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New Way of Counting Scientists Utilize New DNA Analysis of Deer Feces to Estimate Population of Pacific Herd

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New Way of Counting Scientists Utilize New DNA Analysis of Deer Feces to Estimate Population of Pacific Herd Story by Kyle Orr New Way of Counting Scientists Utilize New DNA Analysis of Deer Feces to Estimate Population of Pacific Herd nvironmental scientists with the aircraft over dense forests is not practical California Department of Fish due to poor visibility through the natural and Wildlife and researchers canopies. Road surveys have their own from the University of California drawbacks and are considered unreliable Davis are testing a new way of in forested environments because of the Edetermining the abundance of key deer limitation to accessible roads. populations. The method, which was first Consequently, CDFW wanted a cost tested in Alaska, involves the collection analysis of implementing a long-term moni- and analysis of DNA contained in deer fecal toring program for mule deer using recent samples. developments in non-invasive fecal DNA The shift in survey methods should technology. A research paper, “Noninvasive lead to more accurate estimates and correct Genetic Spatial Capture-Recapture for Esti- some of the inherent inaccuracies that oc- mating Deer Population Abundance,” pro- cur from roadside surveys, as well as spare vided a detailed explanation of the process. the animal the stress from hovering helicop- CDFW environmental scientist Terri ters during aerial counts. Weist was one of three authors of the re- Mule deer (Odocoileus hemionus) abun- search paper on a migratory herd of black- dance has fluctuated significantly over the tailed mule deer along the western slope past century in the western United States, of the central Sierra Nevada. The research and understanding the complex reasons for involved DNA sampling of deer pellets to such fluctuations is vital. Management of provide a genetic “fingerprint” with enough deer herds in California requires knowledge information to eliminate the need to cap- of population parameters in order to ef- ture animals. CDFW funded the research fectively determine hunting quotas, season and UC Davis conducted the laboratory dates and direct activities that will ensure work and statistical analysis. Similar field population viability. However, few existing work has been conducted elsewhere in the methods of determining abundance are state to estimate the population of other equally effective across all habitat types, herds. so over the years the need has grown to “This method provides us with another Kristof Toshimi © develop alternative methods. tool in the toolbox for obtaining accurate Estimating populations of mule deer by information on the population health of our Photo 8 MARCH—APRIL 2017 March_April_2017.indd 8 5/4/2017 3:49:06 PM Estimating the population abundance of deer herds along the western slope of the central Sierra Nevada has been challeng- ing for researchers because of the animals’ natural habitat of dense forests and heavy vegetation. A new method being tested by the California Department of Fish and Wildlife and UC Davis promises to provide better estimates in herd counts through DNA extracted from pellets. The innovative procedure will eventually free researchers from reliance upon the more costly and less reliable aerial and roadside surveys. OUTDOOR CALIFORNIA 9 March_April_2017.indd 9 5/4/2017 3:49:07 PM CDFW File Photo CDFW file photo A researcher with the UC Davis uses deer herds,” Weist said. “It has proven to be species is hunted for subsistence by local a plastic vial to collect pellets left by a effective and provides reliable estimates of residents, as well as for sport. migrating deer herd along the western wildlife species that may be elusive, low in At 2,577 square miles, Prince of Wales slope of the central Sierra Nevada. numbers or otherwise difficult to detect.” Island is considered the fourth-largest Through information collected through California researchers based the pro- island in the United States and is among the extracted DNA, researchers will cess on a precursor study of Sitka black- the 100 largest islands in the world. Even identify individual bucks and does. tailed deer undertaken over the last decade with all the open land, by the late 1990s, Biologists will follow up with field in Alaska. There, scientists extracted DNA hunters on the island struggled to harvest samples, and through the matching of from deer pellets rather than the traditional sufficient deer to meet their needs. State DNA information, will be able to better means (hair or tissue samples). The research wildlife management authorities offered up estimate ungulate abundance, size, served as the source for a seminal study, three possibilities for the decline: overhunt- health and migration patterns. “Estimating Abundance of Sitka Black- ing, predators or a decline in deer habitat Tailed Deer Using DNA from Fecal Pellets,” quality due to past logging operations. by Todd J. Brinkman, an assistant professor Wildlife experts concluded that they needed in the Human Dimensions of Wildlife Labo- to better understand the current status ratory at the University of Alaska Fairbanks. and emerging trends of the population to Brinkman, who has a doctorate in wildlife determine whether the problem arose from ecology, published the article in 2011 for the inadequate deer numbers or other factors. Journal of Wildlife Management. “Previous to this work we had no idea The study was conducted on Prince what the deer densities were in south of Wales Island, one of the islands of the Alaska or the entire range of Sitka deer,” Alexander Archipelago in the Alaska Pan- Brinkman said. “The approach was born of handle. Brinkman called the study the first necessity.” in the nation to precisely estimate ungulate For three years, from 2006 to 2009, abundance using DNA from fecal pellets. Brinkman and his colleagues collected deer According to Brinkman, Sitka black-tailed dung along identified trails, marking and re- deer (Odocoileus hemionus sitkensis) is a surveying numerous times. They identified subspecies of mule deer and serves as the 10,569 pellet groups and retrieved pellets most important big game species both on from 2,248 of them for DNA extraction. the island and in southeast Alaska. The Pellets were preserved in plastic vials filled 10 MARCH—APRIL 2017 March_April_2017.indd 10 5/4/2017 3:49:07 PM with ethanol. Researchers then extracted Lake. They divided the space into three sub- tive and procedures are being increasingly DNA from 1,156 samples and genetic mark- sections to ensure complete coverage. The streamlined.” ers specific to deer were used to identify 737 scientists cleared the collection area of fecal Using statistical programs, researchers individuals. pellets and then re-sampled the area three estimated the Pacific herd consisted of 2,600 The evidence helped researchers more times to determine how many of the animals in 2013 and 2014. In this case, DNA discover potential causes for the difficulty previously identified individuals were re- analysis determined the sex but not the age hunters had encountered in harvesting deer. encountered and how many new individuals of the deer. Brinkman determined “the most plausible also were present. CDFW deer surveys using the fecal cause of the deer hunting dilemma is habi- Testing and analysis of the pellets was DNA process are underway in other parts tat change stemming from the boom and performed by Dr. Benjamin N. Sacks, a UC of the state, including Tehama, Plumas, bust of the logging industry. Those changes Davis adjunct professor at the Mammalian Imperial, Riverside, Sacramento and Marin have dramatically altered hunter access to Ecology and Conservation Unit, Veterinary counties. CDFW scientists expect to use the preferred hunting habitats, with negative Genetics Laboratory. Sacks co-authored the technique on an even larger scale, as similar consequences for hunter success.” California study on the noninvasive esti- studies are planned for 14 deer herds across Brinkman subsequently was contacted mation of deer population with Weitz and a dozen counties in the north central por- by numerous wildlife departments, includ- Jennifer L. Brazeal, a doctoral candidate at tion of the state. Once baseline population ing CDFW, about his study and has offered the university. The analysis was jointly con- data can be collected, researchers will shift encouragement and advice to wildlife agen- ducted with CDFW, and Sacks said scientific to periodic monitoring to track the trends cies that face situations similar to those advances are making the process increas- throughout the state. highlighted in the Alaska study. CDFW ingly feasible. Sacks credited Brazeal with began to test its version of the process in playing a “leading role” in the study, praising 2011 in Mendocino County before beginning his colleague for refining the data analysis. Kyle Orr is an information officer with the the Pacific deer herd study in 2013. “Genetic technology is moving fast,” California Department of Fish and Wildlife. His The migratory Pacific herd roams over Sacks said. “It is becoming more cost effec- stories have appeared before in Outdoor California. approximately 568 square miles of public and private land along the western slope of the Sierra Nevada in El Dorado and part of Placer counties. The herd’s summer range shrinks significantly to nearly 330 square miles, but the terrain remains steep, ris- ing from 4,800 feet to nearly 9,900 feet in Joey Johnson elevation. The land consists primarily of © Ponderosa pine, red fir, lodgepole and white bark pine mixed with shrubs of huckleberry Photo oak, snowberry and sagebrush. Meadows provide important grasses and forbs during fawning season. CDFW and UC Davis researchers col- lected deer pellets during the summer from the range near Icehouse Reservoir and Loon There are six subspecies of mule deer in Cali- fornia: Columbian black-tailed deer (Odocoileus hemionus columbianus), Rocky Mountain mule deer (O.h. hemionus), California mule deer (O.h. californicus), Inyo mule deer (O.h. inyoensis), burro deer (O.h. ermicus) and southern mule deer (O.h. fuliginatus). The natural habitat for deer is thick vegetation and heavy forest with an overhead canopy that offers concealment and protection from predators.
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