PHYLOGENETIC2 (1)

*Pick one of the trees you generated and plot the physical traits on it in the most parsimonious way. Lab Activity 3: Generating a tree with physical traits 1. If not already done, convert your trait table from the previous lab to the format from today’s prelab with 1s and 0s. Remember, the platypus is the outgroup so all traits in its column MUST BE 0 . Adjust other species appropriately. Trait: 1 2 3 4 5 6 8 9 10 Species Has teeth Has >12 incisor s Has canines longer than incisors Has Cutting/shreddi ng cheek teeth Has large braincas e Has occipit al crest Has Sagittal Crest Has Short Rostru m Has sutures Platypu s 0- absent 0- absent 0- absent 0-absent 0- absent 0- absent 0- absent 0- absent 0- absent Deer 1 0 0 0 1 1 0 0 0 Mink 1 0 1 1 0 1 1 1 0 Monkey 1 0 1 0 1 1 0 1 0 Opossu m 1 0 1 1 0 0 1 0 0 Cat 1 0 1 1 0 1 1 1 0 Rabbit 1 0 0 0 0 0 0 1 0 Coyote 1 0 1 1 1 1 1 0 0 1. Generate a distance matrix for the seven species of your ingroup. 1. Generate a tree for mammals using the distance matrix as done in pre-lab. 1. Plot the traits on the tree in the most parsimonious way possible.

Homework: Phylogenetics Lab 1 and 2 Write-Up 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? The trees generated with DNA are more accurate than the ones I made with physical traits. DNA is factual, while the one I made with physical traits is just what I see. 1. 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? Yes, there were autapomorphic traits, one in particular was the mink because it was the only one that didn’t have a saggital crest like the others. I think autapomorphic traits are evolutionary significant because they mark a point where evolution has changed in a species. 1. 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? Yes there were analogous traits, the cat and rabbit both have teeth but that doesn’t mean that they are related. I think this happens because they just need to be there for functional purposes but it doesn’t mean that they are related. 1. Given your results from two genes and physical traits, what relationships between species are you certain of? Which ones are you uncertain of? Why? Given the results, I am certain that the mink, coyote, and cat are related because based on all the results from two genes and physical traits we can see they are related. I am uncertain of the rest because it isn’t very clear from the results. 1. 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?