Effects of Exposure on Genotyping Success Rates of Hair Samples from Brown and American Black Bears

Abstract

Noninvasively collected hair samples have been used in numerous studies to answer questions about the demographic and genetic status and trends of wildlife populations. In particular, these methods are well-suited for researching and monitoring ursid populations, which are typically difficult to study because of their rare and cryptic nature. Recently, researchers have taken increasing advantage of natural bear behaviors to obtain hair samples for genetic analyses by conducting surveys of bear rubs (objects that bears rub against such as trees and power poles). The low quality and quantity DNA in noninvasively collected samples, however, can result in low genotyping success rates, which may be exacerbated by potentially lengthy duration of environmental exposure. We investigated the effects of environmental exposure (sunlight, moisture, and duration of exposure) on genotyping success rates of brown bear Ursus arctos and American black bear Ursus americanus hair samples. We exposed a total of 238 hair samples from one brown bear and one black bear to multiple treatments for either 30-d or 60-d, periods consistent with collection intervals of recent bear rub survey projects. Sample treatments consisted of full or dappled sunlight, kept dry or saturated with water one to two times daily. We genotyped each sample at three microsatellite loci commonly used in noninvasive genetic studies of bear populations. Our results were consistent with predictions, with all three factors significantly reducing genotyping success rates. Based on our results, we recommend that the specific conditions of field exposure be considered when selecting a suite of microsatellite markers for noninvasive genetic sampling projects, and that researchers carefully consider the duration and environmental conditions that hair samples will be exposed to when designing field studies. Limiting exposure to moisture and sunlight by collecting hairs from bear rubs at relatively short intervals and selecting dry and shaded sites should reduce DNA degradation and thus result in higher genotyping success rates.

Seeking efficiency with carnivore survey methods: A case study with elusive martens

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Genetic tagging in the Anthropocene: scaling ecology from alleles to ecosystems

“…Developing new means to counteract the drawbacks of MIS approaches can help address research costs and enhance the welfare of study animals (e.g., Stetz et al. , Lamb et al. ).…”

Optimizing Selection of Brown Bear Hair for Noninvasive Genetic Analysis

“…The success rate of laboratory analyses is affected by many aspects of hair sample quality aside from tuft size, including the length of time hairs are on the wire or other capture device (related to the frequency with which the sampling sites are checked; Stetz et al 2015), the type of hair (e.g., guard hairs vs. underfur), and weather conditions (e.g., moisture; Mowat and Strobeck 2000, Beier et al 2005, Kendall and McKelvey 2008). Amplification success rates are also strongly influenced by extraction and genotyping protocols used in the lab (Waits and Paetkau 2005, Broquet et al 2007).…”