Body Remains Left by Bird Predators as a Reliable Source for Population Genetic Studies in the Great Capricorn Beetle Cerambyx cerdo, a Veteran Oak Specialist

SIMPLE SUMMARY: Molecular genetic techniques can support species conservation by providing information about processes critical to population survival. Unfortunately, obtaining biological material for DNA extraction is often associated with an adverse impact on the animals under study. In legally protected or threatened species, non-invasive sampling (i.e., sampling without injuring or disturbing an animal) is preferred as it carries no risk to the population’s survival. Here, we tested the possibility of using body remains left by bird predators for microsatellite genotyping in Cerambyx cerdo, a veteran oak specialist. We compared results obtained from such remains samples with samples of fresh beetle tarsi (i.e., invasive and destructive but non-lethal samples). We found that the sample type had no significant effect on PCR amplification efficiency; instead, it was strongly affected by allele length and individual heterozygosity. Allele frequencies were perfectly correlated for both sample types (R(2) = 0.94). Although point estimates of individual inbreeding were higher in remains than fresh samples (medians 0.08 vs. 0.02, respectively), both groups were not significantly different from each other and zero. Our study demonstrated that non-invasive remains samples could provide satisfactory data for population–genetic studies. However, we highlight the problem of potentially biased inbreeding estimates, which may result from allelic dropout. ABSTRACT: Obtaining biological material for DNA extraction is often challenging in organisms of conservation interest. Non-invasive sampling (i.e., sampling without injuring or disturbing an animal) is preferred as it carries no risk to the population’s survival. Here, we tested the possibility of using the body remains left by bird predators for microsatellite genotyping in Cerambyx cerdo, a veteran oak specialist. We compared results obtained from such potentially degraded samples with samples of fresh beetle tarsi (i.e., invasive and destructive but non-lethal samples). Using 10 SSR loci, we genotyped 28 fresh, and 28 remains samples. The analysis indicated that PCR amplification efficiency was not influenced by sample type but allele length and individual heterozygosity. Allele frequencies were perfectly correlated for both sample types (R(2) = 0.94). Additionally, null allele frequencies and genotyping failure rates were not significantly different from zero. Although the point estimates of individual inbreeding rates (f(i)) were higher in remains than fresh samples (medians 0.08 vs. 0.02, respectively), both groups were not significantly different from each other and zero. Our study demonstrated that non-invasive remains samples could provide satisfactory data for population–genetic studies. However, we highlight the problem of biased inbreeding estimates, which may result from samples affected by allelic dropout.