PTC Assessment-Student Version

ARISE Curriculum.

PTC Lab Inquiry-based Assessment

S. Gell draft 5 2.2.1

In the PTC lab we examined natural variation in a human gene for tasting PTC. Use what you learned in this laboratory exercise to help you answer questions about guppies and their ability to see colored patterns.

Guppies are small fish that live in warm fresh water. Male guppies are known for their brightly colored patterns. These patterns are thought to be important for mate choice, with females preferring males that have bright and unusual coloring patterns1.

”Sexy” Male Guppy (Image from Ref 1)

Q1: For a male guppy, what would be one a major advantage and one major disadvantaged of having very brightly colored tails in the wild? [Broad area 1.1]

Scientists studying guppy behavior noticed that the females needed to be able to detect Ultra-Violet (UV) light to make decisions about the quality of the markings on males2. Humans cannot see colors in this range, but many animals can. In order to detect UV light, animals must have a UV-light receptor in their eye. This receptor gene is called opsin. Scientists sequenced the opsin gene from two related species of guppies.

The genomic sequence for part of the UV-light receptor (opsin) for the two guppy species is below.

Species 1: P.reticulata

CTG GTT TGC TGG ACA CTT TAC GCC AGT GTA GCC TGG TAC ATC TTC TCA AAT CAG

______

Species 2: G. holbrooki

CTG GTT TGC TGG ATA CCT TAC GCC AGT GTG GCC TGG TAC ATC TTC ACA CAT CAG

______

Q2: [LS1(9-11)-2a,c]

A. Translate each DNA sequence into an amino acid sequence using your codon table. Write the answer on the line provided below the sequence.

B. Circle any coding changes in the amino acid sequence.

C. Put a box around any silent or non-coding changes in the DNA sequence.

Q3: A light receptor, like a taste receptor, is used to sense a particular signal and then transmit that information to the brain. How might changes to amino acid sequence effect a light receptor? [LS1(9-11)FAF+POC-2b]

Q4: You noticed that sequence TTCTCA (P. reticulata) is recognized by the restriction enzyme FshI, but the sequence to TTCACA in G. holbrooki is not.

A. How could you use the restriction enzyme FshI to distinguish between samples of DNA from these two species?

Q5. You have discovered a new population of guppies and want to determine if the opsin gene in this population has the same polymorphisms (nucleotide changes) as the other species.

A. Explain how the FshI enzyme could be used to help you determine this.

A1. If the restriction enzyme cuts the DNA from fish in the new population of guppies, can you be confident that the fish carry the P. reticulata allele? If the enzyme does not cut the DNA what does that tell you about the DNA sequence?

B.(II, CC) Starting with DNA isolation describe the 4 major steps in this experiment and briefly explain why you need to do each.

1. DNA isolation –

C. After you cut the DNA with FshI what would you expect to see if the new population contained fish that were homozygous for the P. reticulata allele? For the G. holbrooki allele? What would you see if there were heterozygous fish?

D. What controls would you include in this experiment to show the genotypes of fish from the new population of guppies? [Broad Area 2.5]

Q6: You tested 6 individuals from the new population of guppies. Based on the data below determine if each individual is homozygous for the P. reticulata allele (P/P) or the G. Holbrooki allele (G/G) or is heterozygous for the two alleles (G/P) [Broad area 3.10, LS1(9-11)-2b, LS3(9-11)-7a]

U = uncut (not digested with FshI), C = cut (digested with FshI)

Genotype of individual samples. (G/G, P/P G/P)

1. ___

2. ___

3. ___

4. ___

5. ___

6. ___

Q7: Following your observation that different populations of guppies have different alleles of the opsin gene,you want to determine which allele represents the ancestral state of the guppy opsin gene. How might you do this? [Broad area 2.4, LS3(9-11)-6a]

Q8: By looking at the data below, determine which allele (P. reticulata or G. holbrooki) is most likely the ancestral state of the guppy opsin and explain how the data supports your hypothesis. [Broad area 1.2 and 4.12, LS3(9-11)-8d]

P.reticulata: TGG ACA CTT TAC GCC AGT GTA GCC TGG TAC ATC TTC TCA AAT CAG

G. holbrooki:TGG ATA CCT TAC GCC AGT GTG GCC TGG TAC ATC TTC ACA CAT CAG

Zebrafish* TGC ATA CTT TAC GCC AGT GTA GCC TGG TAC ATC TTC TCA AAT CAG

Answer here:

Q9: Imagine that P. reticulata live in only clear, fast moving, rocky streams while G. holbrooki live in slow moving water with lots of green algae that can block the light. Make a hypothesis regarding what selective pressures could be driving the evolution of the opsin gene of these fishes. Remember opsin is important for detection of light in the eye. [LS3(9-11)-7c,8a Broad area 1.1]

Q10. Based on your data from the newly discovered population of guppies, what type of environment do you think these fish might have come from? Explain your reasoning. [Broad area 1.1, 4.12]

References

1. Olendorf et al. Frequency-Dependent Survival in Natural Guppy

Populations. Nature. Vo1 144. 1 June 2006.

2. Smith et al. Ultraviolet Vision and Mate Choice in the Guppy. Behavioral Ecology. Vo1 13. 2002.

* Not based on real data.