lab 4

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?

Phylogeneticists cannot only use DNA to determine phylogenetic trees. This is because mutations can occur and can cause vastly different species to become more similar. Even though physical traits aren't as reliable, they still can help determine the evolutionary history between mammals.

0 means

"ancestral version of a trait, shared with the outgroup"

1 means

"derived version of a trait."

Learning Objectives

1. Construct a phylogenetic tree in MEGA using the skull morphological characters you collected in the last lab period. 2. Construct a second phylogenetic tree from the same set of organisms using DNA sequence data for the genes RAG1 and OPNSW that came from Genebank. 3. Describe how changes in included characters can impact the appearance of your tree and its similarity to the current best consensus mammalian tree.

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?

An example of an analogous trait is not having forward facing orbitals. The deer and the rabbit both share the trait of having orbitals on the sides of their heads. This trait has a similar function in each mammal, but it may not be derived from a common ancestor. Some traits are seen multiple times on a tree because the traits might not be genetically related but rather have a similar function. For example, both deer and rabbits need to have their eyes are the sides of their head rather than the front of their heads so that they can see their predators better.

Given your results from two genes and physical traits, what relationships between species are you certain of? Which ones are you uncertain of? Why?

I am certain that the American Mink and the Domestic Cat are very closely related because they have similar physical characteristics and similar DNA. I am also confident that the platypus is the out group because it does not contain a majority of the physical traits shared between the mammals. This was confirmed after looking at the DNA trees. Lastly, I can agree that the opossum is not as closely related to the other species because it also is lacking many of the shared characteristics. But overall, the rest of the relationships are hard to determine. Phylogenetic trees are only hypotheses and are constantly changing. The physical traits are not very reliable since everyone might interpret the characteristics differently. My personal tree I drew is based on 14 traits and is only looking at the physical aspects. My tree does not look like the DNA trees because the DNA trees are more accurate and predict the relationships better. Many of the mammals share specific traits but are far away on the DNA trees which makes it even harder to predict which ones are related.

lab safety

Lab Safety Concerns: 1. Wear closed-toed shoes. 2. Wash your hands with soap and water after you complete the lab and before you leave.

analogy

Similarity Due to convergent evolution not common ancestry Convergent evolution occurs because the compared species and have it similar habitats

Which of the following are true about outgroups?

They help identify plesiomorphic traits in the phylogeny They are a taxa that is known to not be within the species group in question

Maximum Likelihood

This is actually doing both an optimizing tree search (another computationally heavy statistical method) and bootstrapping those searches.

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 based on the physical traits was less accurate than the DNA trees. This is because DNA evidence is based on facts while the physical traits are based on interpretation. For example, just looking at the coyote and European rabbit one might think that they are not closely related since they look nothing alike. However, based on the 2gene maximum likelihood tree, the coyote and the European rabbit have similar DNA resulting in a sister taxa between the two. There were some similarities between the one I drew and the generated ones, such as the cat and mink being closely related. However, the majority of the physical characteristics tree is different from the DNA trees. Many of the animals share similar traits but using DNA can help distinguish which ones are more closely related.

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?

There were autapomorphic physical traits on the gene trees such as there is no sagittal crest for the mink. Everything else in the entire tree has a sagittal crest while a mink does not. Another example is that the domestic cat is the only one with a postorbital plate. These traits are specific to one mammal and must have derived separately from the rest. An example of a synapomorphic trait is the gap between its incisors and its molars which is present in the European rabbit, the Virginia Opossum and the Whitetail Deer. Scientists call synapomorphic and autapomorphic traits "evolutionarily significant" because derived traits arise from natural selection or a change in the environment. All mammals are connected by a common ancestor, but physical traits become different when evolution occurs. For example, the Platypus is the only mammal that has a flat skull. This is an autapomorphic trait because it is only present in the platypus. Evolution effected this trait because a platypus might need a flat skull in order to survive in its environment while the other mammals do not need a flat skull.

"Construct/Test UPGMA Tree.

This will use that distance matrix to make a tree like you did in pre-lab, but with all the DNA sequences. We want to know how good it is, so we're going to run a bootstrap test as well.

homology

Traits inherited by two different organisms from a common ancestor

Safety precaution for this lab include:

Wearing closed-toe shoes Washing hands when finished with the computers and lab exercises.

From the video: What term should we use to decribe the evolution of body types in the Anole lizards?

analogous

From the video: What piece of information was most useful in determining the relationship among the anole species?

dna

plesiomorphic traits

do not help resolve a phylogeny so we don't need to consider traits at the base of the tree.

MEGA i

is a program preferred by many phylogeneticists because of its simple and elegant interface for visualizing and aligning DNA sequences.

Bootstrapping

is a statistical tool used to repeatedly sample information to generate the data. The more times a random sampling of the data supports the conclusion, the more confidence we can have in the result.

The uncertainty between the two trees comes down to lack of information and one way to solve that is to

look for more traits.

The numbers at the nodes represent

the percentage of trees which agree that all the species after that node belong there, thus higher values represent more support.