What Can Wild Boar Feces Tell Us About Their Genetics?
By Tyjaha Steele
A pile of wild boar feces might seem like an unlikely place to look for clues about an animal’s life, but it can contain something researchers are looking for: DNA. Because animals leave genetic material behind as they move through the landscape, researchers can sometimes use those traces to learn about wildlife without having to capture the animals themselves. The challenge is that not every sample contains enough usable DNA to provide the same information.
Noninvasive genetic sampling, which uses materials such as feces, hair, or urine instead of samples collected directly from an animal, allows researchers to study wildlife without having to capture or handle individual animals. These samples can contain DNA from the animal that leaves them behind, although the amount and quality of that DNA can vary depending on the sample and the conditions it experiences.
For wild boar, researchers are interested in using genetic information to understand how populations are connected and how they differ from one another. Researchers from the University of Georgia’s Savannah River Ecology Laboratory (SREL) and Warnell School of Forestry and Natural Resources, Iwate University, the National Institute for Environmental Studies, the Fukushima Prefectural Centre for Environmental Creation, and the Wildlife Symbiosis Centre tested whether DNA from wild boar feces could provide enough information to study those differences.
“Accurate estimates of wild boar population size are essential to optimizing management strategies. Because of their size, lack of distinguishing markings, and secretive nature, traditional mark-recapture techniques are not cost-effective for large-scale population assessments, and so non-invasive techniques like fecal based mark-recapture are a promising alternative for this species,” explains Beasley, a researcher and professor from the University of Georgia’s Savannah River Ecology Laboratory (SREL) and Warnell School of Forestry and Natural Resources.
The researchers were testing a method called multiplexed inter-simple sequence repeat genotyping by sequencing, or MIG-seq, which looks for small differences in an animal’s DNA. These differences, known as genetic markers, can be used to compare individual animals and examine how animals within a population are genetically connected. MIG-seq has been used to study wildlife genetics because it can work with relatively low-quality DNA, but it had not previously been tested using fecal samples.
The researchers wanted to know whether feces could provide enough DNA for this type of analysis, and they also wanted to see how the quality of the sample affected the amount of genetic information they could recover. To test the method, researchers collected different types of samples from wild boar in Fukushima, Japan, including muscle tissue, feces collected directly from the animals, and feces left behind in traps.
Muscle tissue provided a reference point because it contained a larger amount of the animal’s DNA, allowing researchers to compare how much genetic information they could recover from each type of sample. The team then compared the genetic information found in the different samples to see how closely the fecal samples matched the information found in muscle tissue.
The results differed depending on where the fecal samples were collected. Feces collected directly from the animals contained substantially more usable genetic information than feces collected after being left in traps and exposed to the environment. On average, the samples collected directly from the animals contained 165 effective genetic markers, compared with 279 in the muscle samples, meaning they captured about 59% of the markers found in muscle. Trap-collected feces, however, contained an average of just 10 effective markers, or about 4% of those found in muscle.
That difference means the condition of a fecal sample can affect what researchers are able to learn from it. Feces contain cells from the animal, but once they are left in the environment, the DNA within those cells can degrade and become fragmented over time. Feces can also contain DNA from other organisms, which can make it more difficult for researchers to separate the wild boar’s genetic information from everything else in the sample.
The researchers found that the trap-collected samples also had higher error rates than the samples collected directly from the animals, and the amount of usable genetic information decreased as the quality of the DNA declined. Based on those results, the researchers concluded that the trap-collected samples did not provide enough genetic information to conduct population-level analysis using the MIG-seq method tested in this study.
The results were different for the samples collected directly from the animals. Those samples contained enough DNA to recover more than half of the genetic markers found in the muscle samples, while the field-exposed samples contained far fewer.
The researchers suggest that future work could focus on improving the method so it can better identify wild boar DNA and recover more genetic information from samples exposed to the environment. They also point to other approaches that could be tested, including higher-throughput sequencing and additional types of noninvasive samples.
“Due to their extensive use of wetland habitats where DNA degradation can be more severe, wild boar represent a particularly challenging species for genetic mark-recapture studies. These results, combined with prior studies examining field degradation of wild boar DNA in fecessuggest that further optimization of methods is needed to maximize the potential of molecular-based mark recapture techniques for this species,” states Beasley.
The study tested whether DNA from wild boar feces could provide the information needed for genetic analysis, and the results varied considerably depending on how the samples were collected. Feces collected directly from the animals produced substantially more genetic information than feces that had been exposed to the environment, providing researchers with a clearer picture of the conditions under which this method can and cannot recover genetic information.
The full study, Methodological Test of Genetic Population Structure Using MIG-Seq Analysis from Noninvasively Obtained Wild Boar (Sus scrofa) Feces DNA, was published in Mammal Study. Authors include Rie Saito, Natsuko Ito Kondo, Masanori Tamaoki, JaeIck Jo, Kenji Inami, and James C. Beasley.