Abstract
BackgroundThe collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditional sources of DNA, such as blood or other tissues, few investigations have verified fecal samples as a valid source of DNA by directly comparing the results to high quality DNA samples from the same individuals. Our goal was to compare DNA from fecal and blood samples from the same 50 American plains bison (Bison bison) from Yellowstone National Park, analyze 35 short tandem repeat (STR) loci for genotyping efficiency, and compare heterozygosity estimates.ResultsWe discovered that some of the fecal-derived genotypes obtained were significantly different from the blood-derived genotypes from the same bison. We also found that fecal-derived DNA samples often underestimated heterozygosity values, in some cases by over 20%.ConclusionsThese findings highlight a potential shortcoming inherent in previous wildlife studies that relied solely on a multi-tube approach, using exclusively low quality fecal DNA samples with no quality control to account for false alleles and allelic dropout. Herein, we present a rigorous marker selection protocol that is applicable for a wide range of species and report a set of 15 STR markers for use in future bison studies that yielded consistent results from both fecal and blood-derived DNA.
Highlights
The collection and analysis of fecal Deoxyribonucleic acid (DNA) is a common practice, especially when dealing with wildlife species that are difficult to track or capture
The allelic dropout rate, calculated as the instances where only one of the two alleles in a blood sample were present in the matching fecal sample, was 0.023 overall, which means allelic dropout accounted for 60.3% of all mismatches between fecal and blood samples observed in this study
We evaluated 35 short tandem repeat (STR) markers for use with fecal DNA by comparing genotypes generated from paired blood and fecal samples from 50 bison and investigated how heterozygosity is affected by using different types of samples
Summary
The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. Some studies compared results from genotyping fecal samples under different conditions [16,17,18] and different methods for DNA extraction, such as rehydrating and carefully removing only the mucosal coat of the scat [19] or using a magnetic bead protocol [20], but to our knowledge, a direct and comprehensive comparison between a large number of paired samples at numerous loci has not been performed in any wildlife species. In wildlife studies using fecal DNA markers, allelic dropout was often high, determined as 8% in a study on mountain lions [11], 11.1% in wolves [22], and up to 49% in chimpanzees [23] All of these studies inferred dropout rates by re-amplifying DNA from the same fecal samples several times and comparing those results (the multi-tube approach); none of them used matching high quality DNA samples for comparison
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