Review of Phylogeny EC

Review/Discuss Phylogeny
What did I learn?:
Through this activity I learned a lot more about phylogeny and the cladograms. For example, it is important to know the relationship of the lines and how they represent the amount of time that separates each species. This is important to know because it makes reading the cladogram much easier and we get to compare common ancestors and which species are related to each other. Through this activity I learned a lot more about phylogeny vocabulary such as the root, branches, and what each branch separation represents. It was also interesting to see how to tell different sequences apart and this is important because it helps us learn about how related two different species are. I also learned about SNP and Indels which are important to understanding mutations in DNA and how different sequences are made. Overall, I feel a lot better about phylogeny and learning about evolution now that I know the basics of cladograms.

Answers to Worksheet:1. Briefly explain how scientists draw relationships between organisms based on shared anatomical features.A: Scientists base the relationships between organisms on how many features they share together. The more anatomical features that are shared, the more likely the species are to be closely related in evolution. Shared anatomical features (ex: presence of a backbone) are used to study relationships between organisms

2. How are DNA sequences used to deduce evolutionary relationships? A: Molecular sequences such as DNA, RNA, and protein sequences are used to compare and study relationships. Scientists use sequence comparison (like anatomical comparison) to look for similarities and differences between organisms that help them deduce evolutionary relationships.
3. What is one advantage of building phylogenetic trees using DNA comparisons rather than anatomical features?A: Building phylogenetic trees using DNA comparisons is often more objective and less ambiguous than building phylogenetic trees using anatomical comparison.
4.  Watch the video clip on slide 3 and then draw a simple tree illustrating the evolutionary relationships between gorillas, chimpanzees, humans, and orangutans.A:
5. Watch the short video on slide 4. How has biotechnology affected the process of building phylogenetic trees from DNA sequences?A: Biotechnology has increased the amount of sequencing by 50,000-fold in the past ten years. This large database is also very accessible, costing only a dollar.
6. What do evolutionary related organisms share?A: Evolutionary related organisms share a common ancestor with an ancestral DNA sequence.
7. What are two common types of mutations?A: Two common types of mutations are called SNPs and Indels.
8. Watch the short animation on slide 6 and describe a SNPA: A SNP is a change of one DNA base pair to another.
9. Watch the short animation on slide 7 and describe an indel.A: An Indel is a mutation in which one or more nucleotide pairs in a DNA strand is lost or gained.
10. Explain the difference between distantly related and closely related organisms in terms of their DNA sequences.A: More distantly related species have had more time elapsed since they shared a common ancestor, which means that they have had more time for mutations to occur and accumulate in their DNA. Closely related species have not had as much time to accumulate mutations since their last common ancestor, so their DNA sequences are much more similar.
11. What does it mean to compare “apples to apples” when referring to DNA sequences from different organisms?A: Comparing the sequences from different organisms is like comparing “apples to apples” because they are homologous, meaning they are evolutionarily related. Comparing non-homologous sequences, however, is like comparing apples to oranges.
12. Watch the short animation on slide 10 and explain what is meant by “aligning” DNA sequences.A: “Aligning” DNA sequences is maximizing the number of matches among all sequences being aligned by changing the positions of the sequences relative to one another and/or by adding gaps.
13. How is a SNP identified in an alignment?A: A SNP in an alignment is a position where the letters in a column do not match. For example: ACAGAC -- ACATAC
14. How is an indel identified in an alignment?A: An indel is an addition or removal of a pair of DNA bases so it would be a gap in an alignment (can be represented by a dash) For example: ACAGAC-GA -- ACAGAGAGA
15. Look at the information on slide 15. From right to left, identify the base in each box as an indel or a SNP. Write your answers in the spaces below.Box 1 (left): Indel  Box 2 (center): SNPBox 3 (right):Indel
16. Watch the video clip on slide 17. How can you identify the two sequences that are most similar?A: You can identify the two sequences that are most similar by looking at how many nucleotides differ between the two sequences. Then you find the best tree topology that fits the data to indicate which sequences are more alike to one another.
17. Watch the video clip on slide 18 and describe the link between the length of the line and time.A: The link between the length of the line and time is that the longer the line is the more time has passed. With this data we can learn more about different species and see which one is more closely related to the other. For example, the closer they appear to one another on the cladogram, or the shorter the line is, the more related they are to one another.
18. What is surprising about the placement of hippos on the phylogenetic tree?A: It is interesting to see that the hippos are more closely related to the whale than they are to pigs because they are placed next to the whale on the cladogram. Another way to notice this is by comparing the lines and the hippo line is much shorter than the pig, so the hippo is more closely related to the whale.
19. Define a branch point (also called a node) on a phylogenetic tree and describe what it represents.A: It is the place where two branches split. It represents the most recent common ancestor of all the species on those branches.
20. What is the root?A: The root the single branch point from which all other branches originate.
21. What does the node closest to the root represent?A: The node closest to the root represents the most recent common ancestor for all organisms in the tree
22. Describe what an unrooted phylogenetic tree represents.A: Unrooted phylogenetic trees represent only relative relationships among compared organisms and they do not tell you where the common ancestor is among a group of species
23. On slides 22 and 23, notice how phylogenetic trees can rotate around nodes and have different shapes. Notice the relationships between the organisms do not change.A: The relationships between the organisms do not change.
24. Using the information on slide 24, explain how DNA evidence supports the known biology of the seven cone snails.A: Here, the shape of each snail reflects how it was placed on the cladogram. However, the DNA sequencing data supports that classification as well. For example, two cone snails that have similar shell shapes, C. aulicus and C. textile, also are the most related in terms of sharing a similar genetic sequence.
25. Write three conclusions drawn from the information provided in this Click and Learn.A: DNA sequence comparison augments and sometimes clarifies anatomical comparison. Phylogenetic trees can be generated using DNA sequence alignments. With increased amounts of sequence data, we have more confidence than ever in the phylogenetic trees that can be generated.

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