Assessment of genotyping accuracy in a non‐invasive DNA‐based population survey of Asiatic black bears (Ursus thibetanus): lessons from a large‐scale pilot study in Iwate prefecture, northern Japan

Abstract

AbstractNon‐invasive DNA genotyping using hair samples has become a common method in population surveys of Asiatic black bears (Ursus thibetanus) in Japan; however, the accuracy of the genotyping data has rarely been discussed in empirical studies. Therefore, we conducted a large‐scale pilot study to examine genotyping accuracy and sought an efficient way of error‐checking hair‐trapping data. We collected 2,067 hair samples, successfully determined the genotypes of 1,245 samples, and identified 295 individuals. The genotyping data were further divided into 3 subsets of data according to the number of hairs used for DNA extraction in each sample (1–4, 5–9, and ≥10 hairs), and the error rates of allelic dropout and false alleles were estimated for each subset using a maximum likelihood method. The genotyping error rates in the samples with ≥10 hairs were found to be lower than those in the samples with 1–4 and 5–9 hairs. The presence of erroneous genotypes among the identified individuals was further checked using a post hoc goodness‐of‐fit test that determined the match between the expected and observed frequencies of individual homozygotes at 0–6 loci. The results indicated the presence of erroneous genotypes, possibly as a result of allelic dropout, in the samples. Therefore, for improved accuracy, it is recommended that samples containing ≥10 hairs should be used for genotyping and a post hoc goodness‐of‐fit test should be performed to exclude erroneous genotypes before proceeding with downstream analysis such as capture‐mark‐recapture estimation.