Lefkovitch Model

Introduction Because the age of some adult animal such as Green Sea Turtles is
difficult to determine, some researchers have used a Lefkovitch matrix,
which divides the populations into stage classes. Some of the life stages
are easily recognizable (eggs, hatchlings, nesting adults), but the juvenile
stages are long-lasting, and age is difficult to determine. So, size (length
of carapace or shell) is used to define stages. This lesson will introduce a
stage-structured population model based on the distribution of the stages
of a particular species. The population distribution of stages is represented
by a vector and the transition relationship of the stage groups is
represented by a matrix called Lefkovitch transition matrix. We use matrix
multiplication to calculate the new stage population distribution in next
year based on the population distribution of stage in the current year.

Application Crowder, et al (1994) published a stage-based population model for the

Problem Loggerhead Turtle (Caretta) which projected the effects of the use of turtle
exclusion devices (TED’s) in trawl fisheries. These devices allow young
turtles to escape the trawls that trap shrimp, and the model predicted that
the required use of TED’s for offshore trawling would allow a gradual
increase in Loggerheads by an order of magnitude in about seventy years.
Such regulations may save thousands of turtles each year, and help to save
sea turtle species from extinction.

This lesson use Lefkovitch matrix to study the population model based on
Goal and
the staged-structure of a species. The objectives are
Objectives
1. Determine an intrinsic rate of growth of the population.
2. Determine projected population growth rate.
3. Know how to use state diagrams as well as transition matrices to
represent the changes of states of a final state mathematics model
4. Understand the concept and techniques of sensitivity analysis and draw
sound conclusions for the population problem under concern from the
sensitivity analysis.

Reflection Given the initial population distribution over different stage of the animals,
Questions and the transition rates due to the aging process and fecundity (ability to
produce offspring), and number of the mature females, we are interested in
the following questions:
1. What is the difference of stage diagram structures between the aged-
structure and stage structure models? From the observed difference
above, what differences you can observe between Leslie Matrix and
Lefkovitch matrix?
2. What is the predicted time of extinction if the population is decreasing?
Does the population reach a stable distribution if it is increasing?
3. How sensitive is the long-term population growth rate or predicted
time of extinction to small changes in parameters?

MA295; Module 1: Matrix Algebra Page 1

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

Example Morris, Shertzer, and Rice generated a stage-structured model of the Indo-
Use the Pacific lionfish Pterois volitans to explore control of this invasive and
Lefkovitch destructive species to reef habitats (Morris, 2011).
matrix to
This issue is very important because in a Caribbean region study Albins
represent
and Hixon found lionfish reduced recruitment of native fishes (addition of
the staged-
new native fishes) by an average of 79% over a five-week period (Albins
structured
and Hixon, 2008).
model
A lionfish goes through three life stages:
a) larvae (L, about 1 month),
b) juvenile (J, about 1 year), and
c) adult (A).
With one-month being the basic time step, the probability that a larva
survives and grows to the next stage is GL = 0.00003, while the probability
that a juvenile survives and remains a juvenile in a one-month period is
PJ = 0.777.
In one month, GJ = 0.071 fraction of the juveniles mature to the adult
stage, while PA = 0.949 fraction of the adults survive in a month. Only
adults give birth, and their fecundity of female larvae per month is RA =
35,315. Figure 3 presents a state diagram for these circumstances.

State State diagram for lionfish (Morris, 2011) is shown below

Diagram

Quick What transitions in the state diagram above does not exist in the Aged-
Review Structured model (Leslie model)?
Question 1

MA295; Module 1: Matrix Algebra Page 2

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

Now, we use algebraic functions to represent the populations in different

Population
stages. If xL(t), xJ(t), and xA(t) represent the number of female larvae,
Vector and
juveniles, and adults at time t, respectively, we have the following system
Transition
of equations for the distribution at time t + 1:
Matrix
 35315xA (t)  xL (t 1)

0.00003xL (t)  0.777xJ (t)  xJ (t 1)
 0.071xJ (t)  0.949xA (t)  xA (t 1)


Thus, we have the following transition matrix, called a Lefkovitch matrix:

  0 0 35315
 
0.00003 0.777 0 

 0 0.071 0.949 

Using these values, the lionfish monthly growth rate () is about 1.13.
Because adult lionfish reproduce monthly over the entire year, adult
survivorship has a great impact on the population's growth rate. With all
 else being the same, not until the probability of an adult surviving in a
one-month period is reduced approximately 30 percent, from PA = 0.949 to
PA = 0.66 or less, could a negative population growth be achieved.
Harvesting 30% of the adult lionfish each month is quite a challenge.
However, simultaneous reductions of 17% for the probabilities of juvenile
and adult survivorship could also produce a declining population. Thus,
"results indicate that an eradication program targeting juveniles and adults
jointly would be far more effective than one targeting either life stage in
isolation" (Morris, 2011).

Algorithm For an age-structured or a stage-structured problem, we form the

appropriate matrix, L, and the vector representing initial female population
distribution, x, and determine the distribution at time t by calculating Ltx.

For the projected population growth rate, we calculate the eigenvalue, ,

which is available through a command with some computational tools, such
as Maple, Mathematica, and MATLAB.
When not available, to estimate the projected population growth rate to
within m decimal places, we keep calculating the ratio of age distributions,
x(t + 1)/x(t), until two subsequent ratios differ by no more than 10 -m.
For the above example with birds, to estimate population growth to within
4 decimal places, we consider any one of the components, say the first, of
x(t + 1)/x(t) = Lt+1x / Ltx.
After repeated calculation, we discover with
x(15)/x(14) = L15x / L14x = (1.02153, 1.02173, 1.02136) and
x(16)/x(15) = L16x / L15x = (1.02162, 1.02153, 1.02173)
that the first components are sufficiently close to each other:

MA295; Module 1: Matrix Algebra Page 3

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

| 1.02153 - 1.02162 | = 0.00009 < 10-4 = 0.0001

These first elements, 1.02153 and 1.02162, differ by no more than 10 -4, so
our projected population growth rate is 1.0216.
Similarly, we can determine the category percentages of the total to within
m decimal places by finding when each of the corresponding elements of
x(t)/(total population) and x(t + 1)/(total population) differ by no more
than 10-m.

Quick What are the differences in structures between Leslie Matrix and Lefkovitch
Review matrix?
Question 2
Self-Check Australian cane toad data from (Lampo and De Leo, 1998)
Questions
Exercise 1 From To Mean Probability
Egg Tadpole 0.718
Tadpole Juvenile 0.05
Juvenile Adult 0.05
Adult Adult 0.50

a. Draw a state diagram for the model.

b. Develop a Lefkovitch matrix model, L, using the mean probabilities
from Table 14 with a fecundity of 7,500 female eggs and determine the
finite rate of population change, . If the animal could maintain such
annual population growth, would you anticipate the cane toad
population to increase or decrease over time?
c. Use Matlab to Calculate the population of the first 20 years,
X(0)…X(19) based on the mean probability
d. Based on your answers to c, what is the intrinsic rate of growth of the
population?

MA295; Module 1: Matrix Algebra Page 4

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

The relative sensitivity or sensitivity of  to parameter P in a transition

Sensitivity
matrix is the partial derivative of the dominant eigen value of the matrix
Analysis
() with respect to P, ∂/∂P, or the instantaneous rate of change of  with
Definition respect to P. Thus, this relative sensitivity of  with respect to P is
approximately the change in  divided by the corresponding small change
in P:
 new  
sensitivity of P   ,
P Pnew  P
where Pi,new is the new value of Pi and new is the resulting new value of .
For example, P1 = 0.15, and P1 + (10% of P1) = P1 + 0.10P1 = 1.10P1 =
0.15 + 0.015 = 0.165. With P1 = 0.15, the original dominant eigenvalue 
is
1.0216. Replacing the chance of a Year 1 bird surviving with P1,new =
1.10P1 = 0.165, the new dominant eigenvalue new is 1.06526, and new - 
= 1.06526 - 1.0216 = 0.04366. Thus, the relative sensitivity of P1 using
+10% is approximately (new - )/( P1,new - P1) = (new - )/(0.10P1) =
0.04366/0.015 = 2.9067. Similarly for -10% of P1, the sensitivity is
3.0677. However, the relative sensitivity of  to small changes in P2
(+10% and -10%) is much smaller (0.2480 and 0.2562, respectively).
From these calculations in Table 4, we see that  is most sensitive to
changes in survivability of Year 1 birds, P1. This analysis indicates that
conservationists might concentrate their efforts on helping eggs and
nestlings survive.

Table 1 Sensitivity of  (originally 1.0216) to changes in survivability

Survivability Percent Pi,new new new -  Pi,new- Pi new  
Parameter Change
Pi,new  Pi

P1 = 0.15 +10% 0.165 1.0653 0.0437 0.015 2.9111

P1 = 0.15 +20% 0.180 1.1069 0.0853 0.030  2.8435

P1 = 0.15 -10% 0.135 0.9756 -0.0460 -0.015 3.0677

P1 = 0.15 -20% 0.120 0.9268 -0.0948 -0.030 3.1599

P2 = 0.50 +10% 0.550 1.0340 0.0124 0.050 0.2480

P2 = 0.50 +20% 0.600 1.0460 0.0244 0.100 0.2443

P2 = 0.50 -10% 0.450 1.0088 -0.0128 -0.050 0.2562

P2 = 0.50 -20% 0.400 0.9955 -0.0261 -0.100 0.2607

MA295; Module 1: Matrix Algebra Page 5

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

Example Using sensitivity analysis, (Morris, 2011) determined that lionfish

Sensitivity population growth  is very sensitive to lower-level mortality parameters of
Analysis for larval, juvenile, and adult mortality and is "most sensitive to the lower-
Stage- level parameter of larval mortality." However, the larvae have venomous
Structured spines, probably making them less appealing prey than many of the native
reef fish. The project explores a lionfish sensitivity analysis and the
(Morris, 2011) model more closely.

Self-Check a. Consider the following Leslie matrix representing a population, where

Task the basic unit of time is one year:
Exercise 2
 0 0.2 1.3 3.5
 
0.1 0 0 0 
 0 0.2 0 0 
 
 0 0 0.4 0 

b. Give the animal's maximum life span, and describe the meaning of
each positive number in the matrix.
 c. Draw a state diagram for the animal.
d. Use Matlab to Calculate the population of the first 20 years,
X(0)…X(19) assume the initial population is X(0) = [30000, 4500, 800, 300].
e. Based on your answers to C, what is the intrinsic rate of growth of the
population?
f. What is your conclusion about the species, population is growing,
extinct, or stay stable in long term? If stable, what is the proportion of
each age group?
g. Determine the sensitivity of  to the second row, first column
parameter (0.1).
h. Determine the sensitivity of  to the first row, second column
parameter.
i. Determine the sensitivity of  to the third row, second column
parameter.
j. Determine the sensitivity of  to the fourth row, third column
parameter.
k. Determine the sensitivity of  to the first row, fourth column
parameter.
l. Based on your answers to Parts f-j, where should conservation efforts
focus?

MA295; Module 1: Matrix Algebra Page 6

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

Exercise 3 Australian cane toad data from (Lampo and De Leo, 1998)
For
Lefkovitch From To Mean Probability
Matrix Probability Range
Egg Tadpole 0.718 0.688-0.738
Tadpole Juvenile 0.05 0.012-0.176
Juvenile Adult 0.05 0.03-0.07
Adult Adult 0.50 0.3-0.7

a. Develop a Lefkovitch matrix model, L, Using the lower and upper

extremes of the probability and fecundity ranges.
Use Matlab to Calculate the population of the first 20 years,
X(0)…X(19) the lower and upper extremes of the probability and
fecundity ranges assume the initial population is X(0) = [30000, 4500, 800,
300].
b. Based on your answers to b on both the lower and upper extremes of
the probability, what are the intrinsic rates of growth of the population
 in both cases?
c. Determine the sensitivity of  to the second row, first column
parameter (0.1).
d. Determine the sensitivity of  to the second row, second column
parameter.
e. Determine the sensitivity of  to the third row, second column
parameter.
f. Determine the sensitivity of  to the fourth row, third column
parameter.
g. Determine the sensitivity of  to the fourth row, fourth column
parameter.
h. Based on your answers to Parts d-h, where should conservation efforts
focus?

MA295; Module 1: Matrix Algebra Page 7

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

High Performance Computing,

Need for Typically, a Leslie matrix is small enough so that high performance
High computing (HPC) is unnecessary to model the long-term situation for one
Performance type of animal. However, one species might be a small part of a much
Computing bigger network of other species of animals and plants and their
environment. Execution of models of such larger problems involves
extensive computation that can benefit from HPC.
For example, PALFISH is a parallel, age-structured population model for
freshwater small planktivorous fish and large piscivorous fish, structured
by size, in South Florida. The model contains 111,000 landscape cells with
each cell representing a 500m-by-500m area and containing an array of
floating-point numbers representing individual fish density of various age
classes. Researchers reported a significant improvement in runtime of
PALFISH over the corresponding sequential version of the program. The
mean simulation time of the sequential model was about 35 hours, while
the parallel version with 14 processors and dynamic load-balancing was
less than 3 hours (Wang et al. 2006).

Parameter Another use of HPC is parameter sweeping, or executing a model for

Sweeping each element in a set (often a large set) of parameters or of collections of
with High parameters. The results can help the modeler obtain a better overall
Performance picture of the model's behavior, determine the relationships among the
Computing variables, find variables to which the model is most sensitive, find ranges
where small variations in parameters cause large output changes, locate
particular parameter values that satisfy certain criteria, and ascertain
variables that might be eliminated to reduce model complexity (Luke,
2007).

Definition An embarrassingly parallel algorithm can divide computation into

and Example many completely independent parts with virtually no communication.
For example, researchers are modeling biological metabolism at a kinetic
level for green algae, (Chang et al. 2008). However, limited knowledge
exists of parameters for enzymes with known kinetic responses.
Consequently, the researchers have developed the High-Performance
Systems Biology Toolkit, HiPer SBTK, to perform sensitivity analysis and
fitting of differential equations to the data.
One problem involves 64 parameters and approximately 450,000
calculations for a full sensitivity matrix. (Chang et al. 2008) wrote, "In
moving from desktop-scale simulations of a small set of biochemical
reactions to genome-scale simulations in the high-performance computing
(HPC) arena, a paradigm shift must occur in the way we think of biological
models. A complete representation of metabolism for a single organism
implies model networks with thousands of nodes and edges." Because
parallelism of the calculations is extremely well balanced, the scientists are
optimistic that the code will scale to thousands of processors. Thus,
ultimately, they plan to develop an in silico cell model of metabolism that
contains all reliable experimental data for C. reinhardtii with problem sizes
perhaps thousands of times larger than the current problem.

MA295; Module 1: Matrix Algebra Page 8

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

Please discuss among you study group or use the blogs to discuss the answers to the two
quick review questions with other classmates,

Answers to Self-Check Exercises

1. A) State Diagram

 0 0 0 7500
0.718 0 0 
b. L =  0
 0 0.05 0 0 
 
 0 0 0.05 0.5 
c. X(0) = [30000, 4500, 800, 300], it will be right for you to use any no zero initial
populations.
You can use the Matlab to compute the rest by the formula X(n) = L^(n) * x(0)
d. lambda = 0.9289

2. Solution: a. 0.1 is the probability that in one year a stage 1 animal survives and
advances to stage 2. 0.2 is the probability that in one year a stage 2 animal survives
and remains at stage 2. (Other descriptions are left to the reader.)

b. state diagram

c. >> L = [0 0.2 1.3 3.5; 0.1 0 0 0; 0 0.2 0 0; 0 0 0.4 0 ]

>> x0 = [30000 4500 800 300]’
>> x1 = L * x0
>> x2 = L * x1
……
>> x19 = L^19 * x0
X0 X1 X2 X3 X19
30000 2990 2890 2099 0064
4500 3000 299 289 0014
800 900 600 60 0006
300 320 360 240 0005

d. >> x40 = L^21 * x19

>> x41 = L * x40
>> x41 ./ x40
Result [0.4597 0.4599, 0.4599, 0.4571]’
e. We can conclude that the Lambda =0.46,

MA295; Module 1: Matrix Algebra Page 9

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet
 Lefkovitch Model

f. Practically, you may observe that the population becomes extinct after about 20
generations.
g. Change P1 from 0.1 to 0.12 (20%) increase, the lambda changes from 0.46 to 0.463,
very insensitive increase. (0.003/0.2 = 0.015 = 1.5%. Change P1 from 0.1 to 0.2,
lambda changes from 0.46 to 0.56, the sensitivity is 0.1/1 = 10%.
h. If we observe the population changes, we find that the population of tadpoles drop
fasted. It seems a plausible way to counter attack the problem is to increase the survival
rate p1 of the larva. We can guess that the lambda maybe mostly sensitive to the p1.
We can change the F1 by adding 20%, i.e. change F1 = 0.2 to Fn1 = 0.24, try to see
the new lambda (0.46). It turned out very insensitive to the change. If still unstable,
change p1 to r1 = 0.4 (increase 100%), find the new lambda (0.47). It is again
insensitive.
I, Change P2 from 0.2 to 0.24, (20% increase), the lambda changes from 0.46 to 0.48,
sensitivity is 0.02/0.2 = 0.1 = 10%. Increase P2 by 100% from 0.2 to 0.4, the lambda
increases from 0.46 to 0.55. Sensitivity = 0.09/1 = 9%.
J Change P3 from 0.4 to 0.48, (20% increase), the lambda changes from 0.46 to 0.48,
sensitivity is 0.02/0.2 = 0.1 = 10%. Increase P3 by 100% from 0.4 to 0.8, the lambda
increases from 0.46 to 0.55. Sensitivity = 0.09/1 = 9%. Increase F3 by 100% from 0.4
to 0.8, the lambda increases from 0.46 to 0.53. Sensitivity = 0.07/1 = 7%.
K Change F3 from 3.5 to 4.2, (20% increase), the lambda changes from 0.46 to 0.475,
sensitivity is 0.015/0.2 = 0.075 = 7.5%. Increase F3 by 100% from 3.5 to 7, the
lambda increases from 0.46 to 0.53. Sensitivity = 0.07/1 = 7%.
L From the model, we know that the fecundity rates and survival rate are all very low.
According to our computations, the most effective way to protect the species is to
protect the tadpoles so that more can become juveniles and protect the juveniles so that
more can become adults.

3. The procedure to complete the problem is almost the same as the problem above. So,
we only provide the result below. If you have trouble to use MATALB, please use the
tutorial material and contact the teaching assistant to help you.

 0 0 0 7500  0 0 0 7500
0..688 0 0 0  0.738 0 0 0 
a. L R
 0 0.012 0 0   0 0.0176 0 0 
   
 0 0 0.03 0.3   0 0 0.07 0.7 
b. For lowbound L, X19 = 10^7[4.0788, 3.0958, 0.0265, 0.0004]’,
For the upper bound, x19 = 10^10[4.82. 1.955, 0.016, 0.0010]
c. For low bound L, lambda = 1.25, for upper bound R, Lambda = 1.82,

The sensitivity analysis is the same as the exercise 2. All you need is to use the MATLAB
to compute ratio between the change of lambda and change of corresponding
parameter.

MA295; Module 1: Matrix Algebra Page 10

Unit 1: Introduction to Matrix Operations & Population Studies
This section is adapted from a CSE education module by Drs. Angela and George Shiflet