Lab 3 (1)

Anthropology 270 Lab 3: Cladistics and Evolutionary Relationships Name: Section Time: Part 1: Introduction (read this before coming to labs) Humans are very good at recognizing patterns, which makes our species particularly fond of categorization and organization. To make sense of the natural world humans have long attempted to organize, catalog and classify Earth's “endless forms.” One of these famous organizers was the Swedish botanist and zoologist, Carolus Linnaeus. Known today as the Father of Modern Taxonomy, Linnaeus formalized the Latin-based naming system ( binomial nomenclature ) for categorizing plants, animals, and “minerals.” Although many of Linneaus’ original classifications have been reordered thanks to advancements in technology (e.g., we now know that manatees and whales are mammals, not fish), he was the first to correctly classify humans within the taxonomic order Primates, and was the first to classify bats as mammals (not birds). Another approach to biological classification, cladistics , focuses on grouping organisms based on shared derived traits (i.e., novel evolutionary traits that are unique to a particular species and all its descendants) in order to infer their "true" evolutionary relationships. These groupings are often visualized as a cladogram, or tree . Trees generally follow the Law of Parsimony , a scientific principle that states that the simplest explanation is the most likely, and therefore best, explanation. For example, if all members of a group were blue, the simplest explanation would be that they are blue because their common ancestor was also blue. In this case, the blue trait evolved once in the common ancestor and was passed on to all of its' descendants. To say that the blue trait evolved separately in each lineage is more complex and, therefore, less parsimonious. When organisms share a trait that was inherited from a common ancestor (e.g., the blue trait from the example above), the trait is called a homology . For example, although the arms of bats, humans, whales, and cats look very different on the outside (reflecting differences in locomotion), the bones on the inside are homologous. This is because they inherited these bones (i.e., humerus, radius, ulna, carpals, metacarpals and phalanges) from a common mammalian ancestor who possessed them. Trees made from homologous traits are called phylogenies . Phylogenies reflect evolutionary relationships because they are based on inheritance and common descent.

It is important to note that not all trees show the “true” evolutionary history of organisms. Just because two species look alike or possess the same trait does not mean that they inherited that trait from a common ancestor. For example, both bats and birds can fly and have wings , but they did not inherit wings from their common ancestor. The bat-bird common ancestor did not fly or possess wings. Similarly, whales and seals are both aquatic mammals that possess flippers, but they didn’t inherit flippers from their common ancestor (their common ancestor was a terrestrial mammal). When organisms share a trait, but did not inherit it from a common ancestor (e.g., bat and bird wings), the trait is called an analogy . Analogous traits can arise through reversals (i.e., when a previously gained trait is lost) or convergent evolution , which occurs when species occupy the same ecological niche or live in similar environments (e.g., both whales and seals live in the ocean). Because analogies do not reflect evolutionary relationships, these traits should not be used to build trees! In-Class Lab Activity During lab today you will watch Tree Diagrams and discuss how to build and interpret phylogenetic trees. Once we are familiar with making trees, we will put those skills to the test! For this lab activity we will be making two different types of trees; a cladogram based on phenotypic data (Part 1), and a phylogeny based on genetic data (Part 2). Part 2: Building a Tree from Phenotypic Data First, take a look at the 7 animals in the Lab section of our Week 3 module. The table below shows the presence/absence of 9 traits across the 7 mammals. Using only these traits, make the most parsimonious tree. You’ll need a piece of scratch paper and pencil. Hold onto your tree for the next step, but you will not turn in the tree. Your tree must abide by the following rules: 1. Your tree must be dichotomous (i.e., each branch of the tree must be split in two, usually with the organisms on one branch having the trait and the organisms on the other branch not having the trait), 2. You must put labeled tick-marks on the branches of your tree showing which traits you used to make your groupings (remember that all organisms past the tick-mark have this trait), and 3. Each branch of your tree must ultimately end in one species (i.e., each of the 7 mammals will end up on its own branch at the tip of the tree). Table 1. Presence or absence of 9 traits (rows) across the 7 mammals (columns)

Echidna C A A T T C T G G C C G T C C Pangolin T C A T A G T C G T A T T A G Sloth C T A T G G T C G T A G T C T Armadillo C T A T G G T C G T A G T C T Porcupine T G A T C G T C G T A C T C A Lion T C A T A G T C G T A T T A G Human T G A T C G T C G T A C T C A You will notice that the colorful nucleotide sequences from the table above have been converted to FASTA format in the box below. FASTA format is a popular format for displaying sequence data and is required by many phylogenetic programs like the one we will use today. Table 3. Multiple Species Alignment for 7 Mammals. 1. Go to Simple Phylogeny . 2. Copy the entire multiple sequence alignment from the box above and paste it into the text box under “ STEP 1 - Enter your multiple sequence alignment. ” 3. Under " STEP 2 - Set your Phylogeny options, " change the clustering method to "UPGMA." 4. Click the “Submit” button under “ STEP 3 - Submit your job. ” A phylogeny showing the evolutionary relationships of these 7 species will show up on your screen in under 1 minute! 5. Again, keep your tree because you will need it to answer the questions below. However, you will not be turning in your trees.

Part 3. Questions After you have completed the activity above, answer the following questions. You will need the trees you generated during the activity above to answer these questions. Use proper spelling, grammar and complete sentences. Each question will require about 1 paragraph. You can work as a group, but each person will turn in their own lab worksheet. You do not need to turn in your trees, but you will need to have completed them before answering the questions below. 1. How do the two trees compare to each other? What might be the benefit of looking at both phenotypic features and genotypes for establishing evolutionary relationships? Comparing phenotypic traits and genotypes can help figure out how different creatures evolved together. The genetic make-up of an organism is called its genes, while its phenotypic features are its physical traits. Scientists can figure out how closely related two organisms are and how they developed over time by looking at how their phenotypic traits and genotypes are similar and different. 2. Based on the character matrix (Table 1), all 7 mammals produce milk. Would it be more parsimonious to say that milk production is a homology or an analogy? Why? The character grid (Table 1) shows that all 7 mammals make milk. Making milk is a homology because all seven animals share this trait, which they got from a common ancestor. When two or more creatures have structures or functions that are similar because they evolved from the same ancestor, this is called homology. On the other hand, analogy is when different animals have structures or functions that are similar. This happens because of convergent evolution, which means that similar traits develop on their own in different lineages. It is more accurate to call it a homology instead of an analogy since all seven animals produce milk. 3. Both pangolins and armadillos have scales made of keratin (a protein that makes hairs, nails, horns and feathers). However, the gene tree (phylogeny inferred from genetic data) revealed some interesting evolutionary relationships. Given the results of your gene tree, are keratin scales a homology or an analogy? What would explain the appearance of this trait in these two lineages? The scales on both pangolins and armadillos are made of keratin. However, the gene tree (phylogeny based on genetic data) showed that keratin scales are more like one another than the same thing. In other words, the scales did not come from a shared ancestor but rather evolved separately in these two lineages.