LAB 4: PHYLOGENIES & MAPPING TRAITS
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1 LAB 4: PHYLOGENIES & MAPPING TRAITS *This is a good day to check your Physcomitrella (protonema, buds, gametophores?) and Ceratopteris cultures (embryos, young sporophytes?)* Phylogeny Introduction The goal of this exercise is to understand the concepts behind phylogenetic analysis and to acquire hands-on experience building a phylogenetic tree. To that end, you will first use your newly acquired knowledge of major land plant innovations to intuitively build a phylogenetic tree based on morphology. Second, you will build a molecular phylogeny using a section of nuclear DNA that was sequenced in the Di Stilio lab (Soza et al. 2013). Exercise 1 1. In the matrix below, place an X for the presence of the listed morphological trait in each of the plant groups (you may use lecture notes/readings and other online resources). Plant lineage Charophytes (Chara, Nitella) Trait Oogamy Cuticle Alternation of generations Vascular tissue Seeds Pollen Flowers Fruits Mosses (Physcomitrella) Ferns (Ceratopteris) Gymnosperms (Ginkgo) Angiosperms (Thalictrum) 2. Use the information in the matrix to draw a phylogenetic tree below, using shared characters, or synapomorphies, to define clades. Map the synapomorphies on the tree. Use brackets to mark the following monophyletic groups: land plants, vascular plants, seed plants. 50
2 Exercise 2 The genus Thalictrum (meadow rue), in the Ranunculaceae, consists of approximately 200 species of herbaceous perennials living in temperate regions worldwide. You will analyze a subset of 15 representative species of Thalictrum from Soza et al. (2012; 2013) and one outgroup belonging to the closely related genus Aquilegia (columbine). You will be using a fast and simple distance-based method for generating phylogenetic trees, known as UPGMA. Additional methods often used by scientists are probability-based, such as Maximum Likelihood and Bayesian, but they are computationally intensive and may take several days to run. To conduct your molecular phylogenetic analysis, follow these steps: 1. Log in to the BSA computer as BSA User. 2. Open an internet browser, go to Biol 441 website and navigate to Files, Biol 441 Files, Labs, Lab 04 additional materials and download Lab_04_Thalictrum_Mesquite.nex file (right click, save link as). 3. Go to Applications, Mesquite_Folder, and open the program Mesquite (Maddison and Maddison 2011). A Note window will pop up, hit OK to continue. 4. In Mesquite, open your downloaded file, which contains the DNA matrix (alignment) to be used in phylogenetic analyses and a template Character Matrix for Mapping for you to fill out later for the mapping exercise below. 5. Study the DNA alignment. Rows represent species and columns represent characters, which are the individual positions in a DNA sequence. Each position/character in a DNA alignment has 4 states, i.e. 4 possible nucleotides (A, C, G, or T). Search for similarities and differences in the sequence of nucleotides among species by examining one column at a time to look for similarities/differences among species. The analysis will group species that have similar sequences, depicting the species relationships in a phylogenetic tree. Try predicting these relationships based on your visual analysis of the nucleotide alignment. 6. Run a cluster analysis to estimate the phylogeny: from Analysis menu, select Tree Inference, Cluster analysis, Distances from character matrix, F84 distance, Estimate ambiguity differences, UPGMA, use default of 100 for MAXTREES, and no separate thread, don t save. 7. You will get a new window with a tree. Study your tree and answer the following questions: a. Pick a monophyletic group from your tree, and list all the species belonging to it below. b. Which is the sister species/clade to T. thalictroides And to T. cooleyi? 51
3 Mapping Introduction Certain floral traits have been considered indicative of different pollination syndromes in angiosperms. For example, red flowers are often associated with hummingbird pollination. Using the program Mesquite (Maddison and Maddison 2011), you will map pollination syndrome, sexual system, and 5 different floral traits that are typical of specific pollination syndromes on to the tree you generated from Exercise 2. This will allow you to study the evolutionary history of these characters in Thalictrum and determine which floral traits contribute to wind or insect pollination in this group. Exercise 3 Overview: A. Assemble a spreadsheet in Mesquite using the Thalictrum database ( for character states: a. Sexual system: hermaphroditic, andromonoecious, or dioecious. b. Pollination mode: insect or wind. c. Sepal color green: yes or no. d. Stamens: erect or pendent (dangling down). e. Filaments: thin or wide. f. Anthers: short or long. g. Stigmas: short or long. B. Use Mesquite to conduct a parsimony reconstruction of ancestral character states. 1. Go to the tab for the character matrix (Character Matrix for Mapping), to view and edit the morphological matrix. 2. To see the available states for each character, go to the StateNames (Character Matrix for Mapping) tab. Use these states to fill in your observations for each character for each species in your matrix. 3. Fill in the states for each character in the character matrix by typing in the descriptive term or the state number associated with that state (hitting the Tab key will convert numbers to descriptions). Look up character states in the Thalictrum database ( by observing images of species posted here. For Aquilegia formosa, use the images available for download associated with this lab from the BIOL 441 website. If you are uncertain how to assign a state for a particular character for a species, you can leave it as uncertain (?). 4. Hints: Filaments thin means less than the width of the anthers; wide means equal to or wider than the width of the anther, often widest at top. Anthers short means 1/4-1/3 the length of the filaments or shorter; long means about 1/2 the length of the filaments or longer. Stigmas short means 1/4-1/3 the length of the ovary or shorter; long means about equal the length of the ovary or longer. T. kiusianum carpels are not very vsisible in the photo, they look like the left-hand carpel depicted in the jpg (under additional materials). Download the flower model associated with this lab from the course website to review flower terms. 5. After you have finished filling in your character matrix, go to the tree window to reconstruct ancestral states of morphological characters over the phylogeny. 6. To trace character histories in tree window, under Analysis:Tree menu, select Trace character history, Parsimony Ancestral States, select Character Matrix for Mapping. You can move the trace character legend around on the screen by clicking and dragging. Scroll through the 52
4 different characters and their reconstructions by hitting the left and right arrows in the trace character legend. Reconstructions of ancestral states are indicated by the colored internal branches below the tips of the tree. Hover over an internal branch (ancestral lineage) with your mouse and the state reconstructed is depicted in the trace character legend. 7. To search for visual correlations among characters, we will use mirror trees. Under Tree, go to Mirror tree window. Under Mirror, Left Side, Trace Character History, Parsimony Ancestral States, Character Matrix for Mapping. Do the same for the right side. 8. Use your mirror trees to answer the questions below. a. What is the ancestral condition in Thalictrum for each of the 7 characters studied? b. For pollination syndrome and sexual system, how many times did each state evolve from the ancestral condition in Thalictrum? c. Based on your results, what floral traits are undeniably associated with wind pollination versus insect pollination in Thalictrum, and why might this be? d. Discuss advantages and disadvantages of using morphological vs. molecular traits to build phylogenies. Have your TA initial your trees and answers for credit. 53
5 References Maddison WP, Maddison DR Mesquite: a modular system for evolutionary analysis. Available from: Soza VL, Brunet J, Liston A, Salles Smith P, Di Stilio VS Phylogenetic insights into the correlates of dioecy in meadow-rues (Thalictrum, Ranunculaceae). Mol. Phylogenet. Evol. 63: Soza VL, Haworth KL, Di Stilio VS Timing and consequences of recurrent polyploidy in meadow-rues (Thalictrum, Ranunculaceae). Mol. Biol. Evol. 30:
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