Genetic Sampling in the Superior National Forest


What is Genetic Sampling?

Through collection of biological material such as blood, hair, feathers, or scat, natural resource professionals and scientists can effectively build a database to estimate genetic diversity, population structure, and demographic history (Supple and Shapiro, 2018). Scientists can track individual animals, families, and populations, yielding insights to phenomena such as hybridization, genetic relatedness, and geographic distribution. Solutions to genetic issues including genetic bottlenecking and resulting problems from inbreeding can also be pursued. For example, a recent study by McCartney‐Melstad et al. (2018) described the problem that human development and change happens much more rapidly than genetic accumulation can adapt. In the study, a look at the genome of the endangered eastern tiger salamander (Ambystoma tigrinum) in Long Island, New York revealed an apparent lack of genetic variation resulting from genetic fragmentation. Geographic distance and presence of roads between breeding ponds was considered a major contribution to the restriction of genetic variation (McCartney‐Melstad et al (2018). Genetic variation is very important to the health of wildlife populations because it allows the gene pool to be more diverse. Genetic diversity allows for a range in tolerances to abiotic and biotic factors such as predator avoidance or ability to survive in fluctuating temperatures. These variations allow a population to persist when confronted with unforeseen environmental pressures; especially important for endangered or threatened species.   

Figure 1. Blood samples are collected from a Peregrine Falcon chick for biological records

Figure 1. Blood samples are collected from a Peregrine Falcon chick for biological records


Monitoring of Canada Lynx

(Superior National Forest, Minnesota)


Project Overview:

On the Superior National Forest (SNF) there is an effort underway to monitor populations of Canada lynx (Lynx canadensis) which were listed under the Endangered Species Act (ESA) as "threatened" status since the year 2000 (USDA-FS, 2020). Federal authorities are mandated to implement research and conservation programs towards listed species recovery. Areas within the SNF are surveyed via snowmobile, vehicle, ATV, or on foot to find and follow Lynx tracks in the snow (Barber-Meyer et al, 2018). One main goals of the project is to build upon a database of Lynx DNA by collecting genetic material (mostly scat but sometimes hair). When a scat is collected from an animal in the field its geographic coordinates are mapped and the scat is placed in a paper bag for transport. DNA from Scat samples are analyzed at the USDA Forest Service Rocky Mountain Research Station Genetics Lab. A strength of this sampling method is that scat collection is non-invasive, meaning the research has no impact on the study subjects (do not have to live-trap or drug animals) (Barber-Meyer et al, 2018).

Figure 2. A family of Canada lynx is captured on a remote camera

Figure 2. A family of Canada lynx is captured on a remote camera

What can SNF biologists glean from genetic sampling?

Molecular "scatology" techniques are able to take scat samples and extract DNA from donor cells present on the outer lining (Laguardia et al, 2015). Through genetic analysis, scientists can identify species, determine reproduction information such as recruitment, see persistence and survivorship, and distribution and dispersal (Catton et al., 2019). Since the beginning of the study in 2001 up to the 2019 project report, at least 413 individuals were identified in 10 counties (Catton et al., 2019 and USDA-FS, 2020). Through genetic consistency among lynx kittens, researchers can track family units from year to year. Because family groups will travel together and hunt cooperatively (parent-offspring relationships) scientists can compare genotypes of samples collected in close proximity. In the 2018-2019 survey season DNA analysis confirmed 7 lynx families (Catton et al., 2019). Being able to identify individuals allows biologists to see persistence of individuals over detection years and thus get an idea of reproduction and valuable life history characteristics such as minimum age. According to Lynx researchers at the University of Massachusetts, genetic sequencing may better help scientists understand linkages between populations, connectivity and future viability (Lama, 2018). 

Figure 3. Lynx tracks are followed, GPS coordinates are recorded, and scat is collected in labeled paper bags. 

A challenge of genetic sampling:

One problem with DNA collection is what can happen with the sample itself. For example, paper bags are used to store the scat in this study to preserve the integrity of the DNA. Scats in plastic bag environments may damage or degrade the DNA because plastic can trap moisture and cause mold to grow on the sample (Aubrey et al, 2015). Some samples may be degraded as a result of natural decomposition processes or samples may have poor quality (not enough DNA present). These samples may not yield any significant information, which is a problem considering the sampling effort, time and money that goes into collection. Sometimes the samples are determined to be a non-target species as well, which could result from mis-identifying a scat during collection. According to preliminary results from the 2018 and 2019 surveying seasons, individual and sex identification was determined for 89.1% of samples sent in, leaving 10.9% of the samples useless (Pilgrim et al, 2020). 

Figure 4. A bobcat (Lynx rufus) in the Superior National Forest

Figure 4. A bobcat (Lynx rufus) in the Superior National Forest

Hybridization:

Hybridization between Canada lynx and bobcats has been documented in the United States in Maine, Minnesota, and New Brunswick (Homyack et al., 2008). Hybrids display a range of morphological features common to both lynx and bobcat. Furthermore, evidence suggests that hybrids may be successfully reproducing (Homyack et al., 2008). Over the course of the monitoring for Canada lynx in the Superior National Forest, 13 Canada lynx-bobcat hybrids have been confirmed (Catton et al., 2019). Some research suggests that hybridization will be more frequently documented between closely related species as climates shift (Chunco, 2014). It remains to be seen if lynx-bobcat hybrids will become increasingly common with forecasted climate change in the boreal forest.

Influence on Forest Management and Lynx:

Through tracking, scat collection and genetic analysis, the SNF has confirmed lynx presence, reproduction, persistence, and therefore suitable habitat in close proximity to roads and trails. SNF forest management activities often include the creation and maintenance of forest roads for access to natural resource areas. Many of these system roads and trails have vehicle traffic throughout the year. The SNF expects no more than one lynx to be "incidentally taken" (mortality) due to a collision with a vehicle each year within all ownership types within the boundary of the forest (Catton et al., 2019). Due to this threat, the SNF actively mitigates by "decommissioning" forest roads and limiting new road creation when possible. Approximately 21 miles of road within key lynx habitat has been decommissioned in order to enhance the quality of lynx habitat (USDA-FS, 2020). 

What can YOU do to help the effort?

-- If you see a Canada Lynx in the Superior National Forest, please report it to the U.S Forest Service Office.

-- If you have photographs of a Canada Lynx in the Superior National Forest, please consider sharing with wildlife biologists by contacting the U.S Forest Service Office.

-- Please use caution while driving system roads in the Superior National Forest as to avoid collisions with wildlife. 

-- Keep yourself informed and follow along by visiting the U.S Forest Service web-page


Literature Cited:

Aubry, BK. Zielinski, WJ. Raphael, MG. (2012). Biology and Conservation of Martens, Sables and Fishers: A New Synthesis. Noninvasive Survey Methods. Page 335. Cornell University Press, Nov 15, 2012.  


Barber-Meyer, S., Ryan, D., Grosshuesch, D., Catton, T., Malick-Wahls, S. (2018). Use of Non-Invasive Genetics to Generate Core-Area Population Estimates of a Threatened Predator in the Superior National Forest, USA. Canadian Wildlife Biology & Management. CWBM 2018: Volume 7, Number 1. ISSN: 1929-3100. 


Catton, T, Ryan, D, Grosshuesch, D, Pilgrim, K. (2019). Summary of the Superior National Forest's 2019 Canada lynx (Lynx canadensis) DNA database and population monitoring. 09/04/2019. 


Chunco, A. J. (2014). Hybridization in a warmer world. Ecology and Evolution, 4(10), 2019-2031.


Homyack JA, Vashon JH, Libby C, Lindquist EL, Loch S, McAlpine DF, Pilgrim KL, Schwartz MK. 2008. Canada lynx-bobcat (Lynx canadensis × L. rufus) hybrids at the southern periphery of lynx range in Maine, Minnesota and New Brunswick. Am Mid Nat 159: 504–508.


LAGUARDIA, A., WANG, J., SH I, F.L., SH I, K. & RIORDAN, P. (2015). Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China. Zoological Research


Lama, T. 2018. UMass Amherst Leads Team in First Sequencing of Canada Lynx Genome. University of Massachusetts. News & Media Relations. Retrieved from: 

https://www.umass.edu/newsoffice/article/umass-amherst-leads-team-first-sequencing 


McCartney‐Melstad, E., Vu, J. K., & Shaffer, H. B. (2018). Genomic data recover previously undetectable fragmentation effects in an endan‐ gered amphibian. Molecular Ecology, 27(22), 4430–4443. https://doi. org/10.1111/mec.14892


Pilgrim, K. Ingra, O. Swartz, M. (2020). Minnesota lynx (Lynx canadensis) 2019 samples; Batches 1 and 2. Retrieved from: USFS Rocky Mountain Research Station. National Genomics Center for Wildlife and Fish Conservation. Date Issued: April 27, 2019; updated February 14, 2020. 


Supple, M. A., & Shapiro, B. (2018). Conservation of biodiversity in the genomics era. Genome Biology, 19, 131. https://doi.org/10.1186/ s13059-018-1520-3


United States Department of Agriculture-Forest Service (USDA-FS). 2020. Canada Lynx Survey and Monitoring. Retrieved from:  https://www.fs.usda.gov/detail/superior/landmanagement/resourcemanagement/?cid=stelprdb5209910 


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