Effects of different environmental and sampling variables on the genotyping success in field-collected scat samples: a brown bear case study

Abstract

The paper investigates how different field conditions and sample characteristics influence genotyping success in field-collected brown bear scat samples. Genotyping performance of 413 samples collected in a pilot study in southern Slovenia was evaluated, andstatistical modelling was used to control confounding between pre- dictor variables and to quantify their specific effects ongenotyping success. The best predictors of genotyping success were subjectively estimated scat age, sampling month, and contents of ascat. Even when the other confounded variables were controlled for, genotyping success dropped rapidly with the age estimate, from 89% (82-94%) for 0-day scats to 33% (19-52%) for scats estimated to be 5 days old. Sampling month was also an important predictor, and samples collected during the bear hyperphagia period in late summer/autumn performed considerably better (90%,78-96%) than the samples collected in spring / early summer (66%, 57-74%). This effect was stronger for fresh than for older samples. Effects of different food types were also considerable, but less important for practical use. Since noninvasive genetic sampling already became the key method for surveying wild populations of many species, efficiency of studies is becoming increasingly important. Understanding the effect of the month of sampling allows the field season to be timed for maximum genotyping success, while subjective scat age provides a useful metric that indicates a sample’s viability for genotyping, allowing for prioritization of samples and culling of non-viable samples before resources are wasted for their analysis. This provides higher useful data yields per invested resources and may ultimately lead to better study results.

Keywords

• genetics
• genotyping success
• molecular ecology
• noninvasive sampling
• scat sampling
• Ursus arctos