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IU researcher develops tools with Karst and Carbonate to understand evolutionary biology

Jeffrey Adrion studies effects of mobile DNA elements using DNA sequence data from fruit flies

The question of evolutionary processes has always been an interest to a lot of biologists, including IU graduate student Jeffrey Adrion, Department of Biology. His overarching goal is to use computational techniques and methods to better understand evolutionary biology. Specifically, for his Ph.D. thesis, which is supervised by Prof. Matt Hahn, one of the major areas Adrion is working on is the effects of mobile DNA elements, called transposable elements, using DNA sequence data from fruit fly.

These transposable elements are DNA pieces that can copy or cut themselves out of the genome and move to other locations. On the scale of population genetic data, Adrion has developed a software package to allow researchers to see where the transposable elements have cut themselves and where they have migrated to. This package is called TEFLoN, and it is available for anyone to use on GitHub.

Jeffrey Adrion
Jeffrey Adrion

TEFLoN takes genome sequences from multiple individuals, locates the transposable elements and where they’ve moved, and estimates their frequency in the population. It can be used for the most common types of genetic data one may come across.

While transposable elements were once referred to as junk DNA, they are not always harmful or useless. In fact, Adrion mentions, there are many instances where transposable elements have shown some potentially advantageous effects. They are found in nearly all plant and animal genomes, and roughly half of human genomes are comprised of these elements. Adrion is investigating the roles they play in adaptation. “Transposable elements are just yet another type of mutation that influences how organisms can potentially adapt to their environments”, said Adrion.

Adrion says the biggest challenge for him at the start of this project was his lack of experience with multi-core computing resources. Previously, he did not have access to high performance computing resources which made it difficult for him to develop software, particularly software that can process a large amount of information. He now uses IU supercomputers Karst and Carbonate for his research. While Karst is used for running the program and debugging, Carbonate is used for memory-intensive simulations to test the accuracy and sensitivity of different metrics of the tool. “It’s nice that I can have access to everything from home, office, everywhere," says Adrion.