Faculty Features - Multiple Paternity in Deer

Deer, Who’s the Father?

Multiple paternity in wild white-tailed deer detected using high-throughput sequencing (7 minute read)

Dawn Reding is an associate professor of Biology. Adam Koller is a Junior data science and mathematics student. This past summer, they participated in the student-faculty collaborative research program, studying DNA samples from white-tailed deer.

How would you summarize your research for curious non-experts?

Adam: We are trying to find the prevalence of multiple paternity in wild white-tailed deer. Multiple paternity is when we have a litter that is composed of half siblings, meaning that there was more than one father involved. We are trying to find the prevalence of that across Iowa.

Dawn: Biologists have long assumed that in deer, a few large, dominant males secure most mating opportunities. Recent studies with captive deer herds have started to challenge this assumption because they found many males siring offspring across the herd, and they even saw cases where offspring within a single litter had different dads (i.e., multiple paternity).

Every spring, the Iowa Department of Natural Resources (DNR) does a roadkill survey where they collect female deer carcasses and open them up to see how many are pregnant and how many fetuses they have. Iowa DNR biologist Tom Litchfield collected a small bit of tissue from each of these females and her fetuses for several years. He then approached me about examining the DNA to see if multiple paternity is occurring in wild populations.

I've had a couple of students work on this project, which started a number of years ago. Gabby Blair extracted the DNA, did all the lab work, and started the analysis. Chloe Beck helped with the data analysis. Adam, as a data science student, has been doing more in-depth rigorous analysis and writing detailed annotations for our research techniques.

We found nearly (25%) of our litters contained half-siblings, providing evidence of widespread multiple paternity in wild deer!

Photograph by Kirk Larsen.

You are using some novel techniques for this research. Would you explain those?

Dawn: The technique we are using is 2B-RAD, which is a way to subsample the genome in the same places from lots of individuals without really having to know anything about the genome. This way, we can quickly and cheaply get a lot of genetic data for a new species.

In genetics, we often work with wildlife species where there isn’t a lot of previous work. In those cases, we don’t have the reference genomes that we might have if we were working with humans, for example. In the past, 2B-RAD has primarily been used to study corals but we are applying it to mammals and wildlife species.

Our samples had been left at room temperature before they came to us so the DNA was really degraded. The regular techniques weren’t really going to work. 2B-RAD is a nice tool to use for samples that are degraded, which is a common problem when you are dealing with wildlife, especially with roadkill samples like ours. Rather than capture and potentially stress live animals, we often try to collect DNA samples from alternative sources and make use of animals that die for other reasons.

What obstacles did you face?

Adam: The whole project is one obstacle after another that you’re working through. One limitation is the time that computations take. Some programs I run might take two hours, which can be a real source of frustration.

Dawn: You get a lot of errors, and then your job is to figure out what is causing those errors and how to get around those errors. Often, you find a potential solution and then realize that your solution won’t work so you have to try another solution. Our research was a lot of that, pretty much every step of the way.

What are the ethical implications and impacts of your work?

Adam: For one, it’s a proof of principle for using 2B-RAD with wildlife. Also, there aren’t too many cases where people have their whole computer pipeline uploaded for other people to see. I can imagine a lot of scenarios where you have somebody that's really interested in the biology side of things and wants to do this kind of research, but doesn't know a lot about computer programming. If we can get this code journal uploaded, we can help them do this kind of research.

Dawn: Transparency and reproducibility of your data is important when it comes to science. So we plan to make our data freely available, and make our pipeline freely available. In theory, anybody should be able to replicate our work with the same results. So I think there's the ethics of just kind of science to it. I think the more transparent and open you are with your research and techniques, the better. That way, it’s more likely for somebody interested in using this technique to pick it up and to get running with it. Because otherwise that's a huge roadblock for a lot of people to start something new. Our research was not a straightforward path and we were building off of what other people have done, too. If we can close some of the gaps to help people get from one point to another, I think I think that can be a helpful thing.

"The only way we can make progress and further our understanding is by always questioning and challenging the status quo."

From a deer management standpoint, the ethics behind that is in managing these populations. To do so effectively, we need to better understand the basic biology and I think that's something that we kind of take for granted. Deer are relatively well studied and they are a species that is economically important, so, I think it’s important to realize that we have a lot left to understand about these populations. I hope that when people read our work, it can solidify some of those questions that people have been raising.

Just providing some basic information about mating behavior and who's actually contributing to the next generation in these populations is an important thing to know. A lot of times people like to hunt deer, and they want them to be, you know, big, strong bucks with huge antlers and that sort of thing. When people try to protect deer, they want to make sure that those are the ones siring the offspring, so that those ‘desirable traits’ stay in the population. Our results are showing that a lot more males are contributing to the next generation than just a handful of the strong dominant males, which kind of throws those strategies out the window. The only way we can make progress and further our understanding is by always questioning and challenging the status quo, and by making sure that these things that we think are real are actually real.

What advice would you give to people interested in Biology or research?

Adam: If you're an undergrad student, get to know professors. Be active and take initiative. It seems like once you get the ball rolling, opportunities come to you. But it's about taking that first step. I think if you show initiative, that's what people are looking for.

Dawn: Be open to trying things that you might not be initially interested in pursuing. My guess is that Adam probably doesn’t want to be a wildlife data scientist. But there's always connections, right? I think the skills and tools that you learn from doing a research project are going to be translatable no matter where you end up. Even if you don’t plan to be a research scientist, I’ve heard from students that past research experience is valuable in their current jobs. Research projects taught them how to problem solve, troubleshoot, communicate, and work with a team. In research, you often have to figure out how to approach problems when you don’t have clear manuals or instructions, so you learn to figure out problems on your own. There's going to be connections there and skills that are going to be helpful to you no matter what it is that you want to do.

Upcoming research projects

As they wrap up their work with white-tailed deer, Dawn and Adam will continue working on an on-going project involving gray foxes in the Midwest. Gray foxes, once a common species in the Midwest, are becoming rare. In collaboration with the Indiana Department of Natural Resources and the Wildlife Ecology Institute, Dawn and her students will be examining disease, competitors, habitat, and gene flow barriers. They will also be comparing Midwest gray foxes to their Eastern U.S. counterparts to determine whether the subspecies are distinct, a question that impacts whether Midwest gray foxes could be listed as an endangered species. Because the white-tailed deer project has provided proof of principle for 2B-RAD, Dawn will also be using it to examine regional genetics on the gray fox project.