Lab 3 Write Up Introduction to Evolution II PDF

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Mak Monaco Laboratory 3 Write-Up: Introduction to Evolution II Due to the length of this lab, there are no post lab questions. Each question is worth 0.5 points. II. Stickleback Evolution Virtual Lab 1. Define “model organism.” A “model organism” is a non-human species that is studied extensively to understand biological phenomena. 2. Why is the threespine stickleback a model organism for studies in evolution? (List at least two reasons.) The three-spine stickleback fish are small and have shorter generations. This makes them easier to keep in a lab and makes them useful for genetic studies. 3. How do spines protect ocean stickleback fish? The spines protect stickleback fish by simultaneously flaring out from the pelvic ad dorsal spines. This makes it a lot harder for predators to swallow them. 4. Describe where its spines are located. The stickleback fish has three spines on its dorsal side and two spines projecting from the pelvis on the ventral(front) side. 5. The loss of stickleback pelvic spines is similar to the loss of which body parts in some other fourlegged vertebrates? It is similar to the loss of hind limbs. 6. Name two other vertebrate animals whose evolutionary histories included the loss of hind limbs. Snakes and whales evolutionary histories included the loss of hind limbs. 7. In addition to the spines, what is another component of the “armor” of a stickleback fish? Another component of armor for the stickleback fish are the row of plates on each side of the body. 8. Explain how the stickleback armor protects the fish from some predators. The back spines and pelvic spines stick out making it har for predators to swallow. The plates also make the stickleback fish hard to eat.

9. How did ancestral populations of ocean-dwelling fish come to live in freshwater lakes? At the end of the last ice age, glaciers melted and freshwater lakes formed. As more ice melted, massive ice-sheets elevated, cutting off some lakes connections. Researcher believe that stickleback fish were trapped in those lakes and adapted to freshwater living. 10. What is the difference between marine, sea-run, and freshwater stickleback fish populations? Be specific. Marine stickleback live and breed in the ocean. Sea-run stickleback are freshwater born, spend most of their life in the ocean, and may return to the freshwater to breed. Freshwater stickleback live entirely in freshwater. Marine and seawater stickleback have heavier armor than freshwater. 11. From a researcher’s perspective, what is the benefit of having access to hundreds of postglacial lakes? Because there are so many postglacial lakes, researchers can compare traits in different stickleback populations living in these lakes. This also allows researchers to make predictions about environmental conditions that influence these traits. Describe the following structures: 12. Complete pelvis: A pelvis with a full pelvic girdle with two pelvic spines.

13. Reduced pelvis: A range of structures from a simplified girdle with no pelvic spines, to an oval num for a girdle. 14. Absent pelvis: No pelvic girdle and no pelvic spines. 15. Explain in your own words the overall objective of Experiment 1. The overall objective of Experiment 1 was to analyze pelvic structures of stickleback fish that were collected from two different lakes. The collected data was used to suggest possible environmental factors that influenced pelvic morphology. 16. What lake is located between Bear Paw Lake and Frog Lake just to the north? Prator lake is located between Bear Par Lake and Frog Lake. 17. In a population, what happens to organisms that are better adapted to the environment in which they live?

In a population, individuals that are better fit or better adapted are more likely to survive and reproduce. Over many generations, these traits are passed down, therefore these genetic variants and associated traits increase in frequency in the population. 18. Why do you think it is important to empty the used stain, destaining solution, and water under a fume hood? The hood has a vacuum, which helps limit the exposure to toxic or hazardous fumes. 19. How were the fish you will be using in this virtual lab caught? Scientists threw special traps in the water, which were left overnight. The fish swim into these traps and can’t swim out. Scientists pull out the traps and collect the fish. 20. According to Dr. Bell, what is an important difference between Bear Paw Lake and Frog Lake? Bear Paw Lake is completely enclosed and doesn’t drain at the surface. This doesn’t allow for predatory fish to enter the lake. Frog Lake however, is connected to the water system by a small stream, which does allow for predatory fish to enter the lake. 21. Why are random samples, rather than entire populations, used in most research studies? It would take too much time and money in most cases to study all the individuals of one entire population. Scientists study random samples to estimate properties of a population and then infer conclusions about the population as a whole. 22. What is one advantage of studying larger-sized samples? Larger samples usually are more representative of the population as a whole than smaller samples would be. 23. Give an example of sampling bias. Only collecting fish from shallow water because of the ease in placing and collecting traps for the fish. 24. Why do you think it is important that the labels included in specimen jars be made of special paper that does not disintegrate in alcohol over time? Fish are stored in isopropyl alcohol, which will disintegrate most papers. Labels record important information about the specimens. The labels have to be able to withstand this or scientists would lose data. 25. Examine the pelvic score data you just collected. Does the pelvic phenotype differ between Bear Paw Lake and Frog Lake fish? Explain. Yes, Bear Paw Lake appears to contain mostly stickleback fish that don’t have pelvic spines, and Frog Lake stickleback fish have pelvic spines.

26. How does your data compare to those obtained by Dr. Bell and colleagues? My data compares similarly to Dr. Bell and colleadues. 27. Explain why the stickleback fish in Frog Lake are more similar to ocean and sea-run stickleback than they are to the stickleback fish in Bear Paw Lake. Stickleback fish in Frog Lake are more similar to ocean and sea-run stickleback than they are to the stickleback fish in Bear Paw Lake because they have complete pelvises. Whereas stickleback in Bear Paw Lake have reduced or absent pelvises. 28. In addition to predators, what other environmental factors do you think might be responsible for the differences between Bear Paw Lake and Frog Lake stickleback populations? How would you test your prediction? Stickleback fish in Frog Lake have complete pelvises, whereas stickleback fish in Bear Paw Lake have reduced or absent pelvises. Fresh water isn’t as rich in minerals needed to form complete pelvic structures. I could test this by measuring mineral content ocean water, and comparing that to fresh water. 29. What score would you assign to a fossil specimen that has only one pelvic spine visible? I would assign a complete score. 30. A stickleback fossil may show no signs of pelvic structures. What are possible sources of error associated with scoring the pelvis of such a fossil as “absent”? Animals that are preserved as a fossil may have been damaged by physical process or decay factors. Therefore, some body structures may not be visible in a damaged fossil. 31. In your own words describe the overall objective of Experiment 2 and explain what the data you collect will allow you to estimate. The overall objective of Experiment 2 is to characterize the pelvic structures of fossil stickleback fish from the Truckee Formation. The collected data from this experiment will allow me to estimate the rate of change in the frequency of the complete pelvic phenotype over time. 32. Watch the short video on the Truckee Formation in Nevada. What does each sedimentary rock layer of the Truckee Formation represent? Each sedimentary rock layer represent about one year of deposition. 33. What is one type of information that researchers can gain from studying fossils that they cannot obtain from living populations? Studying fossils can show long-term patterns of evolutionary change. This could allow researchers to then calculate the rate of change for certain traits.

34. Approximately how many years apart are any two adjacent samples? Any two adjacent samples are 3,000 years apart. 35. You will collect data on pelvic structures using fossils from rock layers 2 and 5. Approximately how many years of deposition separate these two layers? Approximately 9,000 years separate layers 2 and 5. 36. Which layer is older, 2 or 5? Explain your answer. Layer 2 is older than 5. This is due to the fact that layers are numbered from oldest on the bottom (layer 1), and youngest on the top(layer 6). 37. Based on the pelvic phenotypes you measured, do the fossils in layer 2 differ from those in layer 5? Explain how. Yes, pelvic spines appeared more in stickleback fossils from layer 2 than in layer 5. Layer 5 stickleback fossils mostly were without pelvic spines. 38. How do your data compare to those collected by Dr. Bell and colleagues? My data compares similarly to Dr. Bell and colleagues. 39. What can be inferred about the presence or absence of predatory fish when the Truckee Formation was a lake? Describe the evidence. Due to frequency of pelvic spines in stickleback fish decreased over time, we could infer that pelvic spines provided no advantage to fish that had them. 40. Complete the tables below as you perform the rate calculations. (The link to the instructions is very helpful.) Sample Layer

Number of Fish with a Complete Pelvis

Total Number of Fish Sampled

1 2 3 4 5 6

20 18 3 1 0 0

20 20 20 20 20 20

Relative Frequency of Complete Pelvis Trait in Population Sampled 1.00 0.90 0.15 0.05 0.00 0.00

Time First 3,000 years (Layer 1 to Layer 2) Next 3,000 years (Layer 2 to Layer 3) Next 3,000 years (Layer 3 to Layer 4) Next 3,000 years (Layer 4 to Layer 5) Next 3,000 years (Layer 5 to Layer 6) Total 15,000 years (Layer 1 to Layer 6)

Decrease in Percentage of Complete Pelvis Trait per Thousand Years (Rate of Change) -0.033 = -3.3% -0.25 = -25% -0.033 = -3.3% -0.017 = -1.7% 0.00 = 0% -0.067 = -6.7%

41. What does it mean when the rate of change is a negative number? When the rate of change is a negative number, it indicates a decrease in the quantity being studied. 42. Describe the trend in the data over time. The pelvic spine frequency decreased over time. The first 9,000 years the decrease was rapid, then the decrease leveled off near the end of the 15,000 period. 43. Why is it important to calculate the rate of change over time? It is important to calculate the rate of change over time because it can be used to infer aspects of the evolution. 44. In what way is the change in the complete pelvis phenotype in the fossils from the Nevada lakebed similar to what might have occurred in Bear Paw Lake from Experiment 1? Marine and sea-run populations, the reduced pelvic phenotype had never been seen. In Bear Paw Lake, most stickleback fish have a reduced or absent pelvis. This suggests that the frequency decreased over time, just as fossil data suggested happened in the ancient Nevada Lake. 45. In your own words describe the overall objective of Experiment 3. The overall objective in Experiment 3 was to analyze reduced pelvic traits by scoring the stickleback fish from two lakes. 46. What is one function of the Pitx1 gene? Pitx1 is an important gene involved in developing the pelvic girdle and pelvic spines of stickleback fish. As well as hind limbs for certain four-legged vertebrates.

47. What is the relationship between changes in body form, the process of development, and genes? Because genes control development, changes in physical forms are due to changes in genes. 48. Why did Dr. Kingsley do genetic crosses with stickleback fish? Dr. Kingsley did genetic crosses with stickleback fish to pinpoint what gene/genes were responsible for pelvic reduction in freshwater fish. 49. Which one of the three pelvic girdle phenotypes is analyzed in more detail in this experiment? The reduced pelvis phenotype is analyzed in more detail in this experiment. 50. What is the difference between left-biased and right-biased pelvic asymmetry? When a pelvis is reduced, the leftover pelvic vestiges are rarely ever the same size. If the pelvic vestige is larger on the left, it shows a left bias, and larger on the right side shows a right bias. 51. How do your data compare to those collected by Dr. Bell and colleagues? My data compared similarly to Dr. Bell and colleagues. 52. The pelvic asymmetry observed in stickleback fish from Bear Paw Lake and Coyote Lake is biased toward which side? The pelvic asymmetry is bias toward the left side. 53. Based on previous research conducted in mice, what does this observed bias among Bear Paw Lake and Coyote Lake stickleback suggest about the genetic mechanisms of pelvic reduction in these two populations? An observed left bias in the Coyote Lake and Bear Paw Lake stickleback suggest that pelvic reduction in these two populations are associated with mutations that affect the function of the same Pitx1 gene. 54. For this analysis, what is the null hypothesis? The null hypothesis for this analysis is that in a given population with pelvic reduction, you could infer that there would be an equal distribution of left and right bias. 55. Bear Paw Lake Phenotype Observed (o) Left Bias 18

Expected (e) 10

(o-e) 8

(o-e)2 64

(o-e)2/e 6.4

Right Bias

2

10

8

64

6.4

Total = 20

Total = 20

χ2 = 12.8

56. Coyote Lake Phenotype Observed (o) Left Bias 20

Expected (e) 10

(o-e) 10

(o-e)2 100

(o-e)2/e 10

Right Bias

0

10

10

100

10

Total = 20

Total = 20

χ2 = 20

57. For each chi-square calculation, how many degrees of freedom are there? 1 58. What are the p values for the data from each lake? Coyote Lake: 0.01 Bear Paw Lake: 0.01 59. Do you “reject” or “fail to reject” your null hypothesis for the data from each lake? Coyote Lake: reject Bear Paw Lake: reject 60. What does it mean to reject the null hypothesis for Bear Paw and Coyote Lakes? To reject the null hypothesis means that any differences between the expected 50/50 distribution of left and right bias is unlikely due to chance. Meaning that there is possibly a biological explanation of the pelvic asymmetry in these populations....