BIOL1108L_BiodiversityWorksheet_online

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Feb 20, 2024

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Purpose: The purpose of this exercise is to describe the diversity of life and the phylogenetic relationships among living organisms. This exercise will solidify your understanding of the tree of life and how to interpret phylogenetic relationships and use these relationships to identify shared derived and shared ancestral characteristics. Being able to compare living organisms in an evolutionary framework will benefit you as you move into upper division science courses and even in your daily lives. Beyond being biophilic and having a general appreciation for life, identifying the properties of different lineages, and describing the evolutionary relationships among different organisms has practical applications which can benefit humans, the society, and the biosphere. Having a foundation in interpreting evolutionary relationships will allow you to evaluate these data and figures when you come across them in your daily lives. For example, we can use this phylogenetics approach to understand the relationships among different strains of COVID-19 and track the spread of COVID-19 across the globe. We could also use this information to evaluate hypotheses regarding its origins. This exercise falls under Course Learning Objects #1 Task : Observe the specimens provided, read the descriptions for each of the major lineages of life displayed in the phylogenetic trees. Trace the phylogenetic relationships among the lineages described. Use the hyperlinks to reveal more information. Based on the information provided, answer the questions. Criteria for Success: To succeed in this assignment, you must:  Read the protocol  Interpret the phylogenetic trees  Carefully read the descriptions of each lineage in the protocol  Explore the hyperlinks The worksheet is worth 25 points (0.5-2 points per question)

QUESTIONS Use the specimens in class, the phylogenetic trees, and if necessary digital sources to answer the following questions. Clicking on the lineages on the phylogenetic trees will take you to the Wikipedia entry for that group. If typing, please use a different font color. You do not need to use complete sentences. 1. a. Which node in the 3-domain supertree (the first tree) represents the common ancestor of eukaryotes and Archaea? (0.5 pts) b. Which node in the 3-domain tree represents the common ancestor of all Eukaryotes? (0.5 pts) c. What are some characteristics that would have been present in the common ancestor of all eukaryotes? Hint: think about characteristics that are shared between your cells and the cells of all these other groups (0.5 pts). 2. Survey the links provided and read the protocol descriptions. Look carefully at the traits you see and think about the evolutionary relationships among the organisms present. Based on this, provide at least 3 nodes that represent instances where multicellularity convergently evolved. (1.5 pts). 3. Look at the images in the file labelled “Unknown Gram- Stained Bacteria” in D2L . Determine which organisms are gram-positive and which organisms are gram-negative. List the organisms by letter and state “gram-positive”, “gram- negative”, or “alive and not stained” and include a brief explanation for how you know which is which (1 pt)

4. Explore the links for the organisms in the Archaeplastida tree beginning with Rhodophyta. As part of this be sure you learn about sporophytes vs. gametophytes. Using this information, identify the node in the Archaeplastida phylogeny where the diploid sporophyte generation became the dominant stage in the life cycle (0.5 pt). 5. Look at the Archaeplastida tree links starting with Rhodophyta. Identify the node in the Archaeplastida phylogeny where “land plants” evolved. (0.5 pt) 6. Look at the Archaeplastida tree links. Which node represents the most recent common ancestor of Seed Plants ? (0.5 pt) 7. a. Find the gymnosperms in the Archaeplastida tree. Which node represents the most recent common ancestor of Gymnosperms ? (0.5 pts) b. Conifers are, by far, the most species-rich lineage of modern Gymnosperms; look at the leaf specimens provided for the conifers, other gymnosperms, and their closest relatives, do you think the most recent common ancestor of seed plants would have had needles like a pine tree or broad leaves more like most angiosperms? (0.5 pts)

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8. a. Find the flowering plants in the Archaeplastida tree. Which node is the most recent common ancestor of Angiosperms (flowering plants)? (0.5 pts) b. These are now the most species-rich lineage of embryophytes by far with approximately 350,000 species. Most of these species (including all monocots) are herbaceous , meaning they don’t form a woody trunk with internal vascular rings or bark. Look at the Amborella trichopoda photo. Amborella is a shrub from New Caledonia that represents the basal branch of Angiosperms (i.e. all other flowering plants are more closely related to each other than they are to Amborella ). (Hint: Amborella have woody “trunks”) Do you think the ancestor of angiosperms was woody or herbaceous? (0.5 pts) c. Expand your research to include all other seed plant links (Both Gymnosperms + Angiosperms) What about the ancestor of all seed plants? Do you think this ancestor was woody or herbaceous? (0.5 pts) 9. Look at the animal tree links beginning with sponges. Sponges have specialized individual cells but lack true tissue (masses of coordinated cells, like muscle, nerve, etc.). At what node in the animal phylogeny did true tissues evolve? (0.5 pt)

10. a. Beginning with sponges, look at the animal tree links until you find bilateral symmetry. At what node in the animal phylogeny did bilateral symmetry evolve? (Hint: sponges are primarily asymmetrical) (0.5 pts) b. Bilaterally symmetric animals have a left and right side, as well as a dorsal and ventral side. Based on the organisms in the animal tree, what do you think this bilateral common ancestor may have looked like? Hint : identify the most common body shapes of bilaterally symmetrical organisms. Consider: does the organism have a distinct left and right, top and bottom, front and back or not? Is this organism long or short, wide, or skinny? Does it lack appendages or does it have appendages? Is there a particular organism you know that you think it would resemble? etc.) (0.5 pts) 11. You have paired appendages two forelimbs (in your case - arms) and two hindlimbs (in your case – legs). Look at the animal tree links beginning with the origin of vertebrates (e.g. lamprey and hagfish) and then answer the following… a. At which node in the phylogeny did the vertebrate paired appendages evolve that eventually led to tetrapod limbs (i.e. at what node do organisms exhibit both pelvic and pectoral appendages)? (Note: this is not asking when Tetrapod limbs evolved) (0.5 pts) b. Explore the links for lineages that descend from that limbed ancestor. Are there instances of paired appendages being lost in vertebrates? If yes, give an example. (0.5 pts) c. Examine the animal links that do not descend from the node where vertebrate paired appendages first evolved (i.e., not from your answer to 11a.). Are there instances of convergent evolution of paired appendages? If yes, give an example (0.5 pts)

12. a. Explore the vertebrate links in the animal tree and identify the node in the phylogeny where your ancestor first colonized land (hint: this is also the common ancestor of organisms with digits like fingers and toes). (0.5 pts) b. Give an example of a descendant from that ancestor that has gone back to living a fully aquatic lifestyle. (0.5 pts) c. Explore the links for animals that do not descend from the node where your ancestor first colonized land (i.e. not from your answer to 12a). List at least 2 other examples of an animal lineage that appear to have colonized land independently of your ancestor (0.5 pts). 13. Explore the links for all animals commonly referred to as “fish” (i.e., jawless fishes, cartilaginous fishes, ray-finned fishes, lungfish). If you group all these “fishes” together into a taxonomic grouping is this group a monophyletic group ? i.e. Do they trace back to a single common ancestor, and are all descendants of that most recent ancestor considered fish? Be sure to answer this completely and explain your response. (1 pt). 14. Chambered nautilus is the basal lineage of Cephalopods. Explore the Cephalopod link and all other mollusk links. Based on this information, do you think Octopuses/Octopi evolved from a shelled ancestor? Explain why you think Octopi did or did not come from a common ancestor (based on their evolutionary relationships) (1 pt) 15. Look at the phylogenetic trees, tracing from the lineage you belong to and working your way backward to older ancestors. List all your ancestors (list of node numbers) from both the animal tree and the 3-domain tree all the way back to when everything shared a single most recent common ancestor. (2 pts).

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16. Go outside and take photographs of 4 different organisms, each representing a different terminal group on the tree. Identify where they belong on the tree and submit photographs. A maximum of 2 animals or 2 plants are allowed, and at least one of your selections must be something other than an animal or plant. One of these can be the photo you may use in Question 19 (2pts) Continues Next Page

17. You are the mad scientist Dr. Frankenstein, and you are determined to splice together the genes of 2 organisms to make a distinct new genetically engineered organism. a. Draw a “monster mash” organism (an imaginary creature) that displays the traits of both an Echinoderm and Cnidarian in the circle below. b. Describe the traits your organism possesses and whether they are traits that are inherited from the Echinoderm or Cnidarian ancestry. c. Describe which inherited traits from its ancestors would be adaptations that increase this organism’s fitness through obtaining and digesting food, escaping predators, and successfully producing offspring. Your drawing does not need to be perfect, but you do need to justify why it possesses certain traits based on its ancestry. Hint: you may want to ensure you know the shared derived and shared ancestral traits of these lineages. (2 points) Continues Next Page

18. Explore the following links: roundworms, segmented worms, and flatworms. Draw an example of two of these 3 lineages. Be sure to identify the species. Describe 2 ways these organisms exhibit unity (i.e. shared traits through ancestry or convergent evolution) and 2 ways these organisms exhibit diversity (i.e. shared derived traits solely found in their respective lineages). This should be share derived and shared ancestral characteristics of the two worm lineages (1.5 points) Continues Next Page

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19. Dichotomous keys are an excellent tool that naturalists and scientist use to identify organisms through a series of 2 choice questions. Go outside (or search around your house) and find an insect (you may want to ensure you know what an insect is). Take a picture of this insect and embed your photo in this document. Using the Insect Order dichotomous key that you can find in D2L, identify this insect to the Order level. Write the order here as well as the answer to each step in the dichotomous key that led you to the correct Order. (2 pts)

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