Estimating wild boar Sus scrofa population size using faecal DNA and capture‐recapture modelling

Abstract

Increasing populations of wild boar and feral domestic pigs Sus scrofa have evoked growing concern due to their potential as disease reservoir and as an origin of agricultural damages. Reliable population estimates are needed for effective management measures of this species. As an alternative to traditional methods, non‐invasive genetic population estimation approaches based on hair or faeces sampling have yielded promising results for several species in terms of feasibility and precision. We developed and applied a non‐invasive population estimation approach based on wild boar faeces in a study area situated in the Palatinate Forest, southwestern Germany. We collected 515 faeces samples along transects in January 2008. We carried out genotyping using six microsatellite markers to discriminate between individuals. During the trial, we identified 149 individual wild boar. Using multimodel inference and model averaging, we obtained relatively consistent estimates. Population densities calculated using the estimated population sizes ranged from 4.5 (2.9‐7.8) to 5.0 (4.0‐7.0) wild boar/km2. In the future, to further improve the precision of population estimates based on wild boar faeces, the detection probability should be increased. However, even when comparing a conservative population estimate to the hunting bag, our results show that the present hunting regime in our study area is not effective in regulating the wild boar population. The method which we present here offers a tool to calibrate hunting or other management measures for wild boar.

Identification of robust microsatellite markers for wild pig fecal DNA

“…Following field collection, a highly useful step to identify fecal samples that likely will yield adequate DNA for robust amplification of microsatellite loci is to incorporate qPCR screening prior to genotyping. Our qPCR results supported the microsatellite results and previous studies (Morin et al , Ebert et al ); samples with higher C t values were more likely to produce mismatched genotypes. Additionally, samples that failed to amplify in our study averaged 35.423 cycles across all loci, which was similar to the cut‐off reported in Ebert et al () of 32 cycles.…”

“…Observed heterozygosities ranged from 0.350 to 0.786. Probability of identity values were similar to other studies using noninvasively collected fecal DNA (Brinkman et al , Ebert et al ), and over all loci, provided considerable power to discern individuals ( P ID = 2.862 × 10 −14 , P SIB = 2.485 × 10 −6 ). Based on the low error rates and high polymorphism of the screened microsatellites, we consider this suite of loci highly useful for CMR of wild pigs.…”

“…Data on abundance and density are needed to evaluate the risks posed by wild pig populations and effectiveness of control measures because invasive wild pig populations in the southeastern United States have grown in the last 30 years (Bevins et al ), causing extensive agricultural damage (Engeman et al , Campbell and Long , Bevins et al ) and threatening native ecosystems (Barrios‐Garcia and Ballari , Bevins et al ). Therefore, we evaluated if microsatellite loci used in European and Asian studies (Fickel and Hohmann , Ebert et al , Choi et al ) could provide reliable genotypes when amplified from fecal samples collected in sub‐tropical or tropical areas, such as those typical of the southeastern United States. Our goal for this study was twofold: first, we aimed to identify microsatellite loci that would be robust for wild pig genotypes from fecal samples collected in the warm, humid environments like the southeastern United States; and second, we examined how sample degradation affected our ability to obtain DNA from fecal material in similar environmental conditions.…”

Surveillance strategies for Classical Swine Fever in wild boar – a comprehensive evaluation study to ensure powerful surveillance

“…The data on the wild boar population was determined using feces and tissue samples22. The data set contained the estimated number of wild boar for all 36 districts of RP.…”

Monitoring wild pig populations: a review of methods

“…Capture heterogeneity weakens population estimates, and if the population is also not closed, density estimates by CMR become more uncertain. Estimating wild pig population size using fecal DNA and CMR modeling shows promise given sufficient detection probability of feces (Ebert et al 2012). …”