Sex identification of northern ungulates using low quality and quantity DNA

Abstract

We evaluated PCR primer sets to determine the most effective technique for identifying sex of northern ungulates. We sought markers that required only a single pair of primers to amplify both X-and Y-linked alleles; that amplified X-and Y-linked products that were easily distinguishable using agarose gel electrophoresis; and that produced short amplicons amenable to amplification using DNA of poor quality and low quantity, as is often found in non-invasively collected samples such as feces. Primer pairs KY1/KY2 and SE47/SE48, which amplify X-and Y-specific alleles of the amelogenin gene, met our criteria and were tested for moose (Alces alces), mountain goat (Oreamnos americanus), Sitka black-tailed deer (Odocoileus hemionus sitkensis), and caribou (Rangifer tarandus). KY primers amplified shorter PCR products than did SE primers; moreover, SE primers inconsistently amplified certain Y-chromosome products, creating potential for misidentification of sex. DNA fragments amplified using KY primers were sequenced for each species, allowing us to characterize a 45-bp deletion for Y-linked alleles (136-bp product) relative to X-linked alleles (181-bp product) in all species and a 9-bp deletion in the X-linked allele of moose relative to other species. This is the first sex-determination technique using PCR reported for several ungulate species of Alaska. Although other protocols exist for cervids and bovids, this is the first report of markers meeting the aforementioned criteria for Odocoileus, the most abundant and intensively managed genus of large mammals in North America.

Estimating sex-specific abundance in fawning areas of a high-density Columbian black-tailed deer population using fecal DNA

“…Unique genotypes obtained from DNA in noninvasively collected fecal pellets or hair samples can be used to identify individuals upon initial capture (i.e., identification via DNA) and recapture, enabling the pellet or hair samples to take the place of physically marked individuals. Fecal DNA also can be used to accurately differentiate sexes (e.g., Brinkman and Hundertmark , Ebert et al ) and assess sex ratios (e.g., before vs. after harvest; Pierce et al ). Lastly, the genotypic data generated in such approaches can be used for additional purposes, such as to evaluate genetic diversity or familial relationships (Waits and Paetkau , Yoshizaki , Colson et al ).…”

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 (2010Brinkman et al ( , 2011. We resampled transects 2-8 times/annual field season (approx.…”

“…Feb-May) at 10-day intervals. During poor conditions (warm summer months with abundant rainfall), Brinkman et al (2010) found that pellets should be collected 10 days following deposition to yield sufficient DNA. Starting and ending date of sampling occasions was dependent on date of snowmelt and green-up.…”

An eDNA-Based SNP Assay for Ungulate Species and Sex Identification

“…A logical further step of this method is to use it for the determination of sex-specific browsing patterns. Some studies have determined sex from eDNA samples using traditional fragment-based methods [11,12]. Forensic applications have used single nucleotide polymorphisms (SNPs) for sexing samples, but fewer eDNA applications use SNPs.…”