Interview with the authors: Parallel introgression and selection on introduced alleles in a native species

Species introductions serve as a natural laboratory to study introgression and selection. In a recent paper in Molecular Ecology, Rachael Bay and colleagues use introduced rainbow trout and native cutthroat trout to study hybridization, introgression, and selection. Bay et al. find evidence that some alleles have repeatedly introgressed from rainbow trout into cutthroat trout in independent populations. Their results suggest that selection has played an important role in this introgression, and highlight the usefulness of species introductions for understanding the predictability of evolution. Below, get a behind the scenes look at this work from author Rachael Bay.

West slope cutthroat trout. Photo by Ernest Keeley.

What led to your interest in this topic / what was the motivation for this study? 
This study combined two of my primary research interests. The first is: How do humans alter the evolutionary trajectories of species? By introducing rainbow trout, we have provided access to an extended gene pool for native cutthroat trout species. Previous studies have shown that hybrids have lower fitness, but with hybridization and recombination continuing over decades we can investigate whether particular rainbow trout alleles might be adaptive in westslope cutthroat trout. This study also speaks to the predictability of evolution. The stocking of rainbow trout has resulted in a highly replicated evolutionary experiment. Do we find the same alleles repeatedly under positive selection in independent watersheds?

What difficulties did you run into along the way? 
One of the main difficulties was trying to understand the null expectation. How much introgression should we expect between the two species and what fraction of that introgression is a result of selection? This depends on not only the strength of selection, but also on other demographic factors like population size, and stocking history. Ultimately, we decided to use simulations in order to understand the level of selection necessary to produce the patterns of introgression we were seeing in hybrid populations.

What is the biggest or most surprising finding from this study? 
We found that across multiple independent locations, the same rainbow trout alleles rose to high frequency in hybrid populations, suggesting they were under positive selection. This is somewhat surprising because previous studies have suggested that hybrids have reduced fitness and have found broad signals of purifying selection against rainbow trout alleles. However, hybridization and backcrossing has been occurring for many generations, allowing plenty of time for recombination and allowing different parts of the rainbow trout genome to segregate more independently. So despite the fact that hybrids have lower fitness, there seem to be a few regions of the rainbow trout genome that may be advantageous to westslope cutthroat trout.

Moving forward, what are the next steps for this research?
While our results suggest that some rainbow trout alleles provide an adaptive advantage we still have yet to identify the selective force. Is there some component of the abiotic environment to which these alleles are better adapted? Do these alleles confer higher reproductive success or fecundity? Rainbow trout have been successfully introduced to many different environments across North America – do alleles at high frequency in hybrid populations also explain the invasion success of rainbow trout?

What would your message be for students about to start their first research projects in this topic? 
I think it’s really important to choose your system carefully. We didn’t start out thinking about this as a project on trout, we started thinking about human-induced evolution and repeatability. It took a long time and a lot of thought to realize that a broadly introduced species was the perfect natural experiment for the questions we had.

What have you learned about science over the course of this project?
One of the cool things about this project is that it is a demonstration of how science evolves as technology evolves. Through a collaboration with Rick Taylor, we were able to learn something new from samples that had been sitting in a freezer for many years. Previous researchers had used these samples to analyze rates of hybridization across British Columbia and Alberta, but the increasing ease of high-throughput sequencing allowed us to take a deeper dive and look at genome-wide signals of introgression. So you never know how experiments you are doing now will contribute to knowledge in the future!

Describe the significance of this research for the general scientific community in one sentence.
Some genes from introduced rainbow trout can confer an adaptive advantage in native cutthroat trout species.

Describe the significance of this research for your scientific community in one sentence.
Rainbow trout alleles show consistently high levels of introgression into the westslope cutthroat trout genome across multiple independent watersheds.

Read the full article:
Bay RA, Taylor EB, Schluter D. Parallel introgression and selection on introduced alleles in a native species. Mol Ecol. 2019;28:2802-2813.

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