Week9_assignment (1)

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Indiana University, Bloomington *

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L111

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Anthropology

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Dec 6, 2023

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Name: __Eleanor Dickie________ Section Leader: Rose_______ Section Time:_8am____ L111 Prof. Ragsdale Discussion assignment 7, due Week 9 Phylogenetics This assignment provides practice toward Learning Outcomes #1 and #4 of the course. Instructions: * Print this worksheet and complete questions #1 and #2 before Discussion . Write your answers with a black pen. * Submit your completed worksheet electronically ( e.g. , completed in Microsoft Word or scanned) to your Discussion section on Canvas before arriving to Discussion. This will be checked for completion. Bring the original, completed hard copy with you to Discussion. * Also bring a blue pen to Discussion section. You will be able to make corrections to wrong answers using blue ink; to get credit for these questions, you must have fully answered them before coming to Discussion. Also, for any corrected answers, you will need to explain why the correct answer really is correct. * Complete question #3 during Discussion. * Show all your work, even for multiple-choice questions. * The completed and (as necessary) corrected worksheet is due to your TA at the end of Discussion section. * To help you study for exams, you may take photos of your work during Discussion, take notes on a separate sheet of paper or on a personal device, or both. * This worksheet counts for 77% of your Discussion grade for the week. Purpose: This assignment designed to reinforce and expand your skills in using phylogenetic logic. Being able to interpret a phylogenetic tree—both the tree’s structure and the characters mapped onto the tree—is essential for studies of macroevolution, or evolution above the species level. (1) Interpreting a phylogenetic tree . Those words and those strings of words mean a lot more still if you can relate them to a phylogeny in practice. Phylogenies are packed with evolutionary information – if you know how to read them. So, let’s look at a phylogeny of fishes (to the left). Note that humans, like other four-legged vertebrates, are “tetrapods”. Humans are particularly fond of eating teleost fishes (salmon, cod, tilapia, etc.). Answer some questions about this phylogeny. (A) Is group 2, the “lobe-finned fish” a monophyletic group? Why or why not? Yes, because the species listed are all common descendants of G which is also in the group. (B) Is group 1, the “ray-finned fishes”, a monophyletic group? Why or why not? Yes, because the most recent common ancestor, E, is within the group, along with all of it’s descendants

(C) What is/are the sister taxon/taxa of a monophyletic group formed by bowfins and teleost fishes? Gars (D) What is/are the sister taxon/taxa of the monophyletic group formed by bowfins, teleosts, and gars? Sturgeon & Paddlefish (E) Which (now almost certainly) extinct taxa forms the most recent common ancestor of the lobe-finned fishes? G (F) Group 1 (lobe-finned fishes) and Group 2 (ray-finned fishes) together form a monophyletic group ( i.e ., clade) called the “bony fishes” (Osteichthyes). They make skeletons out of bone instead of cartilage. Sharks and rays make their skeletons out of cartilage. Based on this description alone: (i) What is the synapomorphy that describes the bony fishes? Skeletons of bone instead of cartilage (ii) Which trait described is ancestral ? Which is derived ? Ancestral trait is skeletons of bone instead of cartilage, and the derived trait is skeletons of cartilage (iii) What is the outgroup for the bony fishes? Sharks & Rays (G) Are tetrapods (four-limbed vertebrates) in the fish clade (monophyletic group)? Explain. Yes, because tetrapods evolved from fish in the fish clade (H) Imagine going home for Thanksgiving and telling your family, “Believe it or not, we are fishes.” Someone at the table gets upset and says that “tetrapods are not fishes!” (assume they know the word “tetrapods” for the sake of the problem, OK?). If they exclude tetrapods from the fish phylogeny, which phylogenetic error are they committing ( i.e. , are they making a paraphyletic or polyphyletic group out of fishes?) Explain. They would be making a paraphyletic group out of fishes because they are failing to include all of the recent descendants of fish, i.e. tetrapods. (I) Which split is more ancient: E or F ? Why? Explain. E is more ancient, because F only evolved once into tetrapods and lungfish, where as E has many steps of evolution ( C, B, A, )

(J) Which is the most common recent ancestor between us (tetrapods) and those teleosts? How recent was that most recent common ancestor? The most recent common ancestor between tetrapods and teleosts is H, which is not very recent, as H evolved 5 times into teleosts. (2) Application of phylogenetic principles through sample exam questions . (A) Which description does NOT describe a synapomorphy ? (a) It is the version (state) of a trait (character) that defines a monophyletic group. (b) It is a trait that organisms share due to homology (i.e., it reflects shared ancestry) (c) We could call it “derived.” Plesiomophies are “ancestral.” (d) It is an evolutionary innovation that unites a group of taxa through common descent. (e) All of the above choices describe a synapomorphy well. (B) When we create phylogenetic trees built around monophyletic groups, we use the principle of parsimony. What statement best describes the rationale behind this principle? (a) Parsimony identifies the outgroup, a vital step in determining which traits are ancestral and which are derived. (b) It is difficult for evolutionary innovations to arise, so they should be rare. (c) Evolutionary innovations typically arise due to convergent evolution; parsimony then groups those homoplasies together in a logical way. (d) Both (a) and (b) are true. (e) Both (b) and (c) are true. (C) “We are fishes.” Which choice best supports the reasoning behind this statement? (a) This statement is true if we include all tetrapods in a fish clade. (b) We share a common ancestor with bony fishes. (c) This statement is not true since walking on four legs is a synapomorphy of tetrapods. (d) Both (a) and (b) are true. (D) When you go home for Thanksgiving break, your grandfather is outraged that you are learning evolutionary biology. He says, “humans did not descend from monkeys, period.” If you were to convey how evolutionary biologists view the issue, what would you say to him? “Gpa, from an evolutionary biologist’s point of view…” (a) “Correct, we did not evolve from modern monkeys, but we share a common ancestor with them”. (b) “Incorrect, we did evolve from modern monkeys because we share a common ancestor with them”. (c) “We share a much more common ancestor with chimps and gorillas than monkeys, actually”. (d) Both (a) and (c) are true. (e) Both (b) and (c) are true.

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(E) Consider the phylogeny of SIV – immunodeficiency viruses that infect simians – and HIV, those that infect humans (see phylogeny below). Phylogenetic evidence here supports the following statement: (a) The ability of HIV to infect humans is a homology : it is a trait that is arises from shared, common ancestry . (b) The ability of HIV to infect humans is a homoplasy : it is a trait that is arises from shared, common ancestry. (c) The ability of HIV to infect humans is a homology : it arises independently, from convergent evolution . (d) The ability of HIV to infect humans is a homoplasy : it arises independently, from convergent evolution . (F). Behold the phylogeny to the below. Imagine that you wanted to make a group using the existing, present- day taxa H, J, and K. Would this group be: (a) Monophyletic (b) Paraphyletic (c) Polyphyletic (d) We cannot differentiate between paraphyletic and polyphyletic groups here.

(3) Inferring a phylogeny. Imagine you study plant-parasitic nematodes (I mean, why wouldn’t you?), and are trying to find plant resistance to economically damaging, sedentary parasites. Whether you can find common resistance mechanisms often depends on whether the pathogenesis trait, in this case sedentary parasitism, is only superficially similar (analogous) or similar due to shared ancestry (homologous). Now that you have sampled a certain gene sequence for several plant-parasitic species, answer the following questions: (A) Use the principle of parsimony to infer the phylogeny of the plant-parasitic nematode species below. How many steps ( i.e. , changes of character state) does this tree require? Use Mesocriconema xenoplax as the outgroup. 5 (B) Given the taxa you have sampled, do sedentary parasites form a monophyletic group, i.e. , to the exclusion of migratory parasites? No, because the most recent common ancestor of the sedentary parasites had other descendants that were migratory parasites (C) Based on the above results, infer whether sedentary parasitism evolved once or twice, assuming that this complex trait is irreversible. Sedentary parasitism evolved twice Note that this problem is simply an expanded version of the four-taxon, five-character phylogeny problem we worked through during lecture. It is more advanced than you should expect to see on the exam, meant to give you the “medicine ball” approach to tackling phylogenetics. And a hint: for a small dataset like this, you might try working out the solution for multiple trees to help find the most parsimonious solution. Type of parasitism Species DNA sequence Sedentary Meloidogyne incognita A-G CAG GTA CTA Sedentary Heterodera glycines ACG CGG GCA CGG Migratory Hoplolaimus indicus ACG CGG G-A CGG Migratory Pratylenchus penetrans ACG CAG GTA CTA Migratory Scutellonema bradys ACG CGG GCA CGA Migratory Mesocriconema xenoplax ACC CAG GCA CTA

Mesocriconema xenoplax Scutellonema Hoplolaimus Heterodera Meloidogyne Pratylenchus bradys indicus glycines incognita penetrans

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Week9_assignment (1)

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