No abstract

The main goal of non‐invasive genetic capture‐mark‐recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success rates and genotyping errors, which substantially bias subsequent analysis. To receive reliable results and to minimize the time and costs required for non‐invasive microsatellite genotyping, one must carefully choose a species‐specific sampling design, methods that maximize the amount of template DNA, and methods that could overcome genotyping errors, especially when using low‐quality samples. This article reviews the literature and the pros and cons of the main methods used along the process described above. The review is strengthened by a case study on Eurasian otters (Lutra lutra) using feces; we tested several methods for their appropriateness to accommodate for genotyping errors. Based on this method testing, we demonstrated that high genotyping error rates are the key problem in this process leading to a severely flawed dataset if no consensus genotype is formed. However, even if generating consensus genotypes minimizes errors dramatically, we show that it may not achieve a definite eradication of all errors, which results in overestimated population sizes if conventional estimators are used. In conjunction with these findings, we offer a step‐by‐step protocol for non‐invasive genetic CMR studies to achieve a reliable estimate of population sizes in the presence of high genotyping error rates. © 2013 The Wildlife Society.

Quantifying population status is a key objective in many ecological studies, but is often difficult to achieve for cryptic or elusive species. Here, non-invasive genetic capture-mark-recapture (CMR) methods have become a very important tool to estimate population parameters, such as population size and sex ratio. The Eurasian otter (Lutra lutra) is such an elusive species of management concern and is increasingly studied using faecal-based genetic sampling. For unbiased sex ratios or population size estimates, the marking behaviour of otters has to be taken into account. Using 2132 otter faeces of a wild otter population in Upper Lusatia (Saxony, Germany) collected over six years (2006–2012), we studied the marking behaviour and applied closed population CMR models accounting for genetic misidentification to estimate population sizes and sex ratios. We detected a sex difference in the marking behaviour of otters with jelly samples being more often defecated by males and placed actively exposed on frequently used marking sites. Since jelly samples are of higher DNA quality, it is important to not only concentrate on this kind of samples or marking sites and to invest in sufficiently high numbers of repetitions of non-jelly samples to ensure an unbiased sex ratio. Furthermore, otters seemed to increase marking intensity due to the handling of their spraints, hence accounting for this behavioural response could be important. We provided the first precise population size estimate with confidence intervals for Upper Lusatia (for 2012: = 20 ± 2.1, 95% CI = 16–25) and showed that spraint densities are not a reliable index for abundances. We further demonstrated that when minks live in sympatry with otters and have comparably high densities, a non-negligible number of supposed otter samples are actually of mink origin. This could severely bias results of otter monitoring if samples are not genetically identified.