ER = f(t)
Environment
![Page 10: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/10.jpg)
![Page 11: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/11.jpg)
Different T
Different f
Von Bertalanffy growth in a constant environment
![Page 12: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/12.jpg)
Predictions of a standard DEB model
• E = f(t)• V = f(t)
• EH = f(t)
• ER = f(t)
• Initiation of feeding (birth): ab, Lb observable
• Initiation of allocation of reserve for future reproduction: ap, Lp ?
• Initial reserve E0 KRER / E0 = number of eggs
![Page 13: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/13.jpg)
How do I get these predictions?
• Matlab code• 8 routines
– Parameters– Initial values– Forcing variables: Food, Temperature– Differential equations, Numerical integration– Compute outputs for comparison with data– Plot outputs vs. data
![Page 14: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/14.jpg)
Coding
• On paper first!
• Which variables V, MV, L, l
E, ME, e
• Parameters list + generalized animal• Initial conditions debtool routines• Forcing variables f
![Page 15: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/15.jpg)
What type of data do I need?
• Elements of answer:– Measurements in time = trajectories – Individual trajectories– At different food levels– And at different temperatures
– Stage transitions: age, size
– Ultimate size
![Page 16: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/16.jpg)
What type of data do I need?
• Elements of answer:– Measurements in time = trajectories --> better than end point– Individual trajectories better than population mean– At different food levels much better than one food level only– And at different temperatures
– Stage transitions: age, size very informative but could be tricky
– Ultimate size -> which one? Max ever observed, mean of max observed?
![Page 17: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/17.jpg)
Why should we consider the full life cycle?
• What happens during one stage impacts the next one• Constraints for parameter estimation• More information from data
• Growth pattern: juvenile and adult data (anchovy)• Reproduction investment: Weight / Condition factor as a function of
length (anchovy)• Survival of larvae up to metamorphosis (critical for recruitment): Age
and length at metamorphosis (anchovy)• Evolution of life-history traits: Fecundity /Egg size data (egg size can
be selected but reproduction investment (physiology) is the same among different species (salmon)
• Development and migration: Length of adults when migrating back to the river. Could not be interpreted without egg development data (salmon)
![Page 18: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/18.jpg)
Auxiliary theory
• Core theory: set of assumptions that leads to the standard DEB model
• DEB state variables cannot be observed/measured directly
• Auxiliary theory: second set of assumptions that links DEB variables to particular /quantities that we can measure
• Auxiliary theory can then be tested and validated or falsified and modified without having to reconsider all the assumptions of the core theory right away
![Page 19: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/19.jpg)
Length data
• Physical length = length we measure
• A1: organism is an isomorph
• A2a: only depends on structure– Physical length does not depend on food history, i.e. reserve
• A2b: = product that does not change in shape and which formation can only be expressed as an overhead of the growth process (e.g. length of a shell)
![Page 20: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/20.jpg)
Age (years)
Leng
th (
cm)
![Page 21: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/21.jpg)
![Page 22: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/22.jpg)
![Page 23: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/23.jpg)
Reproduction data
• Number of oocytes prior spawning event / oocytes diameter
• Number of eggs spawned / Egg size• Number of offspring / size (live bearing fish)• Gonado-somatic index prior spawning
![Page 24: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/24.jpg)
![Page 25: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/25.jpg)
![Page 26: Application of DEB theory to a particular organism in (hopefully somewhat) practical terms Laure Pecquerie University of California Santa Barbara.](https://reader030.fdocuments.in/reader030/viewer/2022032704/56649d575503460f94a3619d/html5/thumbnails/26.jpg)
Weight data
Wet weight (non-destructive)
+ We are including gut content (e.g., earthworm)
+ Water content may depend on energy content
vs. Ash-free dry weight (closer link to chemical composition)