How to build a better rattrap with population genetics

azandis@gmail.com

A team I worked with just published a population genetics study looking at the effectiveness of rat eradication programs in Salvador, Brazil.

Figures 1 and 3 from the paper. Sample locations in three valleys of Salvador, Brazil (left) and genetic difference between populations (right) before (blue), 1-month after (red), and 7-months after (yellow) the eradication campaign.

Rats have traveled around the globe alongside humans. Where we make our homes, they are happy to make their own, too. Unfortunately, they can make terrible neighbors, especially when they become vectors for diseases.

The rats that live in the slums of Salvador, are to blame for the widespread of emergence of leptospirosis infections that poses a serious health risk. In response, the municipality planned a multi-year rat-eradication project.

The bad news is that it is nearly impossible to fully eradicate rats from large territories. After just a short time, the populations tend to rebound, either because some rats were missed and then repopulate from within or because new rats migrate from outside and colonize the area. Understanding how rats repopulate after eradication efforts is important for deciding how best to proceed with future management strategies.

To test which of these scenarios was at play in Salvador, my collaborators trapped rats before, during, and after the eradication campaign in three contiguous geographic regions within the slums. We looked at the genetic relatedness of the populations across the three time-points. If the rebound populations were more similar to each other post-eradication, it would suggest that the populations were recolonized from source populations outside. However, if the regions became more genetically distinct post-eradication, it would suggest that the rebound populations were seeded from the few local genetic lineages that persisted.

We found that the populations showed distinct genetic differences immediately after the eradication effort, suggesting that remnant rats from the original populations had repopulated from within. Those difference persisted after 7 months.

In addition, we looked at the genetic signatures of population expansion and contraction. We found that post-eradication populations had pronounced reductions in genetic diversity. As animals were removed from the population during eradication efforts, it created a bottleneck. Since the new populations arose from the few remaining rats, only those few genetic variants left over persisted.

If enough genetic diversity is lost, and is not replaced by migrant mice from outside the original population, it might eventually lead to inbreeding and reduced fitness. If that is the case, it means that creating serial bottlenecks in the population through eradication efforts could be an effective way to weaken the rat populations to manageable levels, even if the overall population number rebounds in the short term.

I think my collaborator Dr. Jonathan Richardson (@JRichardson_44) did a nice job of succinctly outlining our findings in this Twitter thread: