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Ecological factors shaping the genetic quality of seeds and
seedlings in forest trees.
A simulation study coupled with sensitivity analyses
Project BRG-Regeneration 2003-2005
Reproduction cycle in trees
ADULT TREES
SEEDLINGSdispersal then germination
SAPLINGS
SEEDS
dispersal
growth / mortality
Pollen Ovules
fecundation
Sexual allocation
Pseudo -cycle :
Evolution in space
And in demographic and genetic composition
growth / mortality
Experimental « calibration » of input factors: project BRG-Reneration, 6 species
Demographic et genetic evolutions in natural regenerationFrom seed… …..to sapling
Impact of : sur :
A) Stand structure (seed trees density) -> mating system, seed genetic quality (in situ) [1]
B) Temporal variation in fertility, phenology -> mating system, seed genetic quality (in situ + simulation)[5]
C) Seed G.Q. in controlled conditions -> phenotypic value of des saplings (ex situ : germination test in lab, nursery) [2]
D) Seed G.Q. in natural conditions -> demography (survival, growth) : installing sapling plots in forest (in situ) [3]E) Q. G. of natural regeneration -> demography (survival, growth) : monitoring natural regeneration in forest . (in situ) [4]
[1]
[5]
[2]ex situ
[3] in situ [4]
Simulation model (TranspopRege, under Capsis4)
Input and output variables
ADULT TREES
SAPLINGS
Growth / mortality
SEEDS
Pollen dispersal
fecundation
Pollen Ovules
Male versus female fertility
Density, spatial distributionPhenotypic diversityGenetic diversity and structure
Seed dispersal then germinationSEEDLINGS
Genetic quality:― Level of diversity (drift)― Spatial structure
OBJECTIVES
•How these different processes (adult stand characteristics), mating system, survival rate) respectively affect saplings genetic quality (factor screening)•How the way each process is modeled affects the output variable
• “The study of how the variation in the output of a model (numerical or otherwise) can be apportioned (qualitatively or quantitatively) to different sources of uncertainty in the model input” Andrea Saltelli, Sensitivity Analysis
• Originally, SA focuses on uncertainty in model inputs, then by extension to the very structure of the model (hypothesis, specification)
What is sensitivity analyses ?
Sensitivity analyses : Morris method
Screening the factors that mostly affect the variance of output variable (Y)
Economic method in terms of computation/simulation (# evaluations = a# parameters)
Identifying factor(s) that can be fixed without significant reduction in Y variance
Method presentation
• k input factors X
• Each factor Xi takes p values
• Variation space = grid kp
• Elementary effect of factor Xi :
)(,...,,,,...,
)( 111 xyxxxxxyxd kiii
i
=incremented ratio defined in a point x of the variation space
Property : the transformed point x+eiΔ also belongs to the variation space
Distribution of elementary effects associated to factor Xi = Fi
• # of elementary effects = )1(1 pppk
• Gi = distribution of absolute values of elementary effects (Campogolo et al. 2003)
k = 2p = 5Δ = 1/4
X1
X2
How to measure the sensitivity of Y to factor Xi (Fi, Gi)
• μ = mean of distribution Fi • μ* = mean of distribution Gi
• σ = standard deviation of distribution Fi
• High μ* value & low μ value large effect of factor Xi + effects of different signs according to the point in space where it is computed
• High σ value the values of elementary effect are greatly affected by the point in space where they are computed (strong interaction with other factors)
An exemple of graphical representation of Morris sensitivity measures
σ
μ*
Estimation of the distribution statistics (μ*, μ and σ )
• Problem = sampling r elementary effects associated to factor Xi
• # runs needed to obtain r values of each Fi, 1≤i ≤k : n=2rk ↔ économy = rk/2rk=1/2
Morris sampling method• B* = matrix k k+1, each row = input parameter set
so that k+1 runs allow estimating k elementary effects ↔ economy = k/k+1– Choice of p and Δ:
• p uniforme entre 0 et 1• Δ = p/[2(p-1)]
Morris sampling method
• Randomly select an input parameter set x*; each xi drawn randomly in {0,1/p-1, 2/p-1,…, 1}
• 1rst sampling point x(1) : obtained by incrementing one or more elements in x* by Δ
• 2d sampling point x(2) : obtained < x(1) so that x(2) ≠ x(1) only at its ith component (+/- Δ), i Є {1,2,..,k}
• 3rd sampling point x(3): so that x(3) ≠ x(2) only at its jth component (+/- Δ), j Є {1,2,..,k}
• … Two consecutive points differ only for one
component, and each component iof the base vector x* is selected at least once to be increased by Δ
Visualisation
)1(
)2(
)1(
...kx
x
x
Orientation matrix B*Example of trajectory for
k = 3
Estimation
• For a given trajectory, k+1 evaluation of the model, and each elementary effect associated with each factor ican be computed as : :
)()1(
)(ll
li
xyxyxd
)1()(
)(ll
li
xyxyxd
ou
• With r trajectories, one can estimate :
r
ji rd
1
/
r
ji rd
1
2 /
Implementation
11
01
00
B
Triangular matrix, (k+1)k, with two consecutive rows
differing only for one column But the elementary effects produced would not
be random
13/2
3/13/2
3/10
3/10
1
1
1
' BB
X*
Jk+1,1
1. Which orientation matrix B* ??
Consider a model with 2 input factors taking their values in {0, 1/3, 2/3, 1}; we have a k=2; p=4; Δ=2/3.
**22/3/10
1
1
1
* ,1,1 PJDJBB kkkk
X*
Jk+1,1
11
11
11
22
02
00
02
22
20
11
11
11
11
11
11
1. Which orientation matrix B* ??
11
11
11
10
01
Diaginal D matrix with either 1 or -1 randomly
2. Choice of p = number and value of the levels of the input factors
• If Xi follows a uniform law divide the interval of variation in equalsegments
• For any other distribution, select the levels in the quantiles of the distributions
• # of p-values ?– Linked to r : if r small, p high is of no use
– Simulation study show that p=4 and r=10 not bad
Implementation
Conclusion on Morris method
• Elementary effect are basically local sensitivity measures
• But through μ* & μ, Morris method can be seen as global
• Do not allow to separate the effects of interaction between factors from that of non linearity of the model.
Simulation model (TranspopRege, under Capsis4)
Adult stand
Input parameters in TranspopRege
Density (1P)
Spatial distribution : Neyman Scott (1P)
Mean and sd diameter (2P)
# locus, # allèles (1P)
Spatial genetic structure (1P)
Mating system
Growth, mortality
Input parameters in TranspopRege
1. Density/distribution of adult trees
Poisson, 100 trees, DBH = 50 cm, σ = 7 cm Neyman Scott, 100 arbres, 10 agrégats (~ 50 m) DBH = 50 cm, σ = 7 cm
Poisson, 100 trees, DBH = 50 cm, σ = 7 cm Poisson, 100 trees, DBH = 50 cm, σ = 14 cm
Input parameters in TranspopRege 2. Phenotype/Genotype of adult trees
Adult stand
Mating system
Growth, mortality
Input parameters in TranspopRege
Pollen dispersal type (panmixy/ibd = 1TP)
Mean distance and form of pollen dispersal function (2P)
Mean distance and form of seeds dispersal function(2P)
Male fecundity = f (diameter) (1P)
Female fecundity = f(diameter, year, individual) (3P)
Input parameters in TranspopRege 3. Panmixy/ isolation by distance
Random pollen dispersal
Adult under considerationMaternal progenyPaternal progenySelfed progeny
Dispersal folowing a gaussian law
b
a
yx
ba
byxba
22
exp )/2(Γ π2
),;,(2
b = 2 Normale b = 1 ExponentielleAutres b : Exponentielle puissance
b > 1 « light-tailed »b < 1 «fat-tailed»
Input parameters in TranspopRege 4. Pollen/seed dispersal function
Input parameters in TranspopRege 5. Fecundity = f(diameter)
Input parameters in TranspopRege 5. Fecundity = f(diameter)
Depends on tree growth model
Model with year effect : cones ~ A * (cir - 100)^0.25 - (2.8 * A + 25.7)+ stochastic variability
700
4571977873982210
58478227743
Ne=31
Ne=92Ne=76Ne=36Ne=57
Ne=59Ne=85Ne=83
Ne ~ (4N-2) / (V+2)
(Krouchi et al, 2004)
Input parameters in TranspopRege 6. Stochastic variations in female fecundity
(example : cedrus atlantica)
Input parameters in TranspopRege 7. Male fecundity vs female fecundity
Adult stand
Mating system
Growth, mortality
Input parameters in TranspopRege
Mortality = f(genotype, survival rate on plot) (2P)
Adult stand
Mating system
Growth, mortality
Input parameters in TranspopRege
4P
9P
2P
15 parametersr = 100 > 20 trajectories
1600 runs > 320 runs
Problems…solutions ?
• Script mode OK, but within simulation, out of memory errors
• Necessity to include routine for population genetics computation