BIOD59 / EEB1420 Homework 2: Population viability analyses

20 points total (weighted as 10% of your final mark in BIOD59, and 8% of your final mark in EEB1420).

Few have ever seen a Bigfoot, but rumors have it that there is a small
population in the forests of Oregon. You managed to obtain a huge grant
from the newly founded Ministry of Fake Science to conduct a census, and
you indeed found a small population of 62 individuals [5 newborns, 7 1-yr
olds, 15 2-yr olds, and 35 adults (3-yrs or older)]. Moreover, conducting a
post-breeding census you managed to determine some basic demographic
parameters:

In a good year, the probabilities of surviving one year are

P0 = 0.30, P1 = 0.70, P2 = 0.85, P3 = 0.99, whereas in a bad
year they are P0 = 0.10, P1 = 0.30, P2 = 0.75, P3 = 0.85.
Fecundity is m3 = 1.2 in all years.

1. To determine whether this population is viable, first consider their deterministic dynamics in a
stable and average environment. Assume constant survival probabilities that are the average
between good and bad years (i.e., P0 = 0.2 etc.), and project the population 40 years into the
future. Provide a plot (or several subplots) that shows the time series of population abundances
in each age class (n0, t = number of newborns at time t, n1, t = number of 1-yr olds at time t, n2, t =
number of 2-yr olds at time t, n3, t = number of adults at time t), the total population size at time
t, Nt = n0, t +n1, t +n2, t +n3, t, and the annual population growth rates Nt/Nt-1 [7 points]. Calculate
the asymptotic population growth rate λ (the dominant eigenvalue of the projection matrix),
and the stable stage distribution of Bigfoot (the corresponding eigenvector, normalized so its
elements sum to one) [3 points]. Approximately, how many years of transient dynamics do you
observe? That is, how long does it approximately take until the age distribution and population
growth rate have stabilized? [2 points] Based on these initial analyses, do you expect the
population to persist over time? [1 point]

2. Recognizing that survival probabilities depend strongly on the environment, next we explore
the effects of environmental stochasticity on our projections. For this, assume that a year is
good with probability p and bad with probability 1-p. Using the survival and fecundity values
provided above, set up the transition matrices for good and bad years, respectively (denoted
Agood and Abad below).
a. If there were only good years, at what rate would the population grow? Would it
persist? What if there were only bad years? [2 point]
b. Using a random number generator to decide each year whether it is a good or a bad
year and assuming that good and bad years are equally likely (p=0.5), run 100
simulations for 40 years each (starting with N0 Bigfoots). Show the time series of total
population size (Nt) and all age classes (n0, t, n1, t, n2, t, n3, t) for the first 9 runs (9 subplots)
[4 points]. What proportion of your 100 runs results in quasi-extinction? For the
purpose of this exercise, we define quasi-extinction as occurring when total population
size in the last year of the simulation is less than 20% of the initial population size [1
point]
c. As in b, run 100 simulations for 40 years each, but now with good years only occurring
with p = 0.25. What proportion of runs result in quasi-extinction? Following this, repeat
the analyses but now with p = 0.15 and then with p = 0.05. What patterns do you notice
regarding how the quasi-extinction probability depends on p? [3 points]

+ 3 marks: Automate the process in question 2c to run 100 simulations for p = 0, 0.01,
0.02, 0.03, … and calculate the quasi-extinction probability for each p. Plot the quasi-
extinction probability as a function of p.