Disease can lead to major declines in wildlife populations. Yet after population decline, there is often recovery but what are the long term genetic consequences of this process? In this blog post, Don McKnight from James Cook University in Australia gives us a behind the scenes take on a paper that he led exploring the genetic consequences of frog populations rebounding from chytrid fungus outbreaks. Nice to hear a ‘good news’ story about chytrid for a change! Read the full paper here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15108

• What led to your interest in this topic / what was the motivation for this study?

I have always loved reptiles and amphibians, and the loss of amphibians due to chytridiomycosis is extremely concerning. So, I was interested both in studying the long-term consequences of the disease and in contributing to amphibian conservation efforts, but I was especially excited by this system, because populations here are actually recovering from the outbreak. Chytrid papers are often very bleak and depressing, so to have a system where the frogs are rebounding is fantastic. It is really exciting to be able to write papers about recoveries instead of declines, and studying these recovered populations can shed a lot of light on how populations respond to diseases and what factors allow them to recover.

• What difficulties did you run into along the way?

The field work was challenging. I love being in the field, but the waterfall frog earned its name, and we had to climb quite a few falls to get the samples, especially since our sampling design required us to collect samples from really remote sections of the streams.

The biggest difficulty, however, was a lack of pre-decline samples. Ideally, we would have compared samples that were collected before the decline with the samples we collected after the decline, but the only pre-decline samples we could find were in formalin, and, despite a lot of effort, we couldn’t get enough usable DNA out of them. They were just too degraded. That meant that we had to use our post-decline data to infer what changes were caused by the outbreak, and that’s a much more challenging proposition.

• What is the biggest or most surprising finding from this study?

The biggest finding is that, if you want to retain genetic diversity, it is important to have large sections of high-quality habitat in areas that aren’t ideal for the disease. We’ve always assumed that these refugia were important for frogs in the wet tropics, but no one had previously explored how their habitat quality influences population genetics. Thus, our result isn’t necessarily surprising, but it’s not a result that previous studies have really highlighted or documented in this way, so it’s useful to actually have the data to support the genetic benefits of having large refuge populations and conserving habitat for those populations.

• Moving forward, what are the next steps for this research?

We would like to expand both the number of species and populations that we are working with. Currently, we are examining the genetics of another species in this system, the Australian lacelid frog (Litoria dayi), that went through the same declines but has never recovered, and we want to compare its genetics with the species that have recovered. It would also be useful to replicate these studies over more populations and regions to see if the extent of refuge habitat available reliably predicts how much diversity a population retained during the disease outbreak.

• What would your message be for students about to start their first research projects in this topic?

I have two main pieces of advice. First, plan on everything taking longer than you think it will. Between the field work, laboratory work, and quality control filtering, there is a lot that has to happen before you can even begin analyses, and the analyses themselves are very time consuming.

Second, and most importantly, find knowledgeable mentors and a good group of people to work with. This type of research is very involved, and the learning curve starting out is pretty steep, so having good mentors to teach and support you is critical. I was fortunate to have great mentors and a fantastic group of people around me who really knew what they were doing and took the time to teach me, and that was vital for me as I started doing genetics research.

• What have you learned about science over the course of this project? 

My background prior to this research was in ecology, rather than genetics. So, I personally learned a great deal about population genetics. More generally though, I think that there is a really nice melding of basic ecology and genetics that is often lacking. There are a lot of great ecologists who know very little about genetics, and conversely, a lot of great geneticists who lack a good ecology background, and I think that having both of those skill sets and knowledge bases is really useful and provides a much broader understanding of the system being studied. 

Describe the significance of this research for the general scientific community in one sentence.

This research highlights the importance of habitat refugia in conserving disease-afflicted species.

Describe the significance of this research for your scientific community in one sentence.

This research is one of the first population genetics studies of populations that are recovering from a disease outbreak, and it advances our knowledge of that recovery process and the long-term genetic consequences of disease outbreaks.

Citation

McKnight, DT, Lal, MM, Bower, DS, Schwarzkopf, L, Alford, RA, Zenger, KR. The return of the frogs: The importance of habitat refugia in maintaining diversity during a disease outbreak. Mol Ecol. 2019; 28: 2731– 2745. https://doi.org/10.1111/mec.15108