Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison).
Allelic dropout
Bison
Fecal DNA
Heterozygosity
Microsatellite
STR
Yellowstone National Park
Journal
BMC genetics
ISSN: 1471-2156
Titre abrégé: BMC Genet
Pays: England
ID NLM: 100966978
Informations de publication
Date de publication:
26 02 2019
26 02 2019
Historique:
received:
20
03
2018
accepted:
08
02
2019
entrez:
28
2
2019
pubmed:
28
2
2019
medline:
9
1
2020
Statut:
epublish
Résumé
The 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. We 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%. These 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.
Sections du résumé
BACKGROUND
The 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.
RESULTS
We 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%.
CONCLUSIONS
These 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.
Identifiants
pubmed: 30808294
doi: 10.1186/s12863-019-0722-3
pii: 10.1186/s12863-019-0722-3
pmc: PMC6390568
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Comparative Study
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
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