In her lab, Rebekah Rogers, assistant professor of bioinformatics, and her students explore how the genetic instructions of certain animals remodel during evolutionary change. Their research can better predict a particular species’ ability to survive disease and environmental threats like climate change.
Chromosomal rearrangement mutations can copy and shuffle DNA around the genome, the genetic material of organisms. Sometimes these mutations can even produce novel gene sequences. Those sequences can evolve as animals adapt to new environments or create mutations that break gene sequences and cause genetic diseases.
Untangling how and to what extent genes and chromosomes affect animal evolution is no small task. Roger and her students analyze genomic datasets as large as 20 million cell phone photos. They use University Research Computing’s high-performance computing resources to extract, store and examine the information from genome sequences in days, which would otherwise take months or years on individual workstations.
“We would not be able to get preliminary data for our grant proposals without the HPC,” Rogers said. “It’s essential to get and to keep National Institute of Health funding and part of our work that we have submitted to the National Science Foundation.”
In addition, Rogers and her students developed software to help identify mutations and signatures of natural selection. They employed similar techniques to analyze the evolutionary changes of elephants, freshwater mussels, and Drosophila (a type of fruit fly). Using the high-performance computing resources and their software, Rogers and her students can quickly study multiple species at one time. This approach streamlines research on the evolutionary forces that reshape genetic diversity in nature to help species adapt to adverse conditions.
In their studies, graduate student Rittka Mallik evaluates how genomes of the Asian elephant may have been affected during endangerment. Mallik focuses on “selfish” DNA, which enhances its own transmission in part by creating copies.
Theory indicates that natural selection weeds out harmful genetic mutations, but with persistence possible in limited gene pools. In the past, Rogers’ students found these signs of genetic declines in Woolly mammoths. Now, Mallik works to uncover if Asia’s largest land animal displays comparable marks of genomic meltdown.
Mallik’s research also focuses on how parasitic DNA sequences that inhabit a host genome rearrange and clone. The sequence is known as a “transposable element” and can change its position within a genome. Mallik aims to determine whether the transposable elements cause declines quicker than other mutations.
Freshwater bivalves like oysters, clams, and scallops face ecological upheaval in the United States, as manufactured dams block waterways, cause pollution and kill fish that the mollusks inhabit as larvae.
Rogers works with Stephanie Grizzard (Master’s of Bioinformatics, 2018) and postdoctoral students James Titus-McQuillan and Rhyker Ranallo-Benavidez to study the bivalve genomes’ responses under these extreme environmental shifts. So far, they have observed signatures of robust selection on duplicate genes in the Washboard mussel. The team has also identified gene copies that allow adaptation, help animals resist pollution and tolerate stress, and enable larvae to host fish.
Their work has helped the researchers explain how one successful species has adapted while others have suffered. The team hopes to build more genomic resources to study the response of other species, especially threatened and endangered species.
Image: The genetic region with signatures of natural selection across 1,900,000 bp in freshwater bivalves.
Fruit flies thrive in a variety of environments. Rogers, Titus-McQuillan, Ranallo-Benavidez, fellow doctoral student Brandon Turner, and undergraduate student Taylor Conway sequence panels of flies to understand how genomes change in nature. They research fruit flies adapted to island environments, including D. santomea, a high altitude relative of D. yakuba on mainland Africa, and evaluate gene rearrangements and duplications in Drosophila.
The students’ work uncovered genomes that reordered themselves near genes that are tolerant to UV rays. The repair genes spread to high-altitude populations and help flies adapt to higher UV exposure where the atmosphere is thinner than at lower altitudes. Rogers and her students hope to identify other mutations that help flies adjust to new environments, including on other islands.
Fig. 1: The novel gene Quetzalcoatl in Drosophila melanogaster.
Fig. 2: Signature of natural selection at Quetzalcoatl.
Fig. 3: Chromosomal rearrangement at Victoria, a UV tolerance gene in Drosophila.