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Kathryn Adams BSC 2011-008 Lab Report #1

Phylogeny and Evolution This lab activity was conducted in order to grasp a knowledgeable understanding of the interpretation and construction of phylogenetic trees as well as the components involved in evolution. The methods of assembling a phylogenetic tree were utilized after observations were made based on the 10 intricate skeletons of the rat, mouse, chicken, pigeon, shark, human, carp, frog, turtle, and bat. Through the collection of data obtained by observations of each of the 10 skeletal systems, the results of morphological similarities and differences were distinguished. These results included homologous bone structures constructions like the beak, separating the pigeon, chick, and turtle into an individual clade. Although the skeletal structures provided an elaborate

idea of the most accurate phylogenetic tree included in the lab activity, the research based on the cytochrome C oxidase amino acid sequence adequately supported the proposed hypothesis (Figure 1). The cytochrome C oxidase amino acid sequence data showed the differences in the patterns of the related animals. The 10 skeletal structures and the cytochrome C oxidase amino acid sequence research supported the hypothesis of the last phylogenetic tree in the lab activity to be accurate.

Kathryn Adams BSC 2011-008 Lab Report #1

Phylogenic trees are very effective diagrams which show how species evolved from generation to generation by revealing the evolutionary history. When categorizing the various taxa, certain constituents of evolution are questioned including convergent evolution and divergent evolution. How did a particular species evolve? A vast amount of observations and

studies have been executed in order to construct accurate phylogenies. Scientists make every effort to arrange the diagrams so that the common ancestor and all of the most closely related species are grouped together. This is known as a monophyletic group or a clade. A specific example of a study done at University of California Museum of Paleontology demonstrates the characteristics of each breaking point in the phylogenetic tree (Figure 3). The species include sharks, rayfinned fish, amphibians, primates, rodents, crocodiles, dinosaurs, and birds. The first species is a shark which contains vertebrae, but not a bony skeleton. This resulted in the leading breaking point in the diagram, which is referred to as cladogenesis. The ray-finned fish contains a vertebrae and a bony skeleton but does not have four limbs like the remaining species which evolved from the common ancestor. Since the rayfinned fish does not possess four limbs but is related to the

Kathryn Adams BSC 2011-008 Lab Report #1

common ancestor of remaining species, this can be called synapomorphy. The four-limbed creatures exhibit divergent evolution as they exhibit adaptations to assorted environments (Schluter, 2001), yet they all still demonstrate the homologous structures of their common ancestor, the shark. These structures include vertebrae, bony skeleton, and four limbs. This leads to a new species which is an amphibian. Since amphibians, like frogs, do not exhibit an amniotic egg they also show evidence of synapomorphy. The next clade inherited vertebrae, bony-skeletons, four limbs, and an amniotic egg. This monophyletic group is divided into two breaking points. One breaking point contains hair, and the other exhibits two post-orbital fenestrae (as well as all of the traits leading up to the breaking point). This study demonstrated a phylogenetic

tree based on systematics, and aids in the identification of homologies and synapomorphies of the different species. The study done by the University of California presented a detailed method by using homological traits which descended from the common ancestor. This was a method that was used to identify the accurate phylogenetic tree in the experiment of phylogeny and evolution. An additional method used in this lab activity was the ability to validate the hypothesis through

Kathryn Adams BSC 2011-008 Lab Report #1

taking into consideration that each individual species in this lab activity possesses its own unique scientific name in addition to its common name (Figure 2). This is called binomial nomenclature. The genus name and the specific epithet are both used to name a certain species (Brooker, Widmaier, Graham, and Stiling, 2011).The unique name of each species was used in the analysis of the cytochrome C amino acid sequence (Figure 2) through molecular connections. The GenBank BLAST (Basic Local Alignment Search Tool) website associated with the National Association of Medicine. This tool was used to analyze the differences of the protein cytochrome C oxidase through thorough examinations of the generated algorithms. This protein is involved by way of electron transport chain in the mitochondria, and for many years has shown scientists the differences in two species. Scientists believe that phylogenies that have been narrowed into species can provide consequential information from molecular data which exhibits an accurate record of the speciation and evolution potentially leading to reasons of changes in clades and patterns of speciation (Barraclough, 2001). The Principle of Parsimony utilizes several strategies in order to narrow down the accurate hypothesis. It ultimately

Kathryn Adams BSC 2011-008 Lab Report #1

leads to the simplest form of phylogenetic tree based on morphological characteristics as well as molecular or genetic data (Brooker, Widmaier, Graham, and Stiling, 2011). Although evolution can be evaluated by molecular data and morphological characteristics, another factor involves speciation. Allopatric and sympatric speciation encompass differences and similarities in diverging populations. Lately, sympatric speciation is increasingly used to construct new models of phylogenetic diagrams validating credibility and formulating indications of changes that are made in the models and seen in natural populations (Via S. 2001). With geographical data of

speciation, the Principle of Parsimony enables an even more accurate hypothesis to be made. Based on all of the data collected and the sources studied, the cytochrome C oxidase amino acid sequence (Figure 2), and the morphological features of the different species (Figure 4) the shark was labeled as the outgroup of the diagram (Figure 1) due to the common feature of the jaw. The branching point of the frog and the carp was distinguished by the nails and arm features of the frog and the carp contained fins and both exhibited a jaw in comparison to the shark. The amino acid difference between the frog and the carp was 12. The next breaking point includes the

Kathryn Adams BSC 2011-008 Lab Report #1

turtle as its own species, and a chick and pigeon as a separate node. The chick and the pigeon both have feathers whereas the turtle does not, but the amino acid difference between the chick and pigeon compared to the turtle being only 8. The pigeon, chick, and turtle share the homologous traits including the jaw (like the shark, frog, and carp), nails, anatomical arm structures (containing the Humerus, Radius, Ulna, Carpal, Metacarpal, and Phalanges), and a beak. The following clade includes a bat as its own species (most likely because of the difference of cytochrome C amino acid sequence of 14 from the shark) followed by another node including two species with the same amino acid difference of 13, only 1 difference in sequence from the bat. Those species include a rat and a mouse, and on the opposite branch is the human with an amino acid difference of 20 from the shark and 9 from the rat and mouse (Figure 2). The last clade containing the human, mouse, and rat had the many of the same homologous structures including the initial structure obtained from the shark (the jaw), nails, fur/hair, mammary glands, and nails. Yet the human stands in an erect position. Therefore, the hypothesized phylogenetic tree (Figure 1) is the most suitable for the list of species given based on systematics and genetic data. Although only 10 different

Kathryn Adams BSC 2011-008 Lab Report #1

species were examined by the skeletal structures, the analysis of the cytochrome C amino acids sequences among many other sources further validated the hypothesis of the accurate phylogenetic tree (Figure 1).

Kathryn Adams BSC 2011-008 Lab Report #1

Literature Cited Barraclough, T.G. and Nee, S. 2001. Phylogenetics and speciation. Trends in ecology and evolution. 16:391-399 Brooker, R. J., Widmaier, E. P., Graham, L. E., & Stiling, P. D.(2011). Special edition of biology.(2nd ed., pp. 530532). The McGraw Hill Companies. Schluter, D. 2001. Ecology and the origin of species. Trends in ecology and evolution.16:372-380 Understanding Evolution. 2011. University of California Museum of Paleontology. 22 August 2008 <>. Via, S. 2001. Sympatric speciation in animals: the ugly duckling grows up. Trends in ecology and evolution. 16:381390

Kathryn Adams BSC 2011-008 Lab Report #1


Rat Mouse Bat Pigeon Chick Turtle Frog

Carp Shark

Figure 1 Hypothesized phylogenetic tree based on observations and cytochrome C amino acid sequences

Kathryn Adams BSC 2011-008 Lab Report

chicken pigeon

shark bat

Scientific Name Homo sapiens Mus musculus Rattus norvegicus Gallus gallus Columba livia Chelydra serpentine Rana catesbeiana Cyprinus carpio Squalus suckleyi Miniopterus schreibersii

Common name Human Mouse Rat Chicken Pigeon Turtle Bullfrog Carp Shark Bat





0 9 9 13 10 14 18 17 20 12

0 0 8 5 8 9 11 13 5

0 8 5 8 9 11 13 5

0 4 8 11 14 18 8

0 8 12 14 18 6

0 10 13 14 7

0 12 19 10



0 16 11

0 14

Figure 2 A table of the pairwise differences in Cytochrome C oxidase amino acid sequence of the species


Kathryn Adams BSC 2011-008 Lab Report #1

Figure 3 A Phylogenetic tree that distinguishes the characteristics of each node


Kathryn Adams BSC 2011-008 Lab Report #1

shark jaw mammary glands fur/hair feathers beak fins arm structures nails/claws X X

carp X

frog X

turtle chicken pigeon bat X X X X X X X X X X X

mouse X X X

rat X X X

human X X X


Figure 4 A table showing on similar structures of species