Download Pre-lab homework Lab 7: Alleles in populations Name

Pre-lab homework Lab 7: Alleles in populations
Name:
After reading over the lab answer these questions to be turned in at the beginning of the lab!
1. What are allele frequencies. What do they tell us about a population?
2. The Hardy-Weinberg equation describes a population that is not evolving at all. It is only true if
certain assumptions are true - What are these assumptions?
3. In lab we will examine the effects of a very small size on a population’s allele frequencies. What
population size will we be modeling?
Will this population stay in Hardy-Weinberg equilibrium? Why/Why not?
4. What is your blood type? (if you don’t know try calling your parents – if you can’t find out it is not
a big deal)
Lab 7: Alleles in populations
Lab section
Name:
Objectives: Upon completion of this activity, you should be able to:
• Describe a population of organisms using genotype and allele frequencies
• Use the Hardy-Weinberg equation to predict future genotype and allele frequencies
• Explain how the assumptions of the Hardy-Weinberg equation tell you about evolutionary
forces that can change genotype and allele frequencies
• Compare predictions of the Hardy-Weinberg equations to your observations of a real world
population to look for evidence of evolution.
Introduction:
In the early part of the 1900’s as Mendelian genetics was being rediscovered and expanded on
several geneticists were confused by traits that were dominant but rare. A classic example is the trait
called brachydactyly, this trait results in shortened stubby fingers and is the result of a dominant
allele so people who are heterozygous have these shortened fingers. This trait, while it is dominant, is
also very uncommon . While many of the geneticist at the time guessed that this was possible they
couldn’t explain why a dominant trait wouldn’t become more common over time since it masked the
recessive trait. A mathematician named George Hardy working with Alfred Punnett (of Punnett
square fame) developed an equation to describe how allele frequencies would change over time given
some simple assumptions (these assumptions are: large population size, random mating, no mutation,
no migration, and no natural selection). Another person, Wilhelm Weinberg, working on the same
problem developed the same formula independently. This equation, now called the Hardy-Weinberg
equation, is one of the basic tools used in the study of populations and how they evolve. In lab this
week we will learn how to calculate allele and genotype frequencies, we will examine frequencies in
real world populations and we will see how the Hardy-Weinberg equation can be useful even if it is
only an approximation of a population. We will then look at one of the forces, called genetic drift,
that can cause allele frequencies to change over time. Next week we will examine another of these
forces, made famous by Charles Darwin, called natural selection.
Exercise 1: Calculating allele frequencies:
One of the challenges that scientists working on the genetics of populations have is describing
the population. The most basic way to describe a population is to calculate the frequencies of the
different alleles found in the population. Frequencies are simply the proportion of the whole that is of
certain type. You will often see frequencies expressed as percentages – for example if you have 78
red bellied fuzzies in a population of 100 then their frequency is 78/100 or = 0.78 we would often say
that the population is 78% red bellied. One of the difficulties in calculating allele frequencies is that
you cannot always tell what alleles an organism has just by looking at it since recessive alleles can be
hidden by dominant alleles. We will ignore this problem for now by examining flower color in a
population of snapdragons – remember that these organisms have codominant alleles so that it is
possible to know the alleles in an individual by looking at their phenotype.
Calculating allele frequency:
1) Imagine a population of snapdragons. Remember that these plants have flower color determined
by incomplete dominance. If they have two copies of the red allele they have red flowers, two
copies of the white allele and they have white flowers, but one copy of each (a heterozygote) and
their flowers are pink. If this population is made up of 500 plants with 350 white plants and 150
red plants could you calculate allele frequency? Follow these steps:
a) To calculate the frequency of the white allele you first need to know the number of white
alleles. Remember that snapdragons are diploid – so how many white alleles are there?
b) Now you need to know the total number of alleles (both white and red) – what is that number?
c) Now you just need to divide the number of white alleles by the total. In other words the
frequency of the white allele is: Freq. white = #white alleles/total # of alleles
d) Now calculate the frequency of the red allele using the same technique.
Freq. red = #red alleles/total # of alleles
Genotype frequency in a real population:
2) Now we will examine a real population – the students in your lab – and try to calculate
frequencies for this population. The first thing we will need to do is score the phenotypes of all
the individuals in the class. We will use traits that are easy to score and we will act like there is a
simple genetic explanation of their inheritance (although in many cases this is probably not true).
To calculate the frequency of the phenotype we will simply divide the number with that
phenotype by the total number of individuals we have examined.
Genetic Trait
Tongue rolling
# with phenotype 1
Yes =
# with phenotype 2
No =
Widows peak
Yes =
No =
Free earlobe
Yes =
No =
Blue eyes
Yes =
No =
Hitchhikers thumb
Yes =
No =
Hairy knuckles
Yes =
No =
Taste PTU
Yes =
No =
Sickle cell anemia
Yes =
No =
Cystic fibrosis
Yes =
No =
Freq of phenotype 1
a) Notice that what we have calculated here is not allele frequency but rather genotype
frequency. Can you easily calculate allele frequency from this information? Why/Why not?
b) The Hardy-Weinberg equilibrium can help us here – if you know (or assume) the population
is in Hardy-Weinberg then you can calculate allele frequencies from genotype frequencies.
Pick two of the traits above you think are most likely to be in equilibrium – Why did you pick
those traits?
c) Using the H-W equation calculate allele frequencies for these traits.
Exercise 2: Evolving populations – Genetic Drift
In this exercise you will be examine a situation where the allele frequencies of a population
are changing. In this case we will look at a very small population of organisms and see how their
allele frequencies change over time due to simple random changes caused by chance events.
Procedures:
1) To track the evolution of a population over time we will start with a population of organisms with
an allele frequency of Freq. A = 0.6 and Freq. a = 0.4. In order to simulate random mating we will
need a way to generate random offspring – we will pick organisms out of a hat. In this case we
will use different colors of beans to represent the different alleles so you will put together a box
with 60 “A” beans and 40 “a” beans to use as your random offspring generator.
2) After setting up your box you will pick out 5 offspring to represent the next generation. To do this
pick 2 beans from the box for the first individual, record the genotype (which two “alleles” did
you pick), put the beans back in the box, mix and choose the next individual.
3) Once you have the next generation calculate the new allele frequencies and then reset your
“random offspring generator” (the box with beans ) to represent the new allele frequencies.
4) Then repeat step 2 to choose another generation of 5 individuals.
5) Continue on for 10 generations recording allele frequencies in the space below.
Questions:
1) What happened to allele frequencies in your population? Is this evolution? Why/why not?
2) Did all of the populations in lab have the same result? Why do you think this is?
3) Will this process help a population become better adapted to its environment? Why/why not?
4) From a website on the Florida Panther (http://www.panther.state.fl.us/handbook/threats/inbreeding.html) “By the
1980s only 30-50 adults remained in the population.... A 1992 population analysis concluded
that under existing demographic and genetic conditions the Florida panther would become
extinct in only a few decades (24-63 years) (Seal et al. 1992). Congenital heart defects,
poor sperm quality, and high incidence of cryptorchidism (one or two retained testicles that
have not descended into the scrotum) have been cited as possible negative consequences of
inbreeding among Florida panthers (Roelke 1991; Dunbar 1993).”
Shouldn’t natural selection
be reducing the negative consequences of inbreeding? Why do you think it is unable to do so?
Pre-lab homework Lab 8: Natural Selection
Name:
After reading over the lab answer these questions to be turned in at the beginning of the lab!
1. This week's lab uses a mathematical model to simulate the interactions of populations. What is an
advantage of using a model like this over doing research on real world populations?
2. How can you be sure that the results of your model are telling you something about the real
world?
3. Lab this week models natural selection. Briefly explain what natural selection means and how we
will model it in lab.
Biology 102
PCC, Cascade
Lab 8: Natural Selection
Lab section
Name:
Objectives: Upon completion of this activity, you should be able to:
• Explain how predation can affect prey species.
• Describe how predator populations can change depending on the environment.
• Discuss strategies that predators use to improve their chances of survival.
• Relate all of these ideas to the idea of natural selection.
Introduction:
Phenotypic variability exists in all natural populations – some zebra are faster than others,
some plants grow broader leaves. For a wide variety of reasons some different phenotypes (or
morphs) survive and reproduce better than others (faster zebra may survive and reproduce better than
slower zebra). These phenotypes then become more common over many generations. This is the
concept of natural selection. One of the common reasons some organisms have more success than
others is because of how they interact with other species. In lab this week we will look at how one
type of interaction, the predator prey interaction can alter a population.
Today we will use a game to help model how predator and prey populations interact. Using
games to model behavior is a commonly used tactic in many situations since it can allow scientists to
experiment with the different variables that are thought to affect the behavior. Each different version
of the game, with slightly altered variables, is like a hypothesis about how these behaviors occur. As
the variables are altered the results of the game change and can be compared to data about the real
world. The goal is to create a game that seems most like the real world. The closer the match
between the results of real world research and the game the better the hypothesis and therefore the
better we understand the mechanisms that cause the behavior.
In today’s lab we will “play” a game where individual prey are represented by various types
of food (beans, lentils…) and different predators are represented by different utensils (knife, fork,
spoon…). Each different type represents different morphs - slightly different versions of organisms
of the same species (lima beans may be a big slow zebra while the rice grains are tiny fast zebra).
General Rules:
• Predators can use only one hand and must lift the prey into their cups. (No scooping!)
• After every round you need to recalculate the proportion of each morph in the populations.
• The size of predator and prey populations does not change – just the proportion of each
morph in the population. (think of the population as being at its carrying capacity)
• Always try to think about the game you are playing in terms of the how populations
interact in the world outside the lab.
54
Biology 102
PCC, Cascade
Trial 1 – The most wily prey in the carpet!
Basic setup: 4 predators of the same morph (students with knives) will “feed” on a variety of prey
morphs scattered over a small piece of carpet. We will then track the changes in our populations.
Starting conditions: Fill in the starting conditions in the table based on the information given by your
instructor. You will then fill out the rest of the table during the trial.
Prey
Starting
Starting
Population
New
Number at
Frequency
Morph
population
frequency*
after one
frequency* in
beginning of
after 3
round
population
round two.
rounds
1
2
3
4
5
TOTALS

1
1

1
*Frequency = number of individuals of this type alive / total number of individuals alive
 These numbers should match!
Prediction: Which prey type do you think will be the least likely to be “eaten”? Why?
The Game: Have each predator (up to 4 students armed with knives) gather around the
environment, start timing and “eat” for 15 seconds. After you are done count how many of
each type of prey remain then fill out the next three columns of the table. After each round of
predation you will need to reset the prey population to reflect the results of the previous round
(multiply total population size by frequency of the type). Continue until you complete the
third round. Then fill in the last column of the table and answer the questions on the next
page.
55
Biology 102
PCC, Cascade
The Questions:
1. Was your prediction right? If not why do you think the results were different from what you
thought would happen?
2. Did one type of prey disappear? What does this mean is happening to the population? How does
this illustrate natural selection? (Remember these are all the same species so the species is not
going extinct!)
3. Imagine that the phenotype of these prey are not determined by their genetics but only by their
environment. How would this effect the ability of natural selection to change the population?
4. Do you think this simulation has taught you anything about natural selection in the “real world”?
If yes – What? If no – What could be done to make the lab more like the “real world”?
56
Biology 102
PCC, Cascade
Trial 2 – The best of the predator in the carpet!
Basic setup: A new predator morph has appeared – the fork! Now 4 predators of two morphs (replace
one knife predator with a fork) will “feed” on prey species scattered over a small piece of carpet. You
will need to create a data table to track the predator populations over time and you will need to
develop rules to control predator populations.
Starting conditions: Fill in the starting conditions in the table based on the information from round 3
of the previous “game” You will then fill out the rest of the table during the trial.
Morph
1
2
3
4
5
TOTALS
Starting
Starting
Population
New freq.* in
# in round
Freq. after
population
frequency*
after 1 round
population
two pop.
3 rounds

1
1

1
*Frequency = number of individuals of this type alive / total number of individuals alive
 These numbers must match!!
The Game: Have each predator gather around the environment, start timing and “eat” for 15 seconds.
After you are done count how many of each morph of prey remain then fill out the next three
columns of the table. After each round of predation you will need to reset the prey population to
reflect the results of the previous round. You also must decide how to reset the predator
population after each round!! Remember you also must create a predator data table and update
it at least twice (after one round and after three rounds!) Continue until you complete the third
round (a total of 6 rounds now!). Then fill in the last column of the table and answer the questions
on the next page.
Your new rule: After a round of predation you must decide how many forks and knives there will be
in the next generation of predators. How will you reset the population of predators in round
two? (Hint: remember that in general the more you eat the more babies you can make!)
Write your new rule here!
57
Biology 102
PCC, Cascade
The Questions:
5. You set up a rule to determine how many predators you had of each type every round. How well
did your new rule work out? Think of examples in the “real world” that work the same way your
rule does.
6. Attach a graph of predator and prey frequency over the rounds of the trial you conducted.
58
Biology 102
PCC, Cascade
Exercise 4: The Evolutionary Arms Race
In this video we will learn about how the interactions of different organisms can drive
evolution. We will start out looking at the interaction of predator and prey species, including a
predator on humans. Then we will think about other types of interactions that can drive evolution.
Questions:
Read these questions prior to watching the video and answer them during the video!
1. What is special about the newts that Edmund Brody studies?
2. What seems to be causing this trait in the newts? Why?
3. What is the one type of predator that humans should still fear?
4. In the middle of the last century the surgeon general said it was time to close the book on
infectious disease. Was he right? Why/Why not?
5. What disease is running rampant in the Russian prison system?
6. What seems to have happened to the microbes causing the infection in Sasha?
59
Biology 102
PCC, Cascade
7. MDRTB – stands for multi-drug resistant TB. How is natural selection driving the evolution of
this type of TB? (think about how this relates to the activity you did in the first part of the lab!)
8. What conditions caused cholera to become more toxic?
9. What conditions caused cholera to become less toxic?
10. What seems to have happened to all the big cats who are infected with feline immunosuppressive
virus?
11. Do you think a similar thing will happen with humans who are at risk for HIV infection? Why?
12. Leafcutter ants are an example of a symbiotic relationship with what other organism?
13. How do these ants keep pests out of their gardens?
14. What is the most interesting thing you learned from this video?
60
Biology 102
PCC, Cascade
Pre-lab homework Lab 9: Tracing Phylogeny
Name:
After reading over the lab answer these questions to be turned in at the beginning of the lab!
1. Define the following terms in your own words:
•
Phylogeny
•
Taxonomy
•
Derived trait
2. Figure 2.2 in your text shows how evolutionary relationships can be detected by examining
underlying structures that organisms have in common. Structures that developed from a common
ancestor are called homologous structures. One difficulty in identifying homologous structures is
that sometimes structures are similar not due to common ancestry but because they are convergent
features (sometimes called analogous structures). What are convergent features and why do they
occur? (hint: look up analogous in your books glossary)
3. Imagine you are comparing sharks and dolphins and notice that both have dorsal fins that stick up
out of their backs. Do you think these dorsal fins are homologous or analogous? Why?
61
Biology 102
PCC, Cascade
62
Biology 102
PCC, Cascade
Lab 9: Tracing Phylogeny
Lab section
Name:
Objectives: Upon completion of this activity, you should be able to:
• Explain the connection between the scientific naming of organisms and their evolutionary
history.
• Describe the process used to develop evolutionary trees.
• Distinguish between analogy and homology when examining traits on evolutionary trees.
Introduction:
Humans have a strong tendency to place things into categories. We do it with our favorite
restaurants (“our favorite Chinese food place”, “a cute little Italian place”), our music (“a great new
jazz band”, “a cool new hip-hop group”), and we do it with organisms too. The process started in the
1700’s when Carolus Linnaseus developed a system to categorize all of life. You were introduced to
this naming system in biology 101 when you learned about the domains and kingdoms that all living
things are grouped into. In the Linnaean system organisms are grouped together based on similarities
in traits in a hierarchical system where the broadest categories contain several subcategories and each
of these contain several sub-subcategories that each contain sub-sub-subcategories and so on. In the
system that scientists currently use the broadest category is the domain, within each domain are
kingdoms, phyla, classes, orders, families, genera, and finally species (see Fig 2.9). The science of
taxonomy is devoted to naming an organisms correct domain, kingdom, phyla… etc. In other words
a taxonomist tries to place an organism into the correct categories based on similarities with other
organisms in those categories.
Domain
Kingdom
Phylum
Class
Figure 8.1: The hierarchical relationship of categories used in taxonomy
etc…
Initially deciding on what traits to use for the naming system was somewhat arbitrary, for
example was it more important that birds and bats both had wings or that birds had feathers and bats
had hair?. Beginning with Darwin the goal of the naming system changed from simply grouping
organisms together based on shared characteristics to grouping organisms together based on shared
evolutionary history. In other words the goal became to have groups within the same category (say
63
Biology 102
PCC, Cascade
the same genus) to be most closely related to each other than to any other organisms. Scientists now
say that taxonomy should reflect phylogeny, the evolutionary history of a group of organisms. With
this goal in mind it became possible to judge which type of traits would best define naming categories
to show relatedness. Your first activity in lab is to work on a simplified system that will illustrate
these ideas. After working with this simplified system we will look a several real world examples of
the connection between taxonomy and phylogeny and see some of the difficulties that scientists still
have in developing an organisms phylogeny.
Exercise 1: The Great Clade Race
In this exercise you will be working with a set of cards with symbols on them. Your initial job
will just be to sort them into categories. After you do that you will use these cards as clues that will
help you to draw a “map” of a set of paths. Finally you will use this map to answer a series of
questions.
Procedures:
3) Get a set of 8 cards with symbols on them from your instructor and sort them into groups. It
doesn’t matter how many groups you create (as long as there are more than 1 and fewer than 8) or
what characteristics you use to define these groups right now. Just do what ever makes the most
sense to you. Then answer these questions:
a) How many groups did you make?
b) What were the characteristics you used to make your groups?
c) Find another set of students who has divided their cards up in a different way than you have.
Is one way better than the other? Why?
64
Biology 102
PCC, Cascade
Exercise 1 - Procedures continued:
4) Now imagine that these cards represent cards carried by 8 different runners in a special kind of
race. These runners all start at the same point where they all got a stamp on their cards. Then they
started running but soon they came to a fork in the road. Some of the runners took one branch and
others went down the other path. Now both groups of runners pass a check in station and get a
stamp but these stations have different symbols so you can tell by their cards who passed which
station. The runners continue on the race and there are more branch points and more check in
stations until finally the race is over and each of the runners is at a slightly different finish line.
Using the following rules make a map of the race course showing branch points and check in
stations (remember to show the symbol for each check in station) in the space below. Rules:
•
Check in stations are located along the path between branches
•
The path only branched from 1 to 2 paths – never 3 or more
•
Paths never come back together
•
All runners complete the race and they don’t stop part way down a path and turn around.
(hint: some paths may not have check in stations!)
Your Map:
65
Biology 102
PCC, Cascade
Exercise 1 - The Questions:
1. Looking at the map you drew - which runners were most recently together and which runners
seem to have been on different paths for the longest time.
2. What do you think of the suggestion that you can tell which runners have been together the
longest by looking at which runners have a circle on their cards? What does the presence of the
circle on the card tell you?
3. Compare your map to the map drawn by several other groups – do they look exactly the same?
Why would the maps look different if the cards are all the same?
4. Get a copy of the 9th card from your instructor. Does it “fit” on your map? What would you need
to do to make this card “fit”? (hint: What is an analogous structure?)
66
Biology 102
PCC, Cascade
Exercise 2: Animal phylogeny
In this exercise you will be working with a real world data set to build a phylogeny of some
groups of animals. The basic idea is very similar to the “map” you drew for exercise 1 but in this case
instead of stamps you will use physical traits to map an organisms evolutionary history. The
organisms are organized into a table for you. Once again you will have a series of questions to
answer about your phylogeny
Procedures:
6) Get a copy of the data table for animals from your instructor and draw a “map” of the evolution of
vertebrate animals in the space below.
67
Biology 102
PCC, Cascade
Exercise 2: Animal phylogeny – The questions
1. How many different branches did you create?
2. Are there any examples of homology on this evolutionary diagram? If so what are they?
3. Biologists think that dolphins and humans are somewhat closely related. What support can
you see for this hypothesis? (try to use the idea of a derived trait to answer this question)
4. Many paleontologists (people who study fossil remains) think that velocoraptors had feathers.
What evidence does your tree have for this hypothesis?
68
Biology 102
PCC, Cascade
Exercise 3: Great Transformations
In this video we will learn about how the history of evolution is written not just in the fossil
record but also in the traits of all living organisms. We will start out looking at evolution of whales
from land dwelling organisms to marine. Then we will see how similar principles have been
important in evolution for billions of years.
Questions:
Read these questions prior to watching the video and answer them during the video!
1. What are some of the characteristics that all mammals have (including whales and dolphins!)?
2. What was unusual about the skull fragment that Dr. Gingerich found?
3. What did basilosaurus have that other whales seem to have lost?
4. What is the big difference between how fish swim and how whales and dolphins swim?
5. What is a characteristic shared by all land animals?
6. What characteristic does acanthostega have that makes it so surprising?
69
Biology 102
PCC, Cascade
7. What hypothesis does Dr. Clacks put forward on the evolution of limbs in animals?
8. What seems to have happened in the Cambrian explosion?
9. What underlying genetic mechanism seems to have allowed this?
10. How are the genes of fruit flies helping us to understand how evolution can occur
11. What is the most interesting thing you learned from this video?
70