Philip J. Freda, Jr., Ph.D.

Temporal study of microsatellite variation in wild populations of Drosophila simulans

My master’s thesis research investigates variation in microsatellite loci in a close realtive of Drosophila melanogaster – Drosophila simulans. MIcrosatellites are usually found in intergenic regions of the genome or in introns. They are tandem repeats of anywhere from two to six nucelotides. For example, a dinucleotide repeat would look like: AGAGAGAGAGAGAGAG.  Microsatellites arise due to replication slippage and are highly mutable. Due to this, microsatellites are a good way to determine the level of variation inherent in a population.

I am currently using 20 microsatellite loci from across the genome and fly specimens collected from multiple dates over three years to detect changes in the frequency of microsatellite alleles. If allele frequencies change over the course of time, it may be possible to determine how structured the local population of Drosophila simulans is. If these changes are found, tests will be performed in order to determine if natural selection or drift is involved.

 

Temporal study of COI variation in wild populations of Drosophila suzukii

I have been collecting Drosophila from nature for approximately three years using bait traps on the campus of Saint Joseph’s University in Philadelphia, Pennsylvania. In 2011, among the specimens of common, endemic species, I noticed a peculiar male fly in my collection. This male had dark wing spots centered on the first major wing vein. A quick search pointed me to a recent invasive species first detected in 2008 in California. From that point, I have fallen in love with Drosophila suzukii, or Spotted Wing Drosophila (SWD).

I am interested in how this species, which presumably has experienced numerous population bottlenecks, has successfully spread throughout the continental United States in only 3 years. Using the mitochondrial gene, cytochrome oxidase subunit 1 (COI), I am attempting to better understand the invasion and migration of SWD in order to reduce potential agriculture damage.

 

QTL analysis in recombinant inbred lines of Arabidopsis thaliana under elevated and ambient CO2

My undergraduate research, under Dr. Clint Springer, Ph.D., investigated which parts of the Arabidopsis thaliana genome is responsible for variation seen in traits under ambient and elevated carbon dioxide levels. Using the program QTL Cartographer, genetic marker data and trait data were used to locate possible QTL’s, or Quantitative trait loci throughout the A. thaliana genome that are responsible for the observed variation in a number of traits. Traits analyzed included flowering time, axes number, and silique number.

Mendelian traits are controlled by one gene. Cystic fibrosis (CF) is an excellent example of a classic, mendelian disease. If one is unfortunate enough to have two of the recessive alleles in the CFTR gene that cause CF, the person will have the disease. In reality, most of the traits we observe on a daily basis, like height and skin color, are quantitative traits. This means that many genes contribute to the phenotype in varying degrees.