Download Evolution: Simulating Adaptation by Natural Selection

BIO 101L: Principles of Biology Laboratory
Evolution: Simulating Adaptation by Natural Selection
Introduction
The theory of evolution by natural selection is one of the greatest products of modern
science. The name most commonly associated with this theory is Charles Darwin.
However, the idea of the evolution of species had been around a long time before
Darwin. For example, the biologist Jean-Baptiste Lamarck proposed (incorrect)
mechanisms for evolution before Charles Darwin was born, and Georges-Louis Leclerc
wrote treatises on evolutionary change long before that. Even natural selection was not a
wholly new concept; rudimentary forms of the idea first appeared in the writings of
Aristotle.
The major contribution of Charles Darwin and his contemporary, Alfred Russel
Wallace, was to incorporate all of these ideas and produce a coherent and mechanistic
model of how change over time might occur within a species, and how new species might
arise from this change. Their model of evolution by natural selection proved to be a
powerful tool for explaining many patterns found in the living world. Since Darwin’s
time, knowledge of genetics and inheritance has been incorporated into the theory of
natural selection to produce the ‘modern evolutionary synthesis.’ Modern evolutionary
theory has become the bedrock of biology, and has been so thoroughly corroborated by
many independent lines of evidence that it is accepted as ‘fact’ as much as anything can
be in science. Despite minor tweaks arising from modern biological research, the work of
Darwin and Wallace still forms the core of evolutionary theory.
In this lab, we will examine some of the basics of evolutionary theory. We will
focus purely on Darwin and Wallace’s proposed mechanisms and criteria for evolution by
natural selection. To accomplish this, we will use a computer-based simulation available
on the web. Topics like genetic drift and random mutation will be covered in lecture, and
you will learn about genetics in BIOL 102.
Evolution by Natural Selection
Natural populations do not grow infinitely; as they approach the carrying capacity of their
environment, the population growth rate slows to zero. In a closed population, a decrease
in population growth can occur by two means: (1) a decrease in the birth rate, or (2) an
increase in the death rate. In the real world, ‘voluntary’ reduction of the birth rate by
populations approaching their carrying capacity is rare. Thus, the growth of most real
populations is checked by only increased death rates.
The fact that more offspring are produced than can survive forms part of the
theory of evolution by natural selection. Charles Darwin noticed that most living things
produce far more offspring than the environment can support. Most of these offspring die
before producing young of their own, and even those who reach adulthood have widely
varying success in producing offspring. Darwin also noticed that which individuals died
and which lived long enough to produce offspring was not determined by chance. Rather,
organisms struggle with each other and with their surroundings, and some individuals are
better equipped to ‘win’ this struggle than others. The ability to survive and produce
offspring is what Darwin termed ‘fitness.’ Since offspring tend to resemble their parents,
Darwin concluded that this repeated process of overproduction of young followed by
unequal survival could slowly change the nature of a population. This led Darwin (1859)
to propose three criteria for evolution by natural selection to occur:
1. Variation must exist within a population. Individuals within a population must
exhibit variation in phenotype (e.g. differences in wing coloration or beak size).
2. This phenotypic variation must be heritable. Individuals must be able to pass their
traits on to their offspring, at least to some degree.
3. Variation must be linked to fitness (number of successful offspring produced). The
ways in which individuals differ from each other must influence their relative
ability to survive and reproduce.
Simulating Evolution by Natural Selection
To better understand how evolution by natural selection operates, you will use an online
computer program to simulate how changing environmental conditions affect
populations. This program is called EvolutionLab, and it simulates populations of
Darwin’s finches (Geospiza spp.) on two islands in the Galapagos. Darwin’s voyage on
the Beagle in the mid 1800’s played a strong role in the development of his theory of
evolution by natural selection. His observations of the different finch species in the
Galapagos served to illuminate the role environmental factors and competition in shaping
the evolution of species. Thus, for historical reasons, today’s simulation imitates the
situation found on these islands.
The species of Darwin’s finches we are focusing on feed on plant seeds. The
seeds available to foraging birds vary depend on the environment. During rainy periods,
plants that produce small seeds reproduce well, so there are many small seeds available
for the finches to eat. However, during dry periods, plants that produce large, hard seeds
that are resistant to desiccation reproduce well, so there are many large, hard seeds
available for the birds to eat. The finches cannot eat all the seeds easily, however. Finches
with small beaks have trouble breaking open large seeds, and so do much better when
there are a lot of small seeds in the environment. Individuals with large beaks are good at
breaking open large seeds, but have difficulty manipulating small seeds, and forage better
when there are a lot of large seeds in the environment. Because rainy periods result in a
lot of small seeds, small-beaked finches do well under wet conditions. Conversely,
because dry periods result in a lot of large seeds, big-beaked birds do well during dry
periods. Moderate rainfall leads to a lot of medium-sized seeds, and favors individuals of
intermediate beak sizes.
EvolutionLab simulates this evolutionary situation. The program tracks digital
birds feeding on digital seeds on two islands - Darwin and Wallace Islands in the
Galapagos. For each population, the program creates a set of birds of varying beak sizes
and has them forage on the available seeds. Finches that end up eating a lot of food will
have increased survival and reproduction relative to individuals who eat less, and the
whole process is repeated for another generation. Whether or not an individual finch eats
well depends on if it has an effective beak size for the seeds that are available, and, since
there is a random component, a bit of luck. Beak size is heritable in Darwin’s finches;
thus, the digital finch babies tend to have beak sizes close to their parents.
If you look back at the criteria for evolution by natural selection, you should see
that each criterion is met in the Darwin finch scenario. There is variation in beak size, the
variation in beak size is tied to survival, and the variation in beak size is passed on to
offspring. EvolutionLab gives you the power to control parameters like the starting
average beak size of the finch populations, how much rain the islands receive, and how
much variability there is in beak size. Thus, you have the ability to control natural
selection on these populations of finches, and you can use this ability to learn about how
natural selection works. First, let’s get familiar with the program.
EvolutionLab
Using your laptop computer, go to the web site http://biologylab.awlonline.com/. Register
at the site using the code available in your book by clicking on the green “Register”
button and following the directions. Once you have an account name and password, click
on the EvolutionLab button and log in. Click the blue Start Lab button right away. A
second window will open up; maximize this window by clicking the box in the upper
right corner of the window (right next to the ‘X’ which would close it).
On the screen you should see two columns, one labeled “Darwin Island” and the
other labeled “Wallace Island;” these represent the two finch populations you will be
toying with. Below them, you should see the parameter values currently set for each
island (e.g., Beak Size = 12 mm, Variance = 1.00).
1. On the left hand side, you should see a drop down box which currently reads “100.”
Change this to “300” and leave it there for the rest of the lab. This means that when
you hit the “Run Experiment” button, it will run for 300 years, which corresponds to
300 generations in this simulation.
2. Click the Run Experiment button now. You will briefly see two figures depicting the
finches and their beak sizes, along with numeric indications of beak and population
sizes. A graph will then pop up. This graph shows the beak sizes (vertical axis) on the
two islands (red is Darwin Island, blue is Wallace Island) as they change through time
(horizontal axis). In this case, you should see the average beak size rising on each
island. This is because the default parameter settings were for small initial beak size
but for low annual rainfall, which would produce large seeds favoring large beaks.
Thus, the two finch populations both evolved larger beaks over 300 generations. You
just imposed directional selection on the finches, and both populations responded.
3. Click on the Population tab at the top. This should reveal a graph which shows the
population sizes of the two finch populations changing through time. If you ever see
one of the beak size lines in the Beak Size tab get cut short, the population probably
died out. Checking out this tab will let you verify if this has occurred.
4. Next click on the Field Notes tab at the top. Here, you will see a table which gives
you the average beak size, the standard deviation (square root of the variance), and
the population size on each island for each year. Note the beak mean sizes for each
population in the first year, then scroll all the way to the bottom and note the beak
mean sizes in the last year. There should be about a 12 millimeter difference, give or
take a couple millimeters due to randomness. Make sure you remember how to find
this difference between starting and ending beak sizes, because you will have to do it
later in this lab.
Changing the Parameters in EvolutionLab
1. Click on the New Experiment button in the lower left corner; this resets everything
afresh and puts you on the starting page.
2. Click the Change Inputs button. You now have access to all the parameters which
might influence the adaptation of finch beaks. You can alter parameters by clicking
on the corresponding button on the left hand side, then moving the blue bars at the
bottom of the screen left and right. The pictures and numeric representations of the
parameters should change as you shift the blue bar around.
3. Notice that you can alter the parameters for each island separately. For instance, click
on the beak size button. Next, click and hold on the diamond in the blue bar for the
Darwin Island birds. Moving this left and right will change the average beak size that
the Darwin Island population starts out at when you run the experiment. Move the
blue bar all the way to the right so that the Darwin Island finches start with a beak
size of 30 mm. Click Done, then click Run Experiment. You should see that the
Wallace Island population evolved as per the previous simulation because you did not
change the initial beak size for that population. However, the Darwin Island
population did not seem to evolve at all. This occurred because the 30 mm beak size
they started with was already the best beak size for the available seeds, therefore they
experienced no selection for larger or smaller beaks. In fact, any individual finches
that happened to have beaks larger or smaller than 30 mm in this population would
have been worse off than those with the average beak size. Thus, you just imposed
stabilizing selection on the Darwin Island birds.
4. Click on New Experiment, then on Change Inputs. Go ahead and mess with some of
the other parameter values for a while to become more familiar with the program.
Predicting Evolutionary Change in Beak Size
1. When you know the selection pressures, you can predict evolution. Conversely, when
you know how evolution occurred, you can often predict the selection pressures that
caused it. Remember, the capacity to produce testable predictions is one characteristic
of a good scientific hypothesis or theory. Let’s try this out.
2. When you are ready, click New Experiment and Change Inputs again. Reduce the
initial beak size of the Darwin finches to 10 mm, and increase the initial beak size of
the Wallace population to 30 mm. Change the variance of each population to 1.99.
3. Now, suppose you want to end up with finches with beaks that are 20 mm. This is a
medium beak size right in between the starting beak sizes of 30 mm for the Darwin
finches and 10 mm for the Wallace finches. You know that the amount of
precipitation affects what seeds are available to the finches, and the size of available
seeds exerts selective pressure on finch beak size. Thus, you should be able to predict
what amount of precipitation (the same for both islands) will result in both the
Darwin and Wallace populations ending up with beaks at around 20 mm in size by
the end of 300 generations. Write this below
Precipitation: ______________ cm
4. Change the precipitation to this value one each island and run the experiment. Did
both populations end up with a beak size around 20 mm? If not, click the Revise
Experiment button and change the precipitation value to another number. Don’t just
guess though; try to predict the proper amount of rain beforehand. Keep doing this
until you are successful.
Predicting the Effects of Heritability and Variance
1. The term “heritability” refers to how much offspring tend to resemble their parents. In
other words, it tells you on average how good the value of parents’ traits (beak size,
in this case) is at predicting the value of the offspring traits. When heritability is high,
offspring tend have trait values that are close to the average of their two parents.
When heritability is low, offspring trait values tend to be closer to the average of the
trait value for the whole population than to the average of their two parents’ trait
value. Since evolution requires that offspring traits be somehow related to parental
traits (criterion #2), heritability should affect how evolution occurs.
2. Let’s set up two populations that are different only in terms of heritability. Click New
Experiment, then Change Inputs. Change the heritability of the Darwin population to
0.90, and change the heritability of the Wallace population to 0.20. Before you run
the experiment, though, you must make a prediction about what will happen. Both
populations have some heritability for the trait, so evolution will occur in each
population over 300 generations. However, the rate of evolution might be different
for each population. Below, write a prediction about which, if any, of the two
populations will evolve faster. Also write down why you predict this, because you
will need to support your prediction when you write up your lab report.
Prediction: ___________________________________________________________
Why:________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
3. Now click done and run the experiment. If one of your populations went extinct, rerun the experiment by clicking Revise Experiment then Run Experiment. Examine the
graph showing beak size. Are there differences in how fast they changed? Go to the
Field Notes tab. The beak sizes for each population should be pretty close in the first
year. Scroll down to the last year and compare the beak sizes. Are the two
populations still pretty close to each other, or are they fairly different? Is this what
you predicted?
4. Remember, however, that you cannot draw conclusions just based on a single trial of
an experiment. You need to do multiple trials and use statistics. In the table below,
record the beak sizes for each population in the first year and the last year, then
calculate how much the beak sizes changed for each population. Now you can re-run
the experiment.
5. Click Revise Experiment (not New Experiment, otherwise you will reset the
heritability values), then click Run Experiment again. Go to Field Notes, and record
the beak sizes in the first and last years for each population again, and calculate the
differences. Repeat this until you have 10 total trials and have filled up the table
below.
Darwin Island (heritability = 0.90)
Wallace Island (heritability = 0.20)
Starting
Beak Size
(mm)
Starting
Beak Size
(mm)
Final Beak
Size (mm)
Change
(Final-Starting)
Final Beak
Size (mm)
Change (FinalStarting)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
6. Using this data, you should be able to run a t-test to test for differences in the change
in beak size between the Darwin and Wallace populations.
Open up Excel, and enter the changes in beak size into two columns, one for the
Darwin population and one for the Wallace population. Click on Tools->Data
Analysis. Select “t-Test: Two-Sample Assuming Equal Variances,” then click OK.
Click on the text box next to Variable 1 Range, then select the 10 cells which contain
the beak size change data for your Darwin population. Next, click on the text box
next to Variable 2 Range, then select the 10 cells which contain the beak size change
data for your Wallace population. In the Hypothesized Mean Difference, enter the
value ‘0’ (this is your null hypothesis). Click OK. A new sheet will open up which,
among other things, tells you the means, the variances, the degrees of freedom (df),
the t Statistic, and the p-value for your data. Record these below. Use the one-tailed
p-value (probably in row 11) because you had a predicted direction of evolutionary
change for the populations. If your p-value is very small, just record it as ‘p<0.01.’
Did you support your prediction?
Darwin population mean: _________
Darwin population variance: ___________
Wallace population mean: _________
Wallace population variance: ___________
df: ___________
t-statistic: ______________
p-value: _____________
Now you will plot a bar graph of the heritability data for your lab report. Go to the 101
lecture website at http://mama.indstate.edu/angillet/BIOL101/links.htm and click on
‘Creating Graphs in Excel 2007’ for instructions on making bar graphs. Plot the mean
starting and final beak size on each island and include ± standard deviation error bars.
The Effect of Variance:
7. Variance in a population represents how different individuals are from each other
within a population. If there is no variation within a population, then evolution cannot
occur (criterion #1) because there are no differences to be favored by selection.
However, variation, like heritability, is not an all-or-nothing trait. Some populations
have low variance and most individuals within these populations have trait values
pretty close to the average. Some populations have high variance, however, which
means that a lot of individuals have trait values that are much higher or lower than the
average. Variation also affects how evolution occurs.
8. Let’s set up two populations that are different only in terms of variance. Click New
Experiment, then Change Inputs. Change the variance of the Darwin population to
1.99, and change the variance of the Wallace population to 0.50. Before you run the
experiment, though, you must make a prediction about what will happen. Both
populations have some variance for the trait, so evolution will occur in each
population over 300 generations. However, the rate of evolution might be different
for each population. Below, write a prediction about which, if any, of the two
populations will evolve faster. Also write down why you predict this, because you
will need to support your prediction when you write up your lab report.
Prediction: ___________________________________________________________
Why:________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
9. Run the experiment ten times like you did for the heritability experiment, and record
the data below (remember, click Revise Experiment, not New Experiment). Run a ttest on this data in the same manner. Did you support your prediction?
Darwin Island (variance = 1.99)
Starting
Beak Size
(mm)
Final
Beak Size
(mm)
Change
(Final-Starting)
Wallace Island (variance = 0.50)
Starting
Beak Size
(mm)
Final
Beak Size
(mm)
Change (FinalStarting)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
Darwin population mean: _________
Darwin population variance: ___________
Wallace population mean: _________
Wallace population variance: ___________
df: ___________
t-stat: ______________
p-value: _____________
Make a bar graph for this data just like you did for the heritability experiment.
Literature Cited
Darwin, Charles. 1859. On the Origin of Species by Means of Natural Selection, or the
Preservation of Favoured Races in the Struggle for Life. John Murray Publishers.
London, England.