Armored Scale Insects (Hemiptera, Diaspididae) are a unique family of plant-feeding insects including several economically important agricultural pests. This project aimed to combine genetic data from both the lab of Dr. Benjamin Normark here at UMass Amherst, and the lab of Dr. Geoffrey Morse at University of San Diego, focusing on three main loci: the 28s ribosomal subunit (28s), elongation factor 1-alpha (ef1a), and cytochrome oxidase subunits I and II (COI and COII). Combined data sets could be edited and aligned as part of an ongoing process of removing sequences that were poor reads, contaminated, or otherwise unsuited to further study. From these combined data sets, gene trees could be generated using PASTA and related software to elucidate the relations between taxa sampled by the two labs.
For this project I was responsible for combining and aligning sequences for each of the three loci examined. At this stage I helped to identify and remove poorly aligned or suspicious sequences from the analysis. In addition, I was also responsible for generating preliminary gene trees for each of the three loci using PASTA. Following this, I helped to examine and edit the trees, flagging and removing sequences that appeared on long branches or in unexpected locations. These were investigated further by running through BLAST to gauge similarity to other (non-diaspididae) sequences which could indicate contamination, or by examining the original chromatograms of the sequence reads for potential issues.
This project helped to familiarize me with modern methods and tools used in phylogenetics and evolutionary biology, which made it very useful for me academically given the importance of utilizing genetic data in modern biology. The experience I gained over the course of this summer is directly related to my degree and the professional career I am pursuing, making the project invaluable for me as a student. In addition to the professional and academic benefits, this experience was also incredibly rewarding for me personally. Evolutionary biology and genetics are areas that are particularly fascinating to me, so to have the opportunity to gain first-hand experience and guidance in this project was incredibly meaningful.
Naturally, the ongoing pandemic and requirements imparted by social distancing and quarantine procedures posed an obstacle to this project, but given the nature of the work I feel any disruptions were kept to a minimum. In a way, the fact that the majority of the work on my end was done at-home was actually very enlightening, as it introduced me to just how much of a wealth of genetic data is available online now and encouraged me to practice troubleshooting and the technical skills required – areas that I had only minimal experience with previously. The project itself was incredibly rewarding, and is something that I am looking forward to pursuing further.