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Microevolution

For the past two days in Biology, we have been working on a web quest our teacher sent us. This web quest was about guppies, species, and microevolution. Below is the web quest with the links. If you would like to read about it click on the first link. The second link takes you to learn about guppies and their spots. We needed to answer questions and define a few words.

PART 1: EVOLUTION 101

--Go to http://evolution.berkeley.edu/evosite/evo101/IVMicroevolution.shtml and proceed to the definition of microevolution page.

1. How do the authors of this page define microevolution?

            They define microevolution to be evolution on a small scale—within a single population. That means narrowing our focus to one branch of the tree of life.

2. How do they define a population?

            They define population as a group of organisms that interbreed with each other—that is, they all share a gene pool.

--Read the section “Mechanisms of Microevolution”

3. Summarize each of the 4 mechanisms of microevolutionary change that are discussed.

            1) Mutation- Where a gene randomly mutates and causes a change in the alle frequency.

            2) Migration- Where a species with a certain gene immigrates from one population and enters a group with a different gene.

            3) Genetic Drift- When a species mates a certain gene from the immigrated group shows up more than the common gene in the emigrated group.

            4) Natural Selection- A species with a certain gene that can camaflauge them from preditors survive better than those who are bright and easily seen.

--Under “Explore further” at the bottom of the page, click on “examples of microevolution” and read the examples provided.

4.  Summarize the 3 examples of microevolution on this page.

            1) The first example was dicussing the body size of the sparrows. The colder the climate the larger the body the sparrow has. The warmer the climate the smaller the body of the sparrow. Evolutionists say this was due to Natural Selection.

            2) In the second example the scientists discussed the affect of global warming and how it was causeing the environment to change. It would make the summers longer and hotter and the winters colder.

            3) Example 3 was very short and it talked about building resistance. The evolutionists say it was also by natural selection. They say that many different kinds of bacteria have built a resistance to some antibiotics and pestisides.

--Go to the link “Artificial selection in the lab” and read about experiments with the evolution of guppies.

5. Summarize the results of the two different experiments (with and without predators).

            With Predators- The scientists set up a pond to test the spot on guppies. The spots are meant to hide them from predators. The first set of ponds had predators. After less than 15 generations the number of spots seemed to diverge as a result of natural selection.

            Without Predators-  Without the predators the sexual selection of the guppies kicked in. The males attracted the attention of females with their many spots.

6. What types of selection were demonstrated in each experiment?  Are these experiments truly cases of artificial selection? Explain your answer.

            There was Natural selection, sexual selection, and artificial selection. Yes they are cases of artificial selection because each pond had fewer than 15 generations and the ponds were tampered with to get results.

--Click on the quick quiz link to go to the quiz. 

7. Pick your three favorite questions from the quiz and write how you would answer them if you were teaching this class.

1) What are species and how do new ones evolve?

         Species are different types of animals and they evolve over time. For example the dinosaur teridactly is supposed to have evolved into today’s birds.

2) What is macroevolution?

         Macroevolution is basically evoultion, but on a bigger scale. We look at the over-arching history of life.

3) What is an evolutionary trend?

         An evolutionary trend is a directional change within a single lineage or parallel change across lineages, in other words, several lineages undergoing the same sort of change.

PART 2: SEX AND THE SINGLE GUPPY

Go to http://www.pbs.org/wgbh/evolution/sex/guppy/index.html

Use the simulation to test different hypotheses about why some guppies are very brightly colored even thohat makes them easy for predators to find.

1.   Why do some guppies tend to be drabber than others?

To hide from predators

2.   Why do some guppies tend to be more colorful?

 To attract a mate to pass on there genes

3.   What role does color play in guppy survival?

      The more colorful a guppy is the better chances it has to

reproduce, the more drabber a guppy is the better chance it has to

survive

4. Explain the push and pull that the environment (including predators) has on the coloration of guppies in Endler’s pools.

            Places that have  a lot of predators have less colorful guppy as

they are usually eaten. This results in the male guppy being more

drabber as it is pushed toward camouflage.

EXPLORING THE ROOTS OF EVOLUTIONARY THEORY

Awareness of biological evolution emerged over centuries through the cumulative observations of many naturalists, biogeographers, comparative anatomists, and paleontologists. When Darwin and Wallace in the mid-1800s arrived at the idea of evolution by natural selection, they had been influenced not only by their own travels and observations, but also by the writings of many of their predecessors. Darwin's ideas were also influenced by his travels as a young naturalist on the H.M.S. Beagle. The islands he explored off the coast of Ecuador, the Galapagos, are hotbeds of evolutionary change. However, as you will see, Darwin did not entirely recognize the importance of these islands until after he returned from his voyage.

 Activity

In this activity you will access the evolution section of the University of California's Museum of Paleontology to explore some of the roots of evolutionary biology. You will then visit the Why Files site to learn about Darwin's voyage to the Galapagos and the current state of these islands.

Part 1.

Use your browser to go to the "History of Evolutionary Thought" exhibit at the University of California Berkeley Museum of Paleontology athttp://www.ucmp.berkeley.edu/history/evothought.html

Use the links in this section to learn about and briefly describe the background and scientific contribution of each of the following people:

1. Erasmus Darwin:

         Background- Charles Darwin's grandfather, and was a very intellectual man who was also a physician, a well known poet, philosopher, botanist, and naturalist.

         Scientific Contribution- he formulated one of the first formal theories on evolution in Zoonomia, or, The Laws of Organic Life.

2. Jean Baptiste Lamarck:

         Background- He was the youngest of 11 children and joined the French Army until accidental injury forced him to leave the army. He went on to publish a series of books on invertebrate zoology and paleontology.  His works never became popular in his life time. Passed away on Dec. 28, 1829.

         Scientific Contribution- He created a new field of biology and created the Invertebrates lessons. Never won an award for his work or his work was unpopular because other scientists believed that studying “invertebrates” was unworthy.

                 

3. Georges Cuvier:

         Background- Born in Montbéliard, a French-speaking community in the Jura Mountains.  He was a tutor to a noble family in Normandy, there he began to make his reputation as a naturalist.  He was invited to Paris  by Geoffroy Saint-Hilaire and there he became a professor of animal anatomy.

         Scientific Contribution- He established the fact of the extinction of past lifeforms. He contributed an immense amount of research in vertebrate and invertebrate zoology and paleontology, and  he also wrote and lectured on the history of science.

                 

4. Thomas Malthus:

         Background- Malthus was a political economist who was concerned about, what he saw as, the decline of living conditions in nineteenth century England.

         Scientific Contribution- Natural Selection and his theory that in nature plants and animals produce far more offspring than can survive. He said that man could do this too, but it would be the downfall of men.

Part 2.

Use your browser to go to the Why Files' "Treasures of Evolution Island" athttp://whyfiles.org/125galapagos/index.html

Use the information from Sections 3 and 4 to answer the following questions:

1. What interesting evidence of geological change did Darwin observe while visiting the Galapagos?

         Darwin discovered that South America rose from the ocean. He found rocks that had recently been in the water, with barnacles, and they were 6 feet above sea level. He soon realized that quakes probably accounted for the raised beaches he'd seen in Patagonia. He concluded that ancient shorelines dried out when the land was raised.

2. What did Darwin learn about the Galapagos finches when he returned to England? What vital information had he neglected to record when he collected them?

Darwin neglected to record when and where the Finch came from when he collected them. He learned that finches proved that species can be related.

3. Describe the distribution pattern of Galapagos mockingbirds. What question did this raise in Darwin's mind?

         It raised the question of, “Why do you have four different species, when one species certainly seems good for all the islands?”

EXPLORING MOLECULAR EVOLUTION

For the last two days in biology we have done an activity where we learn about relationships of DNA. To do this I set up an account at Biology Benchwork. Using there system I answered the following questions.

Results of your pairwise alignment comparing the beta globin gene in humans and in chimps:

1. Each line in this alignment contains 60 nucleotides. How many nucleotides are there in the beta globin gene for:
1. The chimp?

                                               i.     600

2. The human?

                                               i.     626

2. A blue asterix indicates that the nucleotides in both sequences are the same, we say they are conserved. What percentage of the beta globin sequence is conserved in chimps and humans?
1. 99%

3. Would you expect the protein structure to be highly similar or markedly different in the chimp and the human? Explain.
1. I would expect the protein structure between a human and a chimp to be very similar as we have a 99% identical genes

1. What is the percentage of sequence conservation between the beta globin gene in chickens and humans?
1. 57% 

2. Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or that found in chimps? Explain
1. I would expect the beta globin protein found in humansto be more similar to that of a chimp.

3. Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology? Explain. 
1. Yes because scientist can tell how close something is related to another whencompared with something else.

1. Examine the Unrooted Tree produced. 

Record the species at the end of each branch on the unrooted tree shown below.

2. Based on the information in the unrooted tree:

1. Which two species appear to be most closely related to each other? Explain your choice.

                                               ●         Humans and chimps based on the unrooted tree appear to be more closly related to each other. When you look at a hmans dna and a chimps dna they are 99% similar.

2. Which two species seem to be the least closely related to each other? Explain your choice.

                                               ●         Two species that are least closely related to each other are a chicken and human.

1. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give the comparative evolutionary distance by percent between:
1. The mouse and human

                                               i.     79%

2. The wallaby and the human

                                               i.     75%

3. The chimp and the human

                                               i.     99%

Comment on the significance of these results given your knowledge of mammalian groups.

            a. Humans are more closly realted to the chimp that the mouse and wallaby.

1. Examine your Rooted Phylogenetic Tree and record the species at the end of each branch. 

2. Based on this tree diagram, which species is/are most closely related to:

2. The goldfish: Chicken and Wallaby

3. The mouse: Human and Chimp

3. Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species. Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology. Which two species in the tree above share greatest homology with respect to the beta globin gene?
1. Humans and chimps

4. A node is a branch point representing a divergence event from a common ancestor. Which two species have the most ancestral nodes (divergence events) in the tree above? Explain your answer giving the number of nodes leading to these species.
1. Human and Chicken with 4 nodes

5. Looking at the phylogentic tree above, which two organisms:

1. Diverged from their common ancestor most recently?

                                               i.     Wallaby

2. Diverged from their common ancestor least recently?

                                               i.     Human

6. Draw a modified phylogenetic tree to show how the tree above might change if the beta globin gene for a kangaroo was added to the multiple sequence alignment.

1. It is important to understand that the phylogenetic trees you generated using bioinformatics tools are based on sequence data alone. While sequence relatedness can be very powerful as a predictor of the relatedness of species, other methods must be used in addition to sequence homology, to determine evolutionary relationships. Briefly describe 3 other methods that you think might be used to determine evolutionary relationships.

●       Anatomy/structure

●       Fossils

●      Biogeography

Transformation Lab

For the past two days in Biology, our teacher had us do a lab. We had to take bacteria (E-Coli, don't worry it was not the bacteria that will get us sick). Anyway we needed to follow a procedure to grow our own bacteria. It was quite interesting. First I will talk about the steps and then I will show you pictures of our results. Once I finish that I will show you the questions we were asked and how we answered them based on what we reserved.

Transformation Lab Guide:

Step 1: Label one closed micro test tube +pGLO and another -pGLO. Label both test tubes with your group's name. Place them in the foam tube rack.

Step 2: Open the tubes and using a sterile transfer pipet, transfer 250 ul of transformation solution.

Step 3: Place the tubes on ice.

Step 4: Use a sterile loop to pick up a single colony of bacteria from our starter plate. Pick up the +pGLO tube and immerse the loop into the transformation solution at the bottom of the tube. Spin the loop between your index finger and thumb until the entire colony is dispersed in the transformation solution ( with no floating chunks). Place the tube back in the tube rack in the ice. Using a new sterile loop, repeat for the -pGLO tube.

Step 5: Examine the pGLO plasmid DNA solution with the UV lamp. Note your observations. Immerse a new sterile loop into the plasmid DNA stock tube. Withdraw a loopful. There should be a film of plasmid solution across the ring. This is similar to seeing a soapy film across a ring for blowing soap bubbles. Mix the loopful into the cell suspension of the +pGLO tube. Close the tube and return it to the rack on ice. Also close the -pGLO tube. Do not add plasmid DNA to the -pGLO tube. Why not?

Step 6: Incubate the tubes on ice for 10 minutes. Make sure to push the tubes all the way down in the rack so the bottom of the tubes stick out and make contact with the ice.

-------------------------------------------- 10 minutes Later ---------------------------------------------------------------

Step 7: While the tubes are sitting on ice, label your four agar plates on the bottom ( not the lid) as follows: Label the LB/amp plate: +pGLO; Label the LB/amp/ are plate: +pGLO; Label the other LB/ amp plate: -pGLO; Label the LB plate: -pGLO.

Step 8: Heat shock. Using the foam rack as a holder, transfer both the (+) pGLO and (-) pGLO tubes into the water bath, set at 42 degrees Celsius, for exactly 50 seconds. Make sure to push the tubes all the way down the ram so the bottom of the tubes stick out and make contact with the water. When the 50 seconds are done, place both tubes on ice. For the best transformation results, the change from ice to 45 degrees Celsius and then back to the ice must be rapid. Incubate the tubes on ice for 2 minutes.

Step 9: Remove the rack containing the tube from the ice and place on bench top. Open a tube and, using a new sterile pipet, add 250 ul of LB nutrient broth to the tube and reclose it. Repeat with a new sterile pipet for the other tube. Incubate the tubes for 10 minutes at room temperature.

--------------------------------------------------- 10 Minutes Later --------------------------------------------------------

Step 10 : Tap the closed tubes with your finger to mix. Using a sterile pipet for each tube, pipet 100 ul of the transformation and control suspensions onto the appropriate plates.

Step 11: Use a new sterile loop for each plate. Spread the suspensions evenly around the surface of the agar by quickly skating the flat surface of a new sterile loop back and forth across the plate surface.

Step 12: Stack up your plates and tape them together. Put your group name and class period on the bottom of the stack and place the stack upside down in the 37 degrees celsius  incubator until the next day.

------------------------------------------------ The Next Day --------------------------------------------------------------

Man that is a lot of directions. Now below I will show you our results and questions we needed to answer based on our observations.

This picture shows our LB positive plate. There wasn't any bacteria but it was streaky and smudged.

This was our LB/ amp negative plate. It was very empty and had no bacteria what so ever.

This was our LB/amp/ara positive plate. This plate had a lot (LOT) of bacteria growing on it. Under the UV light it also glows due to the jelly fish DNA.

In this picture the plate is labeled LB/amp positive. The yellow glowing dots are bacteria. They glow under the UV light also due to the jelly fish DNA. 

Now that you have seen my groups results, I will show you are predictions we had to make on the plates before we got to see them. I put the questions red and our answers green. 

Prediction Questions:

1) On which of the plates would you expect to find bacteria most like the original non-transformed E. coli colonies you initially observers? Explain your predictions. 

       In Plate LB you would expect to find bacteria like the original. 

2) If there are any genetically transformed bacterial cells, on which plate(s) would they most likely be located? Explain your predictions. 

       They would most likely be on Plate LB/amp because they have been transformed. Same with Plate LB/amp/ara.

3) Which plates should be compared to determine if any genetic transformation has occurred? Why?

       LB v.s LB/amp because everything will grow on LB but different things will be on the LB/amp.

4) What is meant by a control plate? What purpose does a control serve?

       LB is a good control because we didn't add or take away anything. 

Now I will show you our Data collection questions. The questions will be in blue and our answers in green. 

1) How much bacterial growth do you see on each plate, relatively speaking?

          Either a lot of bacterial growth or none at all. 

2) What color are the bacteria?

          The bacteria colonies are a bright yellow color.

3) How many Bacterial colonies are on each plate?

          There are a lot (LOT) of bacterial colonies, really too many to be able to count. 

4) Which of the traits that you originally observed for E. coli did not seem to become altered? In the space below list these untransformed traits.

           Original Trait                                            Analysis of Observations

         Yellow Blobs                                             Still yellow blobs

5) Of the E. coli traits you originally noted, which seem now to be significantly different after preforming the transformation procedure? List those traits below and describe the changes that you observed. 

            New Trait                                                 Observed Change  

         New yellow blobs                                        Blue tint glows under

       glow blue tint.                                                 UV light.

6) If the genetically transformed cells have acquired the ability to live in the presence of those antibiotic ampicillin, then what might be inferred about the other genes on the plasmid that you used in your transformation procedure?

       We added the arabinose to the plasmid it essentially created the GFP (free florescent protein).

7) From the results that you obtained, how could you prove that the changes that occurred were due to the procedure that you preformed?

       Before we did the procedure the bacteria was normal. Afterwards it went through a transformation when it obtained a blue tinted glow due to obtaining a green florescent protein. 

DNA Detective Work

 Unless you have a twin, no one in the world has a DNA sequence identical to yours. Although 99 percent of the DNA is the same in all humans, certain segments vary widely. Differences in these segments are detected through DNA fingerprinting. A small amount of tissue, such as blood, hair, or semen, is all that is needed to create a DNA fingerprint. The sample is cut up using enzymes and the segments are separated by size through gel electrophoresis. DNA is made visible either with radioactive probes or by staining. This reveals a pattern of bars: the DNA fingerprint. If the two DNA fingerprints match, they probably came from the same person. If they don't match, they certainly came from different individuals. In recent years, a number of people convicted of crimes have been exonerated based on DNA evidence.

Activity

In this exercise, you will learn the basics of DNA fingerprinting and consider the use of DNA in criminal investigations.

Part 1.

Use your browser to go to NOVA’s web site about “Killers Trail,”  the story behind the man who inspired the Fugitive TV series and later the movie version starring Harrison Ford:

http://www.pbs.org/wgbh/nova/sheppard/

Click on the “Chronology of a Murder” section and read about the events that led up to the murder trial of Dr. Sam Sheppard.

1.                 In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?

1.     In my opinion the rle of newspaper stories and editorials played a major part in the outcome of the original trail of Dr. Sam Sheppard. Because of the pressure the police and jury felt from the attacks from the media, they unlawful arrested Sheppard just to please them. The media complained or questioned something they did what they could to please them. Even if it ment putting an innocent man in jail with out a proper trial.

Go back to the Killers Trail homepage and select ”Create a DNA Fingerprint.”

Read about the crime and the suspects then go on to part 2. Answer the following questions about the technique as you go through the simulation:

2.                 What is the function of the restriction enzymes in DNA fingerprinting?

1.     The restriction enzymes work like scissors to cut the long DNA molecules at different locations. Where the enzymes ut depends on the code within the DNA molecule and the code within the enzymes.

3.                 What is the function of  the agarose gel electrophoresis step?

1.     Acts as a molecular strainer, allowing smaller pieces of DNA to move through more easily than larger pieces.

4.                 Why is a nylon membrane used to blot the DNA?

1.     The DNA is sucked into the membrane as liquid traveled up from the gel toward an absorbent material that was placedover the membrane.

5.                 What does a dark spot on the X-ray film indicate?

1.     Your fingerprint

Part 2.

Use your browser to go to Frontline's "What Jennifer Saw" at

http://www.pbs.org/wgbh/pages/frontline/shows/dna/.

The material on this site is about a man convicted of rape but later exonerated by DNA evidence. To read a summary of the case, choose the link to Ronald Cotton's wrongful conviction, then choose "Summary of Cotton's Case."

In the interviews section, read the interviews with DNA expert Peter Neufeld and lawyer Barry Scheck.

Answer the following questions:

6.                 What evidence was initially used to convict Cotton?

1.     A photo identification was made by one of the victims.

2.     A police lineup identification was made by one of the victims.

3.     A flashlight in Cotton's home resembled the one used by the assailant.

4.     Rubber from Cotton's tennis shoe was consistent with rubber found at one of the crime scenes.

7.                 What did the DNA evidence show?

1.     That Cotton was not the rapest and that another inmate in prison for similar crimes had committed the rapes. He ven addmitted it to another inmate but the superior court refused to alow known to the jury.

8.                 How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?

1.     DNA fingerprinting gives us hardcore edvidence on weather or not someone committed. This way those who are innocent won’t be put way for something they didn’t do.

9.                 What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?

1.     25%

10.               The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?

1.     They talked about how though DNA helps in keeping innocents from being wrongflly convicted they can still be wrong, but it depends on if the person working on it makes a mistake.