Individual identification of Sitka black-tailed deer (Odocoileus hemionus sitkensis) using DNA from fecal pellets

Abstract

We tested a protocol for extracting DNA from fecal pellets from Sitka black-tailed deer (Odocoileus hemionus sitkensis) and evaluated genotyping performance of previously developed microsatellite markers as well as a suite of new markers designed specifically for this study. We screened 30 microsatellites, and identified 7 (23%) loci including 4 new markers, that fit well into a single multiplex and consistently genotyped deer with low error rates. DNA was extracted from 2,408 fecal-pellet samples. Of those, 1,240 (52%) were genotyped successfully at all 7 markers allowing identification of 634 genetically unique deer. Using DNA from fecal pellets collected in the field was an effective technique for identifying and distinguishing among deer.Keywords Alaska Á DNA Á Feces Á Microsatellites Á Odocoileus hemionus sitkensis Á Sitka black-tailed deer Densely vegetated environments within Southeast Alaska have hindered the collection of basic population parameters on Sitka black-tailed deer (Odocoileus hemionus sitkensis), the most important terrestrial game species in this region.Because of challenges in sampling deer via direct observation (e.g., aerial surveys), we sought non-invasive methods using genetics (Waits and Paetkau 2005) to answer key population questions. We tested a protocol for extracting DNA from fecal pellets and evaluated genotyping performance of previously developed microsatellite markers as well as a new suite of markers designed specifically for Sitka black-tailed deer. Whereas several studies have been conducted on wild carnivores using noninvasive genetic approaches to identify individuals (Waits and Paetkau 2005; Kendall et al. 2008; Schwartz and Monfort 2008), field research identifying individuals using DNA from the feces of wild ungulates has been rare (Flagstad et al. 2000;Gebremedhin et al. 2009 demonstrated that deer feces collected from the rectum are a viable source of DNA. We now seek to assess the utility of fecal DNA from naturally deposited pellets to genotype deer (Odocoileus spp.).During 2006-2008, we collected 4-6 fecal pellets from pellet groups deposited by deer in three watersheds on Prince of Wales Island in southeast Alaska. To minimize DNA degradation from ambient environmental conditions and to maximize DNA recovery, we collected pellets from transects that were cleared of old pellets 10 days earlier. We preserved pellets in 95% ethanol, and stored pellets at room temperature until DNA was extracted. During collection, pellet samples were classified based on appearance as: good (freshly deposited in a clumped distribution with pellets intact, surface with a glossy sheen, and/or a detectable coating of mucus), average (slightly older or more weathered pellet group that still had intact pellets with smooth surfaces, but that lacked a tightly clumped distribution, glossy sheen, and mucus), or poor (spread-out groups with rough-surfaced pellets which were often showing signs of decomposition). Because early experimentation revealed

Sex Determination of Sika Deer (Cervus nippon yesoensis) Using Nested PCR from Feces Collected in the Field

“…From a population demographic perspective, estimating sex ratios and monitoring trends in abundance can be available [16,29]. By combining them with other genetic analyses using mitochondrial DNA or microsatellite DNA [18][19][20][21][22], advanced details of population dynamics and genetic diversity can be revealed [4]. Finally, it can be expected that these combined analyses would contribute to carry out effective population control and to reduce the extinction risk of sika deer.…”

Fine‐scale spatial genetic structure of deer in a suburban landscape

“…We calculated the probability of identity for siblings for each locus and the combined multilocus assay (Sib P (ID) ; Waits et al ), identified matching genotypes, and calculated the number of unique individuals in GeneCAP (Wilberg and Dreher ). We considered a Sib P (ID) of 0.05 sufficient to correctly identify matching genotypes (Schwartz and Monfort , Brinkman et al ). We applied an iterative approach to identify matching genotypes.…”

Using DNA to test the utility of pellet-group counts as an index of deer counts

“…We collected 4–6 pellets for DNA analysis from each pellet group encountered on deer‐trail transects. We followed sampling, DNA extraction, genotyping, and analysis protocols described in Brinkman et al , ). We re‐sampled transects 2–8 times/annual field season (approx.…”