Modelling Approaches Flashcards
Overview
1.why use /usefulness/build 2mechanistic modelling 1 .SIZE 3mechanistic modelling 2. Thermal PHYSIOLOGY 4Case study : Fisheries -single spp approach -multi spp approach -c trait based 5.Case study : Carbon cycle
why use 3
capture essence
inform us what is important in complex sysyste,
develop accurate predictions (for the future)
who said “all models are wrong but some are useful” and when?
George Box
1987
George Box - why use (b)
all models are a simplification of reality (ie rictionless pendum) - for wrong bit
some models are only a little bit wrong and can be useful in making accurate predictions
How to build (5)
increase complex of same basic
COMPETING models
select using Occam’s razor
select - competing model with FEWEST assumptions
NEED TO UNDERSTAND - mechanistic processes - and thus underlying pattern (in contrast to pheno)
what does a mechanistic model explain?
processes underlying an observed pattern
Example of different bio models
2
Ricker model 1954
Lotka Volterra
Ricker model equation?
N t+1 = N t e^r (1-Nt/K)
what do N T K r and through what mechanism in the Ricker model
N=pop size
T= time step
K=carrying capacity
r- growth rate
What about buikding models in terms of levels?
what are the 3 levels of organisation?
what 3 things to each include?
Need to build model for right level of organisation
Individual
1) metabolic rate
2) growth rate
3) temp rate
Interactions
consumer resource
competition
density depe
Community
top down regulation
bottom up regulation
trophic cascades
why use / usefulness / build overview? (5)
why (3) George box 1987 build (5) Occam's razor Mechanistic - Ricker - Lotka volterra levels + incorporate (AIC)
how do we incorporate the right level? and what is AIC?
1) agrees well wit hdata?
2) agrees best? (right mechanism for prediction?
3) model selection using Occam’s razor for example AIC
Akaike Information Criterion
- shows how much info a modle captures and its suitability for data
- Mechanistic modelling - importance of size overview (4)
magnitude difference
metabolic rate define - Kleiber’s Law
so… Damuth’s Law
Use?
Mechanistic modelling size
a) magnitude dif of ecosystem?
ecosystem can have 10- 20 orders of magnitude different in an ecosystem 10^-16 g to 10^3 g
Mehcnaistic modelling size
b)what is metabolic rate? / resting rate defines what?
rate of individual energy use (watts)
metabolic rate in retsings state (M) sets pace of life
M= M0 m b
(large organisms less of spring)
resting metabolic rate = Kleiber’s law 1947
c) Savage et al universal law?
Savage et al 2004
as mass increases
metabolic mass increases
so… what is Damuth’s law ?
Damuth’s law tells how population density is related to body size (mass).
It says that species with larger body sizes generally have lower average population densities.
More exactly, it states that the average density of a population decreases with body size at a power of approximately 3/4 the body mass (Damuth 1981, 1987, 1991).
Kleiber’s law?? wider
Kleiber’s law, named after Max Kleiber for his biology work in the early 1930s,
is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the ¾ power of the animal’s mass. Symbolically: if q₀ is the animal’s metabolic rate, and M the animal’s mass, then Kleiber’s law states that q₀ ~ M¾. Thus, over the same timespan, a cat having a mass 100 times that of a mouse will consume only about 32 times the energy the mouse uses.
kleibers law
animal’s metabolic rate scales to the ¾ power of the animal’s mass.
why is the mechanistic modelling importance of size thanks to the dif laws useful?
shows that the mechanism underling body size abundance is METABOLISM
this is a universal law useful for fish modelling
- trophic levels dif require dif levels of energy
- Mechanistic modelling importance of thermal physiology overview (5)
importance and Boltzmann constant
Caveats
JF Gilooly and AP Allen - defend Boltzmann
Anthony Dell and Samraat Pawar 90%
Mechanistic model thermal physiology
a) why is it important and what can be used to model?
99.9 % of ectotherms depend on temp
Universal law is the Boltzmann constant
from Arrhenius equation
why?
constant and as increase temp this incrases rate of recations in a universal way –> ie luciferase for bioillimuniscence
Enzme kinetics
- best described using michaelis menten equations (derived from Arrhenius) with a few assumptions about chemical enviro of biological systems
Physiology modelling
b)caveats?
may not include
1) oxygen limitation
2) complexity of metabolic network
3) hormoneal regulation
Physiology modelling
JF Gillooly and AP Allen
main qus and who criticised?
Clarke and Fraser 2004
-so the ydefend use of Boltzmann expression to describe effect of temp on metabolic rate
1) supply or demand?
2) Adaptation /acclimation ?
3) same across spp?
4) is Boltzmann temperature dependence maladaptive?
What did \_\_\_\_\_\_ reply to Clarke and Fraser (2004) supply or demand? Adpatation / acclimation? differen spp? Maladaptive?
JF Gilooly and AP Allen
1) incorrect - BOTH physiology matches DEMANDS more but has CAPACTY to supply more
2)meant to be simple
isolated mitochondria of fish and study shows only small effect of evolutionary adaptation on effect of temp on metaolic rate
3)no assumption
their alternative acnnot be testses “evo trade off hypothesis”
4)true in some cases but more fitness gains with increase metabolism overall
increase met rate –> increase in temp and increase in rate of fish egg laying for example
What was Fraser and Clarkes alternative hypothesis?
“evo trade off”
Thermal physiology
d) Samraat Pawaar and Athony Dell
- what was their research?
metanalysis of 1072 thermal responses
from
bacteria
plants
animals
shows 90% intraspecific rise in response was well fit by Boltsmann constant
BUT not perefcet
What improvements were suggested by metanalysis?
(who was the metanalysis by?
gen problem plus 2 suggestions
Anthony Dell
Samraat Pawaar
not perfect fit - right skew in distributions
1) increase temp range to ensure response over a great ranfe of traits over full temo range
2) look at multiple spp trait in one spp to see how temp influences interaction and integratuin if traits across DIFFERENT levels of organisation
- Case study FISHERIES overview (4)
general - importance of body size not new
single spp approach
multi spp approach
c trait based approach
- Fisheries
1.body size important? known for how long?
Goals of fisheries modelling? (2)
not new
“big fish eat little fish” - Heyden 1557
1) ensure sustainable exploitation (MSY)
2) accounting for implications to wider ecosystem
Fisheries
2. single spp models
examples (2)
clue - what has beverton holt model led to (3)
Ricker model:
N t+1 = Nt e ^r( 1 - Nt/K)
Beverton Holt
discrete time population model - individuals are function of thopse in previous
led on to subsequent work with dif assumptions
1)contest comp
2)source -sink patches
3)within-year resource comp
Fisheries
2. singl spp pro and con
MSY achieved?
what can help?
Pro - detailed info on 1 spp
Pro - used for long time and know models well
Con- no real effect known on wider community
Con- no spp interactions - trophic cascades
Con - missing age? cohort? size? –> mortality depends on these things
extra - beyong certain size tuna acts as an endotherm (tricky to model)
so good for MSY but only for 1 species - what about others? BUT cphort class model enables better MSY as well as next modelling concepts .....
Fisheries
- Multiple spp
a) how are they dif ? what do they account for
b) examples (2)
often complex as multiple spp and interactions
1) spp interactions
2) synamics ie trophic cascade
Ecopath with Ecosim (EwE)
kitchen sink approach (lots of data)
what is
Ecopath with Ecosim (Ewe) who started?
Where now?
free ecosystem modelling software suite,
initially started at NOAA by Jeffrey Polovina,
but has since primarily been developed at the UBC Fisheries Centre of the University of British Columbia.
what are the components pf ecopath with Ecosim?
3
EwE has three main components: Ecopath – a static, mass-balanced snapshot of the system[3] Ecosim – a time dynamic simulation module for policy exploration[4] Ecospace – a spatial and temporal dynamic module primarily designed for exploring impact and placement of protected areas.[5]
Ecopath? component defien
static mass balanced snapshot of the system
Ecosim component define
a time dynamic simulation module for policy exploration
Ecospace
spatial and dynamic module designed for exploring imoact and placement of PAs
multispp approach
- extra - what do they need?
additional consumption rate parameters
BUT - size scaling can help!
Multispecies approaches
overview
1) differences and what it accounts for
2) 2 examples (Ewe) (kitchen sink)
3) what do they need - size scaling - Pawar
4) pros and cons
5) add on source-sink (habitat inclusion)
Multiple spp approaches
3) describe the study that helps understand consumption rates
- size scaling relationships can help
Pawar et al Nature 2012
3D consumption rates - encounter more
2D consumption rates - ecunter less
summary: 3D consumption rates scale differently than 2D
Search rates - drive differences in consumption rate scaling
3D consumption rates scale different that 2D study detail data 3d and 2d explain what does trophic interaction influence needed
376 spp of varying mass
arboreal / pelagic = 3D
terrestrial / benthic = 2D
trophic interaction influences
1) biomass fliuxes
2) stability
important to know how this interaction is influenced by habitat type to iunderstand strength of inteactoions
mutiples spp approach
pros and cons
Pro - account for spp interaction Pro- estimate wider ecosystem impact Con - can become very complex thus 1)some detail must go 2)black boxes 3)can require lots of data that is sometimes unavailable can be too ambitous? LT?
multiple spp approach
explain what source sink dynamics are?
why useful?
theoretical model
decribes how variation in habitat quality may affect population growth or decline of organism
High qual habitat
low qual habitat
C trait based (spp independent approaches)?
Overview (3)
why useful?/compromise
Example - size- spectrum models (COD /herring / mackerel)
Pro/con
C baised (spp independent approach 1- use ? compromise?
it is a compromise but can be useful to estimate size spectrum of a community without underlying complexity
C based
2. (example)
size spectrum model
using body size a s a trait was successfyul for fishery modelling
Big Cod
Herring
Mackarel
folloe size relationships thus fit these model better - better predictions
why needed? Cod is 2/3 size it used to be
Monitoring ecosystem health (link with pracrtical)
C based
Pros/cons
pro - can capture effects ie food web ocmplexty
con - if spp identity matters is a problem
- Case study : global warming and carbon balance
Overview (5)
- importance
- CUE and Net carbon flux exchange
- Response to temp?
- what needs to be done/compensation?
- Gabriel Yvon Durocher - respiration across ecosystem types
Carbon cycle etc
importance of thermal physiology for modelling?
- warming
-carbon cycle
thermal physiology for modelling this is important as
global temp INCREASE
surface temp relative to 1870-1899 BASELINE
not PATCHY - increase in therma;l fluctuations
This effects carbon cycle
earths carbon cycle is temp dependent - thsu can be understoof by modelling
Carbon cycle
CUE and Net Carbon Flux exchange - define
carbon use efficiencyCUE
quantifies organismal growth efficiency and ecosystem product potential
the rate of organismal and ecosystem carbon gain or loss due to metabolism
CUE equation
r?
Pgross
CUE = 1 - R/ P gross
Respiration rate (R) P gross = diurnal gross photosynthesis rate
Net carbon flux equation
R?
Pnet
P net - R
P net = diurnal net photosynthesis rate
(currenlt assumption is that most respiration is at night)
So how do we link carbon cycle to temp?
2
carbon balance depends of dif in thermal responses of
Respiration and
Photsyntehsis (specifically their rates)
Again, both photosynthesis and respoiration respond to temp in similar way –> Boltzmann constant
Equation linking carbon cycle to temp ?
B? T? C? E? K? Ed?
B = Ce ^ -E/KT f (T,Tpk,Ed)
b= metabolic rate c= normalisation constant E = activation energy K = Boltzmann constant Ed = activation T= temp
again basically Arrhenius plots
- what needs to be done / compensation?
option 1 = thimgs become LESS sensitive to temp
option 2 = remain sensitive but increase photosynthesis (compensation)
note research looking into this atm
why link to Arrhenius - again Michaelis mentis for enzyme kinetics derived from arrhenius
- what was Gabriel Yvon Durocher paper about?
what was qu?
what was looked at / method?
Result?
“reconciling temp dependence of respiration across timescales and ecosystem types “
know respiration is modeified by variable but is dependence different between aquatic and terrestrial enviro? YES
opean oceans / lakes /rivers/estuaries
Arboreal and non forest areas
sensitivity to respiration to seasonal changes = similar
annual ecosystem respiration - greater temp dependence across aquatic
Findings can be recognised by similarities in biochemical kinetics of metabolism and subcellular level
Durocher paper
last observation wrt community level?
similarities at biochem level reconciled
differences explained by differemce amd importance of varibales on structure of aquatic and terrestrial at the COMMUNITY level
What is an Arrhenius plot?
what does it display?
What is it used for?
displays the logarithm of kinetic constants plotted against inverse temperature.
Arrhenius plots are often used to analyze the effect of temperature on the rates of chemical reactions.
For a single rate-limited thermally activated process, an Arrhenius plot gives a straight line, from which the activation energy and the pre-exponential factor can both be determined.
