The development of real-time PCR assays for species and sex identification of three sympatric deer species from noninvasive samples

Abstract

Reliably identifying the species occupying an area is an essential part of any wildlife conservation study or sustainable management plan, especially when dealing with a harvested species such as deer. Traditional deer monitoring techniques such as faecal standing crop or faecal accumulation rate estimates cannot accurately identify deer species based on pellet morphology where more than one deer species is present. This study presents real-time PCR assays for the identification of fallow deer (Dama dama), red deer (Cervus elaphus), and sika deer (Cervus nippon) species from pellet samples, and real-time PCR sex determining assays to amplify the ZFX and SRY gene of all three deer species. These assays successfully identified tissue and faecal pellets of all three species with no cross species amplification. Sex determination was successful from both tissue and faecal pellets samples, with the assays amplifying as little as 4 pg of nDNA, making them suitable for use with the often poor quality and low quantity DNA found in noninvasive samples. Application of these assays will provide reliable species presence and distribution data not possible with traditional methods as well as valuable information on sex ratios which can inform sustainable wildlife management and harvest strategies.