Genetic Analysis of Evolution in Fruit Flies

Primary Article: Genome-wide analysis of a long-term evolution experiment with Drosophila by Burke, Dunham, Shahrestani, Thorton, Rose, and Long. doi:10.1038/nature09352

Drosophila melanogaster pictured above is the common species of fruit fly typically used as a model organism for the experimental observation of Mendelian inheritance patterns by scientists of all levels across the world. A recent study performed by the department of Ecology and Evolutionary Biology at the University of California Irvine, and the department of Molecular and Computational Biology at the University of Southern California outlined an experiment using D. melanogaster that compiled data obtained from examining the genome of fruit flies that have undergone sustained selection for shortened developmental time for over 600 generations with the genome fruit flies that had no direct selection on developmental time.  The commonly held genetic theory of evolution can be explained in a model of a classic sweep, which holds that there is a change among the nucleotides in the neighboring DNA of a mutation as a result of natural selection, and that the resulting advantageous allele becomes set within a population. However, in this study, the involved scientists noted that the classical sweep model was not followed, but instead presented a model for the genetic variation caused by selective breeding, which held that a population generally reached a new phenotypic optimum before beneficial mutations have had time to become fixed. The overall conclusion of this study was that selective breeding across 600 generations of fruit flies did not lead to the fixation of newly arising unconditionally advantageous alleles, and that selection doesn’t readily expunge the genetic variation in sexual populations. This study provides evidence against the classically held model of genetic sweeps, whether through a series of small sweeps involving single nucleotide polymorphisms or through classic sweeps in which one advantageous allele becomes fixed within a population. The results of this study were that there was an absence of actual mutations at the genetic level that allowed for the lessened developmental time of the flies selected for shorter developmental time, and that the flies were somehow able to better use the vast array of developmental genes that they already possessed for short term developmental superiority.

This study is a good example of the overall theme that genetics students will come to learn and appreciate, that genetics is much like real life. If you can think of a situation where something might exist, you will most likely be able to find an example of it, often in contradiction to classically held “textbook” type models.

Choosing a Research Topic

One of the most frustrating things that I have experienced in my time at Baker is when a professor tells you “You will be writing a 12 page research paper over a topic of your choice that relates to the topic of the course.”  This is especially frustrating if the course is a history course, because some of them cover a large span of time.  How are  you supposed to come up with a concise topic?

The first thing that we must realize is that there are two separate parts to finding a topic to research and developing a question that will be interesting to readers.

In finding a research topic, I always start with something that is interesting to me.  Why spend hours writing about something if it won’t hold your interest for more than a few hours?  Start thinking about the aspects of the course that you find appealing and think about questions that could be asked.   For example, someone who is interested in the Roman Republic may be interested in the Wars of the Republic, and the specific Consuls who led the soldiers to victory (or defeat).  Great job! You just found a topic that interests you- The Consuls of the Roman Republic and their Military Involvement”

The task is only half completed, however.  Now you must turn your topic into a question that will guide your research and interest your reader.  In my example above we found the topic to be Roman Consuls and their military exploits.  If we were to write a general paper on that topic, it would be too long–This is what books are for.  For a research paper, you need a general idea (a thesis) that will guide your writing, and the best way to develop a thesis is to find a question that can be answered by the research you will perform.  For example, using the Romans again, a good question might be, “Why was Scipio so effective at fighting in Africa when the other Consuls that came before him failed?”.  This question is enough to take up 12 pages, and will interest your reader (usually your professor).  Again, make sure the question appeals to you as well.

Two great books for students who do any sort of research are The Craft of Research and A Manual for Writers of Research Papers, Theses, and Dissertations (Note that this book focuses on Chicago Style of Citation).  If you are in a field that will require you to write multiple papers in your collegiate career, I encourage you to pick up both of these books.  I have included the publishing information below.

The Craft of Research by Wayne C. Booth, Gregory G. Colomb, and Joseph M. Willimas.  Univ. of Chicago Press, 2008.  ISBN:0-226-06566-9

A Manual for Writers of Research Papers, Theses, and Dissertations by Kate Turabian.  Univ. of Chicago Press, 2007.  ISBN:0-226-82337-7

Intervals

One of the most fundamental concepts in music theory is the idea of intervals. An interval is the distance between two pitches. They are usually expressed as a letter followed by a number. The number is an indication of the number of lines and spaces in the staff that the interval encompasses, and the letter is an indication of the quality – that is, the exact number of half steps between the two notes.

So, how can you figure out what note is a given interval above or below a given note? This is one foolproof method:

First, put a note on the line or space that the number in the interval says to.  Do this by counting from the letter of the note you’re given up to until you reach the number the interval says. For example, if you are looking for a major 3rd  above A, count A as 1, B as 2, and C as 3. C is a third above A. If you go above G, then start back at A. If you’re descending, then just count backwards. For example, if you are looking for a perfect 4th below E, then count E as 1, D as 2, C as 3, and B as 4. If you go below A, then continue at G.

Second, find the number of half steps between the starting and ending pitch. Draw a piano from C to C. All of the intervals between white keys are either major or perfect intervals above C. D is the second key above C, which means that it is also two half steps above C. It’s also the second note of C Major, so therefore it is a major second. Likewise, E is the fourth key above C, so it’s four half steps. It’s the third note of C major, so it’s a major third. Using this method, you can determine the distances between major intervals easily. Remember that the fourth and fifth intervals are perfect rather than major, as well as the octave and unison.

So, what do you do if the interval isn’t major or perfect? You just need to add or subtract half steps. If you are looking for an augmented interval, simply add one half step to whatever number you got earlier in this step. Minor intervals also always subtract one half step. Diminished intervals, however, change depending on whether you start with a perfect or a major interval. For perfect intervals, a diminished interval subtracts one half step, but for major intervals, it subtracts TWO half steps.

The last step to notating the interval is to count the number of half steps up from the starting pitch. A major 3rd above A is going to be four half steps above A. So, count up from A, but for this step, DON’T count A. The ending pitch is either C# or Db. In step 1, we found the answer is going to be some form of C, so the answer is C#.

Next time, I’ll give more examples of this process to guide you through it and make you feel even more comfortable.

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The Baker University Tutoring blog is designed to provide our tutors a forum to produce content beneficial for students. This blog will contain tutorials, commonly asked questions, study materials, and posts related to current events within a variety of scholarly fields. Please feel free to leave comments and/or questions for the tutors within each post, or engage in conversation with other students who comment. Take advantage of this site, as it will provide loads of useful information for classes across all disciplines.

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