Phylogenetics_2024Sp-1

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Phylogenetics Lab Turn in all 7 trees you generated in class, including the one you drew by hand and the 6 done on the computer. Be sure two of them have traits (apomorphies) noted on them (the hand- drawn one and one of the computer generated trees). Also turn in a trait matrix for the mammals and answer the following review questions in depth. Review Questions 1. What differences and similarities did you notice between the trees you generated? In particular, how did the trees generated with DNA differ than the one you made with physical traits? In most of the graphs generated, the American mink, platypus, and often the domestic cat would be in the exact same places while the rest shuffled a lot more. With my drawing, the platypus stayed in the same spot, but the cat was higher. In most of the trees, opossum was more closely related with the platypus, but based on the physical characteristics, it as much higher on the tree. 2. Were any of your physical traits autapomorphic or synapomorphic when plotted on the gene trees? Which ones and for which species? Phylogeneticists often refer to these physical traits as “evolutionarily significant,” what do you suppose they mean by this? Some traits were synapomorphic like 1,4,6. Almost all of the animals had these specific traits which were the presence of teeth, the presence of shredding teeth, and the presence of occipital chest. There are more synapomorphic below but are not as common among all animals. The presence of diastema is only found in rabbits and opossums. Automorphic means that it was specific to one animal and that would be the peg teeth that were found in rabbits. When phylogenetics talks about evolutionary significance, they are talking about how an animal has changed or evolved with new characteristics to help them survive based on the characteristics they share with a common ancestor and how derived are those traits. 3. Were any of your physical traits analogous? Which ones? Why do you suppose some traits can occur multiple times on a tree while others don’t? Based on the chart I made, some of the analogous traits would be the presence of a sagittal crest in deer and coyote, then the presence of 12+ incisors between opossum and coyote, and lastly the presence of shortened rostrum between cat, mink, and monkey. This can be possible due to their evolution depending on their environment. A good example would be the 12+ incisors with the coyote and opossum. While the opossum has more traits than the coyote, both are omnivores and carnivores- so they must eat meat. Because the opossum and coyote have an extended rostrum (snout- like feature), it can be said that they can have more incisors to the front to chew or tear on their food. On the other hand, rabbits are herbivores and don’t require the shredding or tearing of meat and therefore can only use fewer incisors to survive. 4. Given your results from two genes and physical traits, what relationships between species are you certain of? Which ones are you uncertain of? Why? Based on the data collected and the trees, I can confidently confirm that the platypus is the outgroup. Another distinction I made would be that the domestic cat is the least similar to the platypus because of how high up it is on the 1

tree compared to the rest of the mammals and even in the generated trees, you can see that the cat is mostly towards the top. The uncertain one would be the mink because in the trees it shows that is the least similar as well but based on analogy and physical traits I found it has more similar traits with monkeys and other mammals as well. 5. If gene trees have more information in terms of base pairs for generating phylogenies, why do you suppose phylogeneticists even bother using and including physical traits in their analyses? The trees based on genes alone cannot display the similar traits the animals have themselves. As I said in the previous question, I was not sure about my placement of the mink because even though it had similar characteristics, it was least similar in regards to gene trees. I believe that gene trees are not as accurate because a lot of it can be due to mutations or other factors that could result in different results. While physical trait trees are not as accurate as gene trees, both trees can be used to display the likeness between the species and can give an idea of a similar ancestor. Required materials: Responses (1 pt. for each question) 1 hand-drawn tree with traits on it (1 pt.) 1 character matrix (0.5 pts.) 6 computer generated trees, 1 with traits on it (3.5 pts. total) 2

Name: sandi mitra Section: 570 Species Traits (Write in trait below number) 1 Presence/ Absence of teeth 2 Presence/ Absence of >12 Incisors 3 Presence/ Absence of canine 4 Presence/ Absence of shredding Cheek teeth 5 Presence/ Absence of large braincase 6 Presence/ Absence of occipital chest 7 Presence/ Absence of sagittal crest 8 Presence/ Absence of shortened rostrum 9 Presence/ Absence of peg teeth 10 Presence/ Absence of diastema Cat 1 0 1 1 1 1 1 1 0 0 Deer 1 0 0 1 0 1 1 0 0 0 Mink 1 0 1 0 1 1 0 1 0 0 Monkey 1 0 1 1 1 1 0 1 0 0 Opossum 1 1 1 1 1 0 1 0 0 1 Platypus 0 0 0 0 0 0 0 0 0 0 Coyote 1 1 1 1 0 1 1 0 0 0 Rabbit 1 0 0 1 0 1 0 0 1 1 3

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2 GENE 6

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