Dartmouth bioinformatician uses dual stressors, IPA for new findings in evolution
New research from Thomas Hampton, a senior bioinformatics analyst at the Geisel School of Medicine at Dartmouth College, and collaborators used a dual-stressor system to discover important aspects of evolution in a fish with unique phenotypic plasticity. QIAGEN’s Ingenuity Pathway Analysis (IPA) helped them make the connection.
In the study, the team collaborators used IPA to characterize genes underlying an important biological mechanism in Fundulus heteroclitus, a type of killifish. Their results were published in Molecular Biology and Evolution in a paper entitled “Natural Selection Canalizes Expression Variation of Environmentally Induced Plasticity-Enabling Genes.”
The paper sheds light on a poorly understood but critical trait in killifish, and would not have been possible without conducting a dual-stressor study, Hampton says. Such studies are rare in science because of concerns about confounding variability, but Hampton and his team were able to carefully craft their experiments and use IPA to determine the meaning of the gene expression data they generated. The result is a new look at the scale of evolution in killifish, which may contribute to a better appreciation of how evolution functions in other organisms too.
Hampton and his collaborators, including Joseph Shaw at Indiana University and John Colbourne at the University of Birmingham, chose to study killifish for a most unusual trait: the fish is equally happy in fresh water or in salt water, due to its ability to change the morphology and function of its gills as needed to adjust for salinity levels in the water. “This is really special. They can remodel their gills on a week-to-week basis,” Hampton says. “This would be like if anytime we needed to fly, we just sprouted a pair of wings.”
During the experiment, the team interrogated gene expression with custom arrays to reveal what was going on during gill remodeling. But in this case, expression analysis was not terribly insightful. “The kinds of genes engaged in this plasticity response were not that interesting, viewed from a distance,” Hampton says. “It looks like a bunch of different genes that are not related to anything that makes a tremendous amount of sense.”
Fortunately, the team used IPA to dig deeper, looking at the genes on a network level. “We found that the genes that facilitate phenotypic plasticity seem to be less connected to other genes, almost as if they’re in their own little world, ready to be activated in one direction or another to facilitate this process without a lot of cross-talk from other systems,” Hampton says. “That’s what Ingenuity helped us figure out. It’s an interesting result that suggests that evolution has acted not just on genes but on gene networks to make phenotypic plasticity happen.”