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Michael Kearney [email protected] of BioSciences, The University of Melbourne
Mechanistic Niche Models
Part I• What is a mechanistic niche model?• Thermodynamic basis to the niche• The importance of temperature• Heat budgets• Microclimates• Water budgets• Play with NicheMapRPart II• Connecting to the Dynamic Energy Budget• Play with NicheMapR• Inferring climatic constraints• Nutritional constraints
Mechanistic Niche Models
Biophysical Ecology
fundamental niche
realized niche
temperature
hum
idity
What is a mechanistic niche model?
What is a mechanistic niche model?
Maxent model
NicheMapR model
Environmental Layers
probability of occurrence
potential reproduction
Correlative Model (process implicit)
Mechanistic Model (process explicit)
51°C
35°C44°C
Military Dragon, Ctenophorus isolepis
Thermodynamic basis to the niche
51°C
35°C44°C
Thermodynamic basis to the niche
Credit: Elia Pirtle
BOUNDARY
SYSTEM
SURROUNDINGSin
out
energy in = energy out + energy stored
in
outmass in = mass out + mass stored
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe dingJJX,I JX,PJX,G JX,R JX,S+ + + +=
brathnig
JO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
Temperature ºC5 15 20 30 50100 45403525
Fitn
ess
survival survivaldeath deathreproduction
optimal
e.g. sprint speedegg developmentfeeding ratedigestion rate
The importance of temperature
Magnet
Reed Switch
Light Sensor on Satellite
Board
Data logger Radio Transmitter
The ‘waddleometer’
Prof. Mike Bull
The importance of temperature
60 Lizards’ Tbs in 2009
The importance of temperature
Tfish = water temperature
Tball ∝ air temperature, wind speed, direct and diffuse solar radiation, infra red radiation, ground temperature, humidity, surface area, shape, thermal mass, solar reflectance …
The importance of temperature
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
Warren PorterUniversity of Wisconsin,
Madison
Ecological Monographs 39(3), 227-244 (1969)
Biophysical Ecology
Solar(gained)
Infra-red(gained)
Conduction(gained/lost)
Convection(gained/lost)
Evaporation(lost)
Metabolism(gained)
Infra-red(lost)
+ +
+ + +
=
(Heat) Energy Balance of a Lizard
0][]273[ 4 =−−+− abcba TThTQ σ
air temperaturewind speed V,
organism size Dinfra-red and solar radiation
gained
infra-red radiationlost
convection
5.0
5.0
49.3DVhc =
Biophysical Ecology – Heat Budgets
What would the body temperature be if …?
Diameter = 0.015 m
Wind speed = 2.0 m/s
0][49.3]273[ 5.0
5.04 =−−+− abba TT
DVTQ σ
Air temperature = 20 ºC
0]20[015.00.249.3]273[700 5.0
5.04 =−−+− bb TTσ
Radiation = 700 W/m2
If we know the environmental conditions, we can find the body temperature which satisfies the energy balance equation
Tb = 26 ºC
Biophysical Ecology – Heat Budgets
weather station
air temperature layer
?
Biophysical Ecology – Microclimates
56545250484644424038363432
http://img1.jurko.net/
Biophysical Ecology – Microclimates
60 Lizards’ Tbs in 2009
Biophysical Ecology – Heat Budgets
60 Lizards’ Tbs in 2009
Biophysical Ecology – Heat Budgets
available range
body temperature
Environmental Layers
Thermodynamic basis to the niche
target (optimal) range
survivable range
selected environments through time
available range
hum
idity
Biophysical Ecology
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
Qevap,cut = Aevaphd (Vd,skin - Vd,air) λ
area wet, m2
mass transfer coefficient, m s-1
vapor density,kg m-3
latent heat of vaporisation,
J kg-1
Greer 1989 Biology and Evolution of Australian Lizards
Aevap
Water budget - evaporation
Qevap,resp = λ(mout,resp – min,resp)
mout
min
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
target (optimal) range
survivable range
selected environments through time
available range
hum
idity
Biophysical Ecology
body temperature
Environmental Layers
water balance
Thermodynamic basis to the niche
Part I• What is a mechanistic niche model?• Thermodynamic basis to the niche• The importance of temperature• Heat budgets• Microclimates• Water budgets• Play with NicheMapR
Mechanistic Niche Models
Biophysical Ecology
NicheMapR – a general system for mechanistic niche modelling
NicheMapR Google Group
https://groups.google.com/forum/#!forum/nichemapr
@NicheMapR
NicheMapR Google Group @NicheMapR
https://github.com/mrke/NicheMapR
Niche Mapper
NicheMapR
MICROCLIMATE
SOLRAD
SFODE IOSOLR
GAMMA
SINEC VSINE
DSUB
OSUB
EVALXZSOILPROPS
WETAIR
MICRO/MICROSEGMT
SNOWLAYER
HUMID
INFIL
DRYAIR
DCHXY
EVAP
DEXPITAB
VAPPRS
f) derived environmental variables d) integration routines
e) soil moisture and snow
b) solar radiation routines
c) hourly interpolation of daily inputs
a) driving subroutine, links to R via function microrun
Microclimate Program Structure
Niche Mapper NicheMapR
-100 0 100
-50
050
microrun.R
rungads
micro_global.R
Fortran microclimate model library
Fortran GADS libraryGADS Tables
cCampNormTbl9_1
global_climate.nc
ccccc
metout
soil
soilmoist
soilpot
humid
soil.mon.ltm.v2.nc
cUser Input (location,
terrain, shade, soil type, …)
b)
a) Call to Fortran
c) User arguments
d) Climate and soil data setse) Global Aerosol Data Set
f) output
-150 -100 -50 0 50 100 150
-50
050
New et al. 2002
CPC soil moistureNicheMapR
Koepke et al 1997
microrun.R
rungads
micro_aust.R
Fortran microclimate model library
Fortran GADS libraryGADS Tables
AWAP tmax, tmin, solr vpr, rr
ccccc
metout
soil
soilmoist
soilpot
humid
SLGA bulk dens, sand/silt/clay
cUser Input (location,
terrain, shade, soil type, …)
b)
a) Call to Fortran
c) User arguments
d) Climate, terrain and soil data setse) Global Aerosol Data Set
f) output
NicheMapR
Koepke et al 1997
McVicarwind
GEODATA 9 Second DEM
50 100 150 200 250 300 350
05
1015
20
Day of Year
Hou
r of D
ay
The Heat and Water Budget Model
ccccc
metout
soil
soilmoist
soilpot
humid
output
ectotherm.Rccc
environ
enbal
masbal
SURROUNDINGS
BOUNDARY
wa er
brathnig
fe ding
The Heat and Water Budget Model
c) Steadystateheat
budget
THERMOREG
f) thermoregulation
GEOM
d) heat (and water) budget components
METRESPSEVAP
SOLARABOVEGRND
BELOWGRND
BURROWIN
ECTOTHERM
b) driving subroutinelinks to R via function ectorun
SELDEP
CONDRADOUTCONVRADIN
SHADEADJUST
WETAIRDRYAIR
VAPPRSZBRAC ZBRENT
FUN
WATER
ccccc
shadmetshadsoil
shadmoistshadpot
shadhumid
ccccc
metoutsoil
soilmoistsoilpothumid
cccc
yearsout1yearsout2yearsout3
yearsout…n
ccccc
environenbal
masbaldeboutyearout
traits
morphologybehaviourphysiologyDEB pars
TRAPHRPHOTOPERIOD
e) Fluid properties
a) functional traits and microclimate datah) microclimate input
The Heat and Water Budget Model
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
TNZ
Thermo-Neutral
zone
5 15 20 30 50100 45403525Temperature ºC
Requ
irem
ents
Upper criticaltemperature (UCT)
Lower criticaltemperature (LCT)
Tcore = 36 ºC
Biophysical Ecology – Heat Budgets
0
1
2
3
4
5
-10 0 10 20 30 40chamber temperature
met
abol
ic ra
te (W
)
23.1 31.1
C
woodrat
weasel
Brown J.H. & Lasiewski R.C. (1972). Ecology, 53, 939-943.
Biophysical Ecology – Heat Budgets
consider an elliptical animal
Predicting Endotherm Energy and Water Requirements
flesh
furwind
air
heat energy balance of an endotherm
body resistance furresistance
environmental resistance
Porter & Kearney (2009) PNAS 106, 19666-19672.
C
R
Predicting Endotherm Energy and Water Requirements
0
1
2
3
4
5
-10 0 10 20 30 40chamber temperature
met
abol
ic ra
te (W
)
0
1
2
3
4
5
-10 0 10 20 30 40chamber temperature
met
abol
ic ra
te (W
)
23.1 31.1
C
22.5 31.7woodrat
weasel
Porter & Kearney (2009) PNAS 106, 19666-19672.
Predicting Endotherm Energy and Water Requirements
NicheMapR – a general system for mechanistic niche modelling
Part I• What is a mechanistic niche model?• Thermodynamic basis to the niche• The importance of temperature• Heat budgets• Microclimates• Water budgets• Play with NicheMapRPart II• Connecting to the Dynamic Energy Budget• Play with NicheMapR• Inferring climatic constraints• Nutritional constraints
Mechanistic Niche Models
Biophysical Ecology
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O heat
pSOLAR
pIR,in
p
MET
pIR,out
pCONV
p
pCOND
EVAP
+
+
+
+
+
fe ding
JJX,I JX,PJX,G JX,R JX,S+ + + +=br
athnigJO2,MET
JCO2,MET
JN,MET
JH,MET
+
+
+
= wa er
JJH,PJH,I +=+ +JH,U JH,S+
p = heat fluxJ = mass fluxX = foodH = waterI = ingestedP = product (faeces)U = urinatedG = growthR = reproductionS = storedO2 = oxygenCO2 = carbon dioxideN = nitrogenous wasteMET = ‘metabolism’EVAP = evaporationSOLAR = solar radiationIR = infrared radiationCONV = convectionCOND = conduction
Kearney et al. Functional Ecology (2013) after Porter and Tracy (1983)
pS+
Thermodynamic basis to the niche
Credit: Elia Pirtle
target (optimal) range
survivable range
selected environments through time
available range
hum
idity
Biophysical Ecology
Dynamic Energy/Mass Budgetgrowth
reproductivemaintenance
reservemetabolicworkgonads
metabolicrate
structuresomatic
maintenance
maturity maintenance
κ
1-κ
body temp/metabolic rate
Environmental Layers
water balance
Connecting to the Dynamic Energy Budget
A year in the life of the Fence Lizard in UtahConnecting to the Dynamic Energy Budget
0
100
200
300
400
500
600
0 5 10 15
wet
mas
s (g
)
time (years)
growth (mass) and reproduction
CO2 H2O O2 N waste
CO2H2OO2N waste
FoodStructureReserveFaeces
=
Inferring climatic constraints
Inferring climatic constraints
Kearney et al.. 2018. Field tests of a general ectotherm niche model …. Ecological Monographs 88:672–693.
target (optimal) range
survivable range
selected environments through time
available range
water balance
hum
idity
Biophysical Ecology
Dynamic Energy/Mass Budgetgrowth
reproductivemaintenance
reservemetabolicworkgonads
metabolicrate
structuresomatic
maintenance
maturity maintenance
κ
1-κ
body temp/metabolic rate
Kearney and Porter TREE 2006Kearney et al. PTRS 2010
target (optimal) range
survivable range
available food 1
available food 2
selected foods through time
Geometric Framework
food ingested
carb
ohyd
rate
Environmental Layers
Nutritional constraints
Food
Faeces
Food
Structure
Reserve
Faeces
Nutritional constraints
iso221
food ingested
pa
faeces
assimilation SUs
carbohydratereserve
κ (1-κ)pC
somaticmaintenance
maintenance SU
structure
growth SU
pG pS
somaticmaintenance
maintenance SU
structure
growth SU
pG pS
reproduction SU
food ingested
proteinreserve
carbohydratereserve
pA*(1-κP)
pa
κM κM (1-κM)(1-κM)pC pC
structure
pG pGpS pS
growth SU
pR pR
maintenance SU
somaticmaintenance
maturation/reproduction
rejection rejection
return flux
retu
rn fl
ux
faeces
assimilation SUs
somaticmaintenance
maintenance SU
pA*κP
maintenance SU
maturitymaintenance
maturitymaintenance
maintenance SU
pM pM
retu
rn fl
ux
κE
κ E
reserve
Kearney et al. PTRS 2010
pRpM
repro SUmaturity maint SU
maturity maintenance repro
Nutritional constraints
iso221
Simpson et al. (2010). Trends in Ecology & Evolution, 25, 53-60.
Nutritional Landscape Agent Behaviour
high P:C
low P:C
• Preference behaviour/targets will change with ontogeny
Nutritional constraints
CLIMATE
MICROCLIMATE
HEAT BUDGET WATER BUDGET
METABOLISM
LIFE HISTORY/PHENOLOGY
VITAL RATES BIOTIC EFFECTS
DEMOGRAPHY
DISTRIBUTION
ABUNDANCE
MECHANISTIC NICHE MODEL
Environment
Indi
vidu
al
PopulationCommunity
predation
competitionresources
Mechanistic Niche Models