Evaluation of in-field DNA degradation of mitochondrial- and genomic DNA in snowsampled faecal pellets from rock ptarmigan (Lagopus muta)

Abstract

The use of non invasive genetic sampling (NGS) have become increasingly relevant in genetic studies applied to ecology. Reliable methods should be tailored to species and environments. Rock ptarmigan (Lagopus muta) spend their entire lifecycle in the alpine region and roost in snow holes to save energy and avoid predation. Faecal pellets (FP) were collected from 20 individual rock ptarmigan snow roosts in the Lifjell mountain area in Telemark, Norway repeatedly between 17 january and 7 july, 2010. DNA was extracted from 146 samples, and degradation evaluated in PCR products of mitochondrial DNA (mtDNA), and 3 genomic DNA (nDNA) microsatellites. For mtDNA, the mean duration in 20 roosts was 73.8 and 59.4 days respectively in a best and worst case scenario. For the 3 nDNA microsatellites, mean duration times varied between 38.8 - 58.1 and 20.9 - 45.8 days respectively in a best and worst case scenario. MtDNA had a significantly longer duration than nDNA, and duration times between individual nDNA microsatellites varied significantly. Overall PCR error rates in the study period were 0.48 for mtDNA and 0.53 - 0.68 for 3 nDNA microsatellites. DNA degradation appeared to accelerate considerably when frozen, snow covered FPs eventually became exposed to higher temperatures and precipitation during the spring snow-melt. FPs from rock ptarmigan snow roosts serves as a promising DNA source in genetic studies, and method may be applied to other snowroosting grouse.