Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates: A case study with Pyrenean chamois

• DOI: 10.1371/journal.pone.0216345
• Publication Date: 2019-05-22T17:28:31Z
• Authors: Johan Espunyes; Carme Espunya; Sara Chaves; Juan Antonio Calleja; Jordi Bartolomé; Emmanuel Serrano
• Keywords: Herbaceous plant

The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) emerging DNA-based methods being most relevant. In this work, we refined optimized a qualitative approach combining PCR amplification long trnL(UAA) ITS2 fragments capillary electrophoresis (PCR-CE), instead short massive sequencing technologies reported. To do so, developed controlled assay using stabled Pyrenean chamois specimen (Rupicapra pyrenaica pyrenaica), which included representative herbaceous shrubby species. We also assessed impact sample freshness determination mountain caprinae by exposing outdoor environment three weeks. Faecal from both experiments were analysed PCR-CE semi-quantitative CMA in order compare pros cons approaches. Our results show that all offered species detected methodologies although over-detected shrubs compared At same time, degradation due sustained climate exposure limiting factor molecular analysis, but not CMA. Taken together, our suggest information obtained can be interchangeable when are fresh (less than one week after deposition) but, afterwards, underestimates probably DNA degradation. CMA, however, accurately at least weeks defecation. Moreover, simultaneous two complementary genes, methodology provides reliable, feasible more affordable alternative multiple routine analyses complex samples. Neither nor seems solve comprehensively quatification herbivore diets thus further research needs done.