Interview with the author: Human activity can influence the gut microbiota of Darwin’s finches in the Galapagos Islands

We interviewed Sarah Knutie (an Assistant Professor at the University of Connecticut) about the research she led examining how humans can shape the microbiota of Darwin’s finches in unexpected ways. Read the full text below:

Knutie, SA, Chaves, JA, Gotanda, KM. Human activity can influence the gut microbiota of Darwin’s finches in the Galapagos Islands. Mol Ecol. 2019; 28: 2441– 2450. https://doi.org/10.1111/mec.15088

Image credits: Kiyoko Gotanda
  • What led to your interest in this topic / what was the motivation for this study? 

The inspiration for this project came from our observations of Darwin’s finches trying to steal food from our plates and my co-authors’ recent paper (De Leon et al. 2018) showing that the diet of finches differed in urban and non-urban areas. Since diet can influence the gut microbiota of the host, Kiyoko and I decided to return to the same field site and look at how the gut microbiota of Darwin’s finches differ among sites with varying exposure to human activity. However, at the time, Kiyoko and I were both post-docs without funding for our idea, so we decided to crowdfund the project (Kiyoko was more successful than me!). With help from our crowdfunding campaign and our own out-of-pocket money, we were able to head to the Galapagos for a few weeks to collect the fecal samples for our study.

De León, L. F., Sharpe, D. M., Gotanda, K. M., Raeymaekers, J. A., Chaves, J. A., Hendry, A. P., & Podos, J. (2018). Urbanization erodes niche segregation in Darwin’s finches. Evolutionary Applications.

What difficulties did you run into along the way? 

We decided to do all of the bacterial DNA extractions in the Galapagos since we were unsure whether we would be able to export our samples immediately after the field season. However, equipment and lab space can be hard to come by in the Galapagos. Therefore, we created a clean extraction space in our apartment with whatever equipment I could buy on the cheap and transport from the US to our Galapagos “lab”. Specifically, I brought a sous vide for the heat step and rigged a vintage vortex for the agitation step of the extraction. Was that just an #OverlyHonestMethods moment?

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

Even though De Leon et al. (2018) found that the diet of Darwin’s finches differed in response to urbanization, I was not confident that we would find parallel differences in the gut microbiota. Although the field sites vary in their exposure to human activity, they are geographically quite close to each other. Therefore, a part of me thought that our samples sizes would not be large enough to detect an effect of site on the gut microbiota. Fortunately, my gut instinct was wrong and our study demonstrated that human activity can impact the gut microbiota and body mass of finches, even among adjacent sites.

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

My lab is currently looking at whether the gut microbiota of urban and non-urban Darwin’s finches influences their immune response to the invasive parasitic nest fly Philornis downsi. Since the gut microbiota can affect the development and maintenance of the immune system and the gut microbiota of finches is affected by human activity, it is possible that urban finches defend themselves differently against the invasive parasite than non-urban birds.

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

Start by being present. My favorite project ideas are inspired by observations in the field.  Once you are inspired, be a sponge. Read everything that you can about your topic and if you have the opportunity, talk with experts in the field. Then, create a solid study design using the scientific method; think through all possible outcomes and draw graphs of your predicted results. Although establishing patterns (like in the published paper) is very important to understand the underlying function of the microbiota, try to determine causation with an experiment, if possible. If applicable, when you start your DNA extractions, especially if you are working with birds, talk to experts in the field. Many colleagues and myself have resolved issues with the extraction protocols and sequencing and might be able to help.  

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

I have learned to find collaborators who I enjoy working with on projects. Science is so much more fun when you can interact with brilliant and kind people.

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

Human presence in the Galapagos Islands is affecting the gut microbiota and body mass of Darwin’s finches.

How genomic data can determine the role of elk in the transmission of bovine tuberculosis in Michigan, USA

Figure credit: Sheri Raifsnider, Michigan Department of Natural Resources

In areas where wildlife and livestock coexist and become infected with bovine tuberculosis (bTB), a major question in disease management is determining the roles of different species in disease maintenance. In Michigan, white-tailed deer are known to be the primary wildlife host for bTB, but controversies continue over the role that elk may play in bTB maintenance and spread. In this study, we used pathogen genomic, spatial and temporal data to identify M. bovis lineages associated with deer, elk and cattle, and quantify the probability of M. bovis transmission between them. A particular challenge in common with many other systems is the reliance on convenience sampling, potentially introducing biases that can influence the inferred roles of each species. Using a suite of carefully chosen down-sampling scenarios, our analyses showed that, while samples from elk are present in two of three phylogenetic clades, there was no evidence for significant transmission between elk and cattle. Our results are consistent with inter-species transmission in Michigan being maintained by deer. Thus, the major management focus should continue to be controlling disease in the endemic deer population. This study shows the value of genomic data for examining bacterial pathogen transmission at the wildlife-livestock interface -Liliana Salvador (University of Georgia) and Rowland Kao (University of Edinburgh)

Salvador, LCM, O’Brien, DJ, Cosgrove, MK, et al. Disease management at the wildlife‐livestock interface: Using whole‐genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA. Mol Ecol. 2019; 28: 2192– 2205. https://doi.org/10.1111/mec.15061

Summary from the authors: What do gut microbes do for their hosts?

Despite a flood of recent interest in this question for humans, the answer remains a mystery for the vast majority of animals. Gut microbiota are often assumed to provide nutritional benefits, but many insects acquire the majority of their nutrients during larval feeding, leaving less opportunity for bacterial contributions to adult nutrition. In fact, when food is scarce the adult gut flora might even impose a net reproductive cost.

Photo courtesy of A. Ravenscraft

We tested this prediction in the Mormon fritillary butterfly (Speyeria mormonia), a denizen of mountain meadows in the American Rockies. We experimentally subjected wild caught butterflies to a brief burst of antibiotics to disrupt their gut flora and then maintained them with either ad lib feeding or a 50% starvation diet. Contrary to our
predictions, the number of bacteria in the gut did not correlate with butterfly fitness even if the butterfly was starved, though a few individual bacteria species were associated with increased or decreased lifespan.

Overall, these results suggest that gut bacteria may have little net
effect on some animals. – Alison Ravenscraft, NIH PERT Postdoctoral Fellow, University of Arizona

Ravenscraft A, Kish N, Peay K, Boggs C. No evidence that gut microbiota impose a net cost on their butterfly host. Mol Ecol. 2019;28:2100–2117. https://doi.org/10.1111/mec.15057

Interview with the author: Do estimates of contemporary effective population size tell us what we want to know?

For our first interview that goes behind the scenes of one of recent paper, it is our pleasure to introduce Professor Nils Ryman from Stockholm University. Read the associated paper here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15027

What led to your interest in this topic / what was the motivation for this study? 
I have since the beginning of my career had a strong interest in conservation genetics, and because the concept of effective population size (Ne) is a key parameter in this field it has long been in my interest to understand this complex and often unintuitive concept. Several years ago my colleagues Ola Hössjer (professor of mathematical statistics) and Linda Laikre (professor of population and conservation genetics) formed an interdisciplinary team aiming at improving the mathematical tools for understanding various types of effective population size in populations under migration, and then applying such tools to practical conservation and molecular ecology questions. This is one of the studies applying the tools to understand what we expect to estimate when assessing Ne for non-isolated populations.

Brown Trout (photo Anastasia Andersson)

What difficulties did you run into along the way? 
Effective population size (Ne) is a difficult concept, and my experience is that you always run into difficulties when working with it. Also, it is difficult to explain, so presenting this study in text that can be understood by molecular ecologists was a challenge. Another difficulty, along the rather long way leading up to the theoretical framework that provides the basis for this study, has been to establish common grounds in our interdisciplinary team. Although we population geneticists and molecular ecologists might think that we are rather strong in theory, we are very far away from the world of a mathematician.

What is the biggest or most surprising finding from this study? 
That the different effective population sizes that quantify different types of genetic change (inbreeding, allele frequency variance, additive genetic variance and linkage disequilibrium in this case) behave so differently in populations that are subject to even small rates of immigration.

Moving forward, what are the next steps for this research? 
We have several planned studies aimed at further improving our understanding of different types of effective sizes in metapopulations. In practical conservation, guidelines and recommendations for such systems are largely lacking. Understanding the effects of subpopulation extinction on metapopulation effective size is one topic. Also, an obvious question is how do we measure inbreeding effective size in populations that are not isolated but parts of metapopulations? This is often the rate of genetic change that we want to quantify, but when we use the most frequently available software we do not measure this rate at all in populations under migration. Further, as we discuss in the paper, there are also good reasons for focusing more on inbreeding itself, rather than the inbreeding effective size.

What would your message be for students about to start their first research projects in this topic? 
Read the classic, theoretical population genetics literature and make sure that you have a good grip on assumptions and definitions! The work by e.g. Crow & Kimura, Wright, Nei, and others are still essential to know and understand. I am actually worried that the theoretical part of population genetics is forgotten in the face of the genomic explosion. I think that would be most unfortunate and I agree with my close friend and colleague Fred Allendorf who is “concerned that current training focuses too much on techniques and too little on understanding the conceptual basis needed to interpret these data” (Molecular Ecology (2017) 26, 420-430).

What have you learned about science over the course of this project? 
When working with Ne, always be prepared for two steps forward and then at least one step back.

Describe the significance of this research for the general scientific community in one sentence.
Currently applied methods for assessing rates of inbreeding and loss of additive genetic variation do not tell us what we want to know – in spatially structured populations they do not measure the actual rates.

Metapopulations (Photo Nihls Ryman)

Describe the significance of this research for your scientific community in one sentence.
Different types of Ne – here the inbreeding, variance, additive genetic variance and linkage disequilibrium effective sizes – behave very differently in populations under migration as compared to completely isolated ones.