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

作者：Uno Reina; Kondo Mami; Yuasa Takashi; Yamauchi Kiyoshi; Tsuruga Hihumi; Tamate Hidetoshi B^*; Yoneda Masaaki

来源：Population Ecology, 2012, 54(4): 509-519.

DOI：10.1007/s10144-012-0328-3

• Allelic dropout
• Error rate
• False alleles
• Hair trap
• Microsatellite

Non-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 a parts per thousand yen10 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 a parts per thousand yen10 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 a parts per thousand yen10 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.

• 出版日期2012-10