In which conditions can species coexist? There are several hypotheses about this, but in this exercise we will investigate the effect of the perturbation regime that an area endures, with differences in the colonization capabilities for the species, as we are still studying the colonization and extinction processes, as described by the metapopulation models.
We will start with the internal colonization model, in which a species dynamics is already familiar to you:
$$\frac{df_1}{dt}=i_1f_1(1-f_1)- p_e f_1 $$
Here:
Now, we will add another species to the system. The second species will be a weak competitor: it will only persist in patches in which the first species is absent. This means that the patches available for colonization are only the empty patches, and that it is excluded from whichever patch is colonized by the first species. The variation of fraction of patches occupied by the second species is given by:
$$\frac{df_2}{dt}=i_2f_2(1-f_1-f_2)- i_1f_1f_2 - p_e f_2 $$
The equation for species 2 does not add any new coefficient, but only combinations of things we have already seen:
* The extinction rate from both species is the same, so we didn't add a subscript.
The fraction of patches that are occupied by species 1 in equilibrium remains the same:
$$F_1=1-p_e/i_1$$
And now the fraction of patches occupied by species 2 in equilibrium is:
$$F_2=p_e/i_1- i_1/i_2$$
So, in order to have a viable metapopulation of species 2 ($F_2>0$), it is necessary that the following inequality is satisfied:
$$p_e/i_1 > i_1/i_2$$
Here you can read a tutorial explaining the mathematical deduction of the fraction of patches occupied by species 2 in equilibrium, that you can run in MAXIMA.
The deduction only needs simple algebraic manipulations. If you are scared of maths, keep in mind that you only need to understand the logic behind each step. To do the algebraic manipulation *per se*, there are lots of symbolic mathematics programs that can help you, such as MAXIMA, which is open source and free to use)).
Download and install the program and the graphical interface wxMaxima, open the script linked above and press crtl-R
to run.
Para prosseguir você deve ter o ambiente R com o pacote Ecovirtual instalado e carregado. Se você não tem e não sabe como ter, consulte a página de Instalação.
Depois de instalar o pacote, execute o R e carregue o pacote copiando o comando abaixo para a linha de comando do R:
library(EcoVirtual)
Let us run a computer simulation to generate a stochastic dynamic following the same rules as the differential model described above. The simulation is very similar to other simulation you have already seen on EcoVirtual :
fi1
and (fi2
), and occupy random patches until you reach the determined fraction.pi = i*f
).pe
.
The arguments to this function are the number of rows and columns for the habitat matrix, the number of time intervals that should be run, initial fraction of patches occupied by each species, and the model parameters i1
, i2
and pe
.
To run the simulation tutorial we will use the function metaComp from EcoVirtual package.
The parameters here are almost the same as the internal colonization model, but adding a second species:
option | parameter | effect |
---|---|---|
data set | R object | stores the simulation results |
Maximum time | $$tmax $$ | number of model iterations to be run |
columns | $$cl$$ | number of columns in the habitat |
rows | $$rw$$ | number of rows in the habitat |
Best Competitor | Parameters for the best competitor | |
initial occupancy | $$f01 $$ | pproportion of initial patch occupancy by species 1 |
colonization coef. | $$i1$$ | c colonization coefficient for sp1 |
Inferior Competitor | Parameters for the inferior competitor | |
initial occupancy | $$f02 $$ | proportion of initial patch occupancy by species 2 |
colonization coef. | $$i2$$ | colonization coefficient for sp2 |
Both Species | Parameters shared by both species | |
prob. extinction | $$pe$$ | extinction probability |
Habitat Destruction | $$D$$ | proportion of patches not available |
Show simulation frames | anima=TRUE | should every step be graphically animated? |
Start a simulation with the following parameters:
tmax = 100 cl = 20 rw = 20, f01 = 0.1 f02 = 0.4 i1 = 0.4 i2 = 0.5 pe = 0.25
Calculate the equilibrium value for each species using the formulas shown above. Verify that the theoretical values are close to the simulations results.
Don't be destructive!
The parameter D in the model controls how much habitat is removed at the start of each simulation. Don't use your immense destructive powers by now, as this will be done on the next tutorial. For now, always leave this parameter as zero.
We have defined the species 2 as the worse competitor. Does this sentence it to extinction? Examine the effect of the difference between the colonization capabilities over coexistence. To do this, we will vary the colonization parameter for species 2, keeping everything else constant. Identify the conditions for coexistence, and for extinction of each species.
Start simulating the following parameters:
tmax = 100 cl = 20 rw = 20 f01 = 0.05 f02 = 0.05 i1 = 0.1 i2 = 0.1 pe = 0.05
Now keep everything unchanged, except for i2. Change i2 to:
What is the interpretation of these results?
Let's start a new simulation with a new combination of parameters, in which species 2 has triple the colonization capability as species 1:
tmax = 100, cl = 20, rw = 20, f01 = 0.1, f02 = 0.1, i1 = 0.1, i2 = 0.3, pe = 0.05
Does this simulation lead to extinction? Vary the extinction probability keeping the other parameters constant, to investigate the effect of the perturbation regime over the results.
If the equilibrium is not being reached:
Tips
Many times, in order to check the predictions of a stochastic models, we need to run the simulation for longer times. When the graphical animation is toggled, it can take a while to process. In order to shorten the required time, turn off the animation by deselecting “Show simulation frames”. (anima=FALSE).
Patch occupancy can be defined as the proportion of available patches that are being occupied by a species. In our model, the initial occupancy for each species is given by fi1
and fi2
.