Evolutionary Biology in the iCompBio REU

University of Tenessee i comp biology

By Isimeme Udu and Taya de Blonk

My name is Taya de Blonk and I am a senior at the University of Tennessee (UTC) at Chattanooga. I am a participant in the iCompBio REU which is supported by the NSF and hosted by Dr. Hong Qin of UTC. I have previously expressed interest in pursuing a career involving evolutionary biology and ecology. After graduating from UTC, I hope to pursue a Masters or PhD program to further my research. To prepare, I have worked under my mentor, Dr. Fernando Alda, since January of this year, and our work has focused on the evolution of Neotropical freshwater fish. Unfortunately, research during the spring semester was cut short by the persistence of COVID-19. Luckily, the iCompBio program has proven to be a successful online REU. Our current project focuses on assembling, annotating, and aligning mitochondrial genomes of several species within the genus Crenichicla so as to create bioinformatic pipelines, do comparative studies, and assess the phylogeny of the genus Crenicichla. Some REU participants, like myself, are beginners to several aspects of computational biology. As we just passed the half-way mark, I can tell that I have come a long way since we first met on Zoom. Skills I have gained include using advanced molecular genetics software such as Geneious and Mitofinder, using both Python and R languages, and learning to deal with metadata. Additionally, the cohort experience of the REU has been enhanced by joint meetings arranged by Dr. Hope Klug and Dr. Fernando Alda, both evolutionary biologists and professors at UTC. These meetings include myself and another iCompBio participant, Isimeme Udu of Spelman College. My skepticism of the quality of learning I would be able to achieve in an online REU has dwindled as I now see that research and networking is possible from the comfort of my own home. Isimeme and I decided to collaborate on this blog to exemplify the quality of iCompBio as an online REU and provide an outlook on evolutionary biology in undergraduate research.

My name is Isimeme Udu and I am a senior at Spelman College. I have never been to the University of Tennessee at Chattanooga, nor have I had any previous contact with anyone there. My interests in computational biology led me to pursue this iCompBio REU. In the future, I hope to enter a MD-PhD program, and I thought this REU would be the perfect way for me to enrich myself and refine my research skills. I am surprised how well this REU was able to transition to a remote space. I initially had my doubts on how effective the interactions within the cohort would be, but those thoughts quelled as the program began. Before, I had only considered evolutionary biology from a phylogenetic lens and gained experience exclusively in tree building. The focus of my current research under my mentor Dr. Hope Klug is different in that it is a project which uses mathematical modelling to explore what basic life conditions influence the evolutionary loss of parental care. Upon learning that this project incorporated the program Mathematica, I was surprised. Although I had coded before, I had never used this program, so I looked forward to the challenge. Through my research, I have a greater understanding of what parental care is. The theoretical work I am doing can stand as a template for future projects by providing testable predictions. Initially, it was difficult to understand the mathematical concepts behind the project as well as how these influence the evolution of parental care. With a lot of reading and practice, I was able to overcome this struggle and strengthen my understanding of relationships between parents and offspring. Furthermore, my REU experience has been supplemented by the meetings held by Dr. Hope Klug and Dr. Fernando Alda. I believe Taya and I have been able to learn more about evolutionary biology and be more assured about our future goals.

In collaborating on this blog post, we hope to exemplify the diversity and success of the remote iCompBio REU. Our host, Dr. Hong Qin, has worked diligently to ensure a quality online research experience despite these extenuating circumstances. We have been successful in assessing evolutionary biology from molecular, phylogenetic, and mathematical perspectives. Our mentors, Dr. Fernando Alda and Dr. Hope Klug, have allowed us to look deeper into evolution by reading scientific articles, reviewing conference talks, and presenting our own preliminary findings. Though the cohort experience has been impacted, we are proof that even in the absence of physical interaction, sustainable relationships can be made. Since we are working from the comfort of our own homes, there are other trade-offs to the online experience.We both regret that we were not able to physically interact with our peers from the iCompBio REU. We must also be conscientious of our time management and be able to acclimate ourselves to this non-typical lab environment where communication relies on video-chatting and emails rather than direct, in-person interactions. Despite the inconveniences of living in the now-online world, we are grateful for the opportunity to continue scientific research and be participants in the iCompBio REU.

Taya de Blonk:

These images show the assembly and annotation of a Crenicichla mitogenome.

crenicichla mitogenome

Isimeme Udu:
These images shows the sample code used to generate plots that can be analyzed qualitatively to find how basic life-history conditions influence the loss of care.

basic life history conditions

This is a screenshot of our Evolutionary Biology Journal Club. At top, from left to right: Dr. Hope Klug, Taya de Blonk. At bottom, left to right: Dr. Fernando Alda, Isimeme Udu.

biology journal club