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In the study of zoology, one of the most important factors in regard to the interaction of species is phylogeny. Phylogeny is the evolutionary development and history of a species or higher taxonomic grouping of organisms.1 In other words, it is the evolutionary history of a species or group of species. It is one of the first things that is considered when inspecting animals to gain a better understanding of their life and physical characteristics. This scientific method relies heavily on DNA to reveal an organism's history. The questions discussed in this study are how can we tell how closely related various organisms are, what is the importance of phylogeny in science, and how does evolution influence phylogeny? Are there any close relationships between a human and a shrimp or a gorilla and a blue whale? To answer these questions, we turn to phylogeny, a key force in revealing the ancestry of organisms in the natural world.
Phylogeny is one of the most important factors when deciding on a species, or group of species evolutionary history. Scientists are interested in understanding life over the course of time-not just in the present, but over long periods of time past. Before they can attempt to reconstruct the physical structures, roles, and lives of extinct plants and animals, scientists have to place these organisms in context. Their relationships to each other are based on the ways they have split off, or diverged, from a common ancestor. A phylogeny is usually represented as a phylogenetic tree which is like the genealogy of species. Phylogenetics, the science of phylogeny, is one part of the larger field of classification, which also includes taxonomy. Taxonomy is the science of naming and categorizing the many diverse organisms. Not only is phylogeny important for understanding evolution, but evolution in turn contributes to phylogeny. Many groups of organisms are now extinct, and without their fossils we would not have as clear a picture of how modern life is interconnected.
There is an astonishing variety of life, both living and extinct. For biologists to communicate with each other about these many creatures, there must also be a classification of these organisms into groups. In theory, the classification should be based on the evolutionary history of life, such that it predicts properties of newly discovered or poorly known organisms. Phylogeny is a way to understand the evolutionary relationships of living things, trying to interpret the way in which life has diversified and changed over time. While classification is mainly the creation of names for groups, systematics goes beyond this to expound upon new theories of the mechanisms of evolution. Cladistics is the method of assuming relationships between organisms. Like other methods, it has its own set of hypotheses, procedures, and restrictions.2 Cladistics is now the best method available for phylogenetic analysis, because it provides an explicit and testable hypothesis for relationships between organisms. The fundamental idea behind cladistics is that members of a group share a common evolutionary history, and are closely related, more so to other members of the same group than to non- member organisms. These groups are distinguished by shared, unique features which were not present in distant ancestors.
In the lab experiment that was carried out, I used a sample of my cheek cells to construct a phylogeny. Each member of the team gently rubbed the side of their cheeks with a flat toothpick to gain DNA to carry out the reaction. The toothpick was then placed into a microcentrifuge tube containing a 6% Chelex solution and stirred to transfer the DNA to the solution. A negative control (NC) microcentrifuge tube was also prepared to check for any possible contamination. The tubes were then boiled at 60° C for 5 minutes, at 97° C for 20 minutes, and held at 4° C until they were removed and refrigerated. The purpose of this step was to denature the DNA proteins and the Chelex kept them from being damaged by enzymes. Afterward, 2 microliters of the prepared DNA was added to another microcentrifuge tube containing 48 microliters of PCR reactants necessary for a PCR reaction. The tubes were then mixed by vortexing and loaded onto a thermal cycler where they were incubated at 94° C for 20 seconds, followed by 35 cycles at the same temperature for 20 seconds more, 51° C for 20 seconds, and 72° C for 40 seconds, incubated at 72° C for 5 minutes, and finally, held at 4° C until they were removed and refrigerated.
Since the agarose gel we were going to use in the rest of the experiment was not provided, it had to be prepared from the raw material that we were given. After the gel cooled, it was placed into the electrophoresis chamber and covered with .5 X TBE. After 1.5 microliters of DNA size standard, 5 microliters of each team member's DNA and the NC was loaded into each of the wells, the reaction was run. After this process was completed and the DNA stain was poured over the gel, the bands where the DNA passed the agarose were clearly visible. Next, the excess matter, such as nucleotides, proteins, and prime was filtered away from the remaining PCR reaction with a vacuum. Next 7 microliters of master mix containing sequencing dilution buffer, BigDye sequencing mix, and forwarding primer was added to 3 microliters of DNA and vortexed. The DNA was then sent to the lab to be sequenced. After being sequenced and interpreted into a spectrogram, I was able to read the DNA sequence, delete the unreadable portions, and convert the spectrogram into a phylogenetic tree.
Fig. 1: The phylogenetic tree showing and comparing the relativity of various organisms, including myself. (12-C1)
The results of the DNA sequencing are shown in the following phylogenetic tree. The tree shows how closely related each species is to the other. In Fig. 1, a general idea is given about the relations between several varied organisms, but more information is needed to gain a clear understanding of the phylogenetic tree. According to scientists, arthropods and chordates, who gave rise to mammals, diverged approximately 525 million years ago. This lets us know that the last common ancestor between any chordate and any arthropod lived around half a billion years ago. That is too great a distance for animals belonging to these two groups to be considered to be closely related. Conversely, humans and chimpanzees are the most closely related mammals with only 5 million years since their last common ancestor was alive.3 Physical characteristics are also helpful in deciding the relativity of two or more organisms, for example a blue whale and a gorilla are both mammals, so it can be inferred that they are more closely related than a mouse and a fly.Phylogeny.TIF
The results of the phylogenetic tree show how closely related the different animals are: a shrimps is very distantly related to humans and chimps are, as expected, very closely related. However, even though physical characteristics can be helpful when constructing a phylogeny, they can also be a stumbling block to unwitting scientists. A prime example of this is the North American and Australian moles. They are similar looking creatures and, at first glance, would be classified as being almost directly linked, but a closer look reveals that the North American mole is, in fact, a eutharian- an animal whose young develops inside its body and the Australian mole is a marsupial. These two animals are so far apart that their last common ancestor was alive 140 million years ago.1 This helps to illustrate the point that phylogeny can be useful when trying to find a common ancestor between species.
Fig. 2: A simplified phylogenetic tree showing mammal diversification over the years. Conversely, the platypus and the other listed mammals are much closer, even though they belong to different groups within the mammal classification. The last common ancestor of the platypus, a monotreme, and the other mammals, which are eutherians, was alive 180 million years ago (Fig. 2) and while that is a great deal less than 525 billion years ago, it still leaves room for considerable evolutionary changes to species over time. Thus, the slight changes in the phylogenetic tree.001.jpg
Phylogeny is influenced by evolution; without evolution there is no phylogeny, but with it, there is a whole world of plants and animals available to research and study. Evolution is formed by natural selection, which operates on the differences that occur in members in a regional species' population. The individuals that survive are the ones whose genes are the most compatible with the environment, and in surviving, they change the genes of their descendants, whose genes may have little in common with the genes of their ancestors. So, the genetic sequence of any descendant cannot be determined with any degree of certainty. In the end, it's the environment that selects for certain physical traits in organisms. And environments have been known to change. Even with the many changes that occur in genetics over time, it is still possible to trace evolutionary history back to an ancestor. To do this, scientists employ the concept of a molecular clock, a gauge that measures the time of genetic change based on the fact that some genes seem to change at a constant rate over time.1 Obviously, no gene can accurately indicate time because the clock measure average change, which can include a number of discrepancies below or above the average rate.
Early development can also lend support to the concept of phylogeny. In 1866, German zoologist Ernst Haeckel proposed an idea and called it the Recapitulation Theory. The theory simply stated that the embryonic development of an individual organism (ontogeny) followed the same path as the evolutionary history of its species (phylogeny).4 While this was not completely true, what is true is the concept that an animal's developmental process reveals facts about its evolutionary history. Animals that are more closely related tend to share more similarities during embryonic development. Even though some are more closely related than others, all life on Earth is related. This relatedness can be depicted by a tree of life (Fig. 3). This diagram shows how interconnected all life is and to what degree, but even though it is widely recognized and used, the tree of life has come under question. Recently, scientists have discovered that there has been significant genome movement between the domains. This phenomenon occurred through horizontal gene transfer, a process in which genes are transferred from one organism to another that is not the offspring of the first organism. It can take place through viral infections, exchange of alien genetic material, or the joining of two organisms, to name a few. The concept of horizontal gene transfer gives rise to the thought that, instead of a tree of life, there is a ring of life. This idea is still relatively new to the world of science, but has the potential to give rise to new studies and theories. http://rds.yahoo.com/_ylt=A0PDoS6Sc75M7lkAmQGjzbkF/SIG=12ahtqp8q/EXP=1287636242/**http%3a/www.theophoretos.hostmatrix.org/treeoflife1.jpg
Fig. 4: The Phylogenetic Tree of Life- Three Domains of Life