Since Darwin, scientists have struggled to find the best ways to


Question Description:

35

Since Darwin, scientists have struggled to find the best ways to represent the evolutionary relationships that exist between organisms. Traditionally, biologists use phylogenic trees to diagram and analyze the evolutionary histories. However, as DNA sequencing has become quicker, easier and cheaper, we now see phylogenetics and phylogenetic trees used to analyze relationships between strains of organisms such as viruses isolated from different outbreaks or bacteria and fungi implicated in contaminated medicines and food supplies. In this assignment, we will walk through how several programs are used and then you will use these programs to study data from several West Nile Virus outbreaks. PART ONE – Ebola Virus Ebola virus was first discovered in 1967 in the Sudan and in Zaire (in the same outbreak) and more than 600 cases occurred with a fatality rate nearing 70%. Similar outbreaks have since occurred in other areas of Africa including the Ivory Coast, and Gabon. Ebola is a member of the filoviridae and causes a hemorrhagic fever. If you have ever seen the movie “Outbreak” – you know how disgusting this is!! If not, and you have a strong stomach, you could do a google image search – but be prepared. Ebola is not pretty. Figure One – Ebola virus Source: http://www.telegraph.co.uk/news/worldnews/africaandindianocean/uganda/9436320/Ebola-virus-kills-14-in-Uganda.html Diagnosis is almost always made by ELISA for specific antibodies to the virus in the blood, but hemorrhagic fevers are not very common. It is spread person to person through blood products, secretions, organs or semen and many human to human spreads occur in the final stages of infection when the patient is vomiting, having massive diarrhea or hemorrhaging. A study of the relationships between various isolated Ebola viruses may help us understand the origins of each outbreak as well as provide insight into the evolution of Ebola viruses. Once viruses have been isolated, often, the genomes are sequenced. Analysis of the genomes of the viruses aides in the determination of common ancestors and what other viral outbreaks it may be related to. In order to do this biologists must align the sequences, and the easiest way for biologists to then analyze these data is by the use of phylogenies and phylogenetics. By identifying similarities in anatomical structures, protein sequences, and nucleic acid sequences biologists are able to make comparisons and determine evolutionary trends. In order to visualize the data, biologists create phylogenetic trees that relate each organism. Each tree consists of a few distinct points of information: nodes, branches, branch length, and the trees can be rooted or unrooted. Figure two show a typical tree. Figure 2 (A phylogenetic tree created off of the sequence homology of the ATP6 Gene along the primate lineage leading to humans) Nodes on a phylogenetic tree represent an organism/ species. There are two types of nodes. Terminal nodes refer to a node at the end of the tree and indicate that we have known data. Internal nodes function to connect two branches and represent a common ancestor. Branches on the phylogenetic tree represent an evolutionary relationship, and often times there is an associated scaler, making the length of the branch indicative of time. Trees can be rooted or unrooted. When a tree is rooted it is connected to a distant relative which is often times called an outgroup. 1. Go to GenBank at http://www.ncbi.nlm.nih.gov/ (Links to an external site.) and from the main page change the search field (pull down menu) to “Nucleotide” and enter “Cote d’Ivoire Ebolavirus” in the search field. In the results, you will see several results. Pick any one that gives you a sequence of the glycoprotein (GP) or spike glycoprotein (these will be about 2000-2400 nucleotides long) and click on the name of the virus. This takes you to a page with more information about the sequence. Immediately below the name is the FASTA link; click on the

Answer

35