Fish Phylogenetic Tree Based on Protein Size

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Fish phylogenetic tree based on protein size
Amanda Reed
Lab partners: Lecia Redwine, Kyle Hatcher
TA: Baneshwar Singh
Biology 117, Section 25
Tuesday 10:30 AM

      Although tree diagrams have been used since the days of Charles Darwin, biologists have only recently adopted the tree model of evolution to read and interpret phylogenies. One of the reasons for this is the confusion that often arises from using a tree model to describe a phylogeny (Baum, 2008a). Many people interpret the trees to show that different species evolve from one another instead of viewing them as ways to trace the common ancestors between species. All species at the tips of the branches should be thought of as being evolutionarily equal; however, many people misinterpret the trees to show how different organisms evolved from one another (Baum, 2008b).       Phylogenetic trees are a great way to represent how evolution led to the differentiation of species. However, to determine how to draw the tree, one must first define what a species is. Unfortunately, there is no black-and-white answer to determining the existence of new species. First, though, one must decide if a new organism is different enough from pre-existing species to constitute a new species or not. One must also have a method to detect new species. According to Ernst Mayr, organisms of the same species are able to reproduce fertile offspring. However, George G. Simpson argued that members of the same species have the same evolutionary history. Today, the two ideas have been combined to create the Biological Species Concept. This is still open for individual interpretation, so scientists, for the most part, have chosen to follow the Phylogenetic Species Concept which uses the most accurate phylogenetic trees available depicting organisms with shared traits to determine if an organism is a new species or not. Currently, the easiest way to depict the most accurate phylogenetic tree without using computer software is to attempt to determine the most parsimonious tree. If organisms have many shared traits, then they can be determined to be of the same species as each other (Hey, 2009).       Another key piece of information used in determining phylogenetic trees is the evolutionary rate. Biologists often use the evolutionary rate to calibrate a “molecular clock” to determine an evolutionary timeline for a species for which we may not have much evolutionary information. This helps to determine missing pieces in a phylogenetic tree, thus allowing us to create a phylogenetic tree when we may not have all of the information. We can presume that the tips of the tree are equally evolved, as well (Ho, 2008).       By using a relaxed molecular clock that presumes that the evolutionary rate varies between organisms along with the Phylogenetic Species Concept, one can get an idea of a phylogenetic tree for a set of organisms, based on their traits. The purpose of this lab was to try to determine a phylogenetic tree for six different fish using the proteins each fish contained to determine their placement on the tree.

3 flip top microtubules and 3 screw top microtubules were labeled. 250 microliters of Laemmli sample was added to each flip top microtubule. A small piece of each fish sample was added to its designated flip top microtubule. Each flip top microtubule was then agitated by flicking it approximately 15 times with a fingertip. The samples were then incubated at room temperature to separate and extract the fish proteins. The buffer solutions containing the fish proteins were then transferred into their designated screw top microtubules. These microtubules were then heated for 5 minutes at 95 degrees Celsius to denature the proteins. The samples were then stored at temperatures less than -20 degrees Celsius until the following lab meeting.

The next lab meeting, the frozen fish samples and actin and myosin samples were reheated at 95 degrees Celsius to...
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