Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy
Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, whic...
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| Published in | Animals (Basel) Vol. 15; no. 4; p. 574 |
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| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
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01.02.2025
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| Abstract | Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (
), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3-58.2%) compared to winter (99.2-84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. |
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| AbstractList | Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (Lutra lutra), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3-58.2%) compared to winter (99.2-84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites.Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (Lutra lutra), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3-58.2%) compared to winter (99.2-84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (Lutra lutra), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3–58.2%) compared to winter (99.2–84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. Non-invasive genetic approaches using fecal samples are valuable for studying endangered species, but they face challenges like poor DNA yield and increased data errors. This study evaluated the impact of sample age and season on DNA extracted from Eurasian otter spraints (feces) in South Korea. We found that PCR amplification success rates and genotyping accuracy decreased more rapidly in summer due to higher microbial growth and fecal degradation. Winter samples showed better DNA quality. We recommend collecting otter spraints in winter or, if summer sampling is necessary, using fresh samples from frequently monitored latrine sites. Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter ( Lutra lutra ), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3–58.2%) compared to winter (99.2–84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. Simple SummaryNon-invasive genetic approaches using fecal samples are valuable for studying endangered species, but they face challenges like poor DNA yield and increased data errors. This study evaluated the impact of sample age and season on DNA extracted from Eurasian otter spraints (feces) in South Korea. We found that PCR amplification success rates and genotyping accuracy decreased more rapidly in summer due to higher microbial growth and fecal degradation. Winter samples showed better DNA quality. We recommend collecting otter spraints in winter or, if summer sampling is necessary, using fresh samples from frequently monitored latrine sites. Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter ( ), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3-58.2%) compared to winter (99.2-84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. Non-invasive genetic approaches using fecal samples are valuable for studying endangered species, but they face challenges like poor DNA yield and increased data errors. This study evaluated the impact of sample age and season on DNA extracted from Eurasian otter spraints (feces) in South Korea. We found that PCR amplification success rates and genotyping accuracy decreased more rapidly in summer due to higher microbial growth and fecal degradation. Winter samples showed better DNA quality. We recommend collecting otter spraints in winter or, if summer sampling is necessary, using fresh samples from frequently monitored latrine sites. |
| Audience | Academic |
| Author | Min, Mi-Sook Cho, Je-Yoel Yang, Yoon-Do Han, Sung Yong Lee, Hang Lee, Jangmi Cho, Sujoo Kim, Jee Hyun Park, Han-Chan Kim, Dong Youn Pandey, Puneet |
| AuthorAffiliation | 6 Association of Korean Otter Conservation, Hwacheon 24135, Republic of Korea; hsy5034@hanmail.net 2 Conservation Genome Resource Bank for Korean Wildlife, Seoul 08826, Republic of Korea; hanchanee@gmail.com 5 Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea 8 Comparative Medicine Disease Research Center (CDRC), Seoul National University, Seoul 08826, Republic of Korea 3 Veterinary Humanities and Social Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea 1 Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; kjhsonic@hanmail.net (J.H.K.); jmhr15@naver.com (J.L.); dreamcat2017@gmail.com (D.Y.K.); rhkcjs6450@naver.com (S.C.); minbio@yahoo.co.kr (M.-S.M.); hanglee@snu.ac.kr (H.L.) 7 Department of Biochemistry, College of Veterinary Medicine, Research Institute for V |
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| Snippet | Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with... Non-invasive genetic approaches using fecal samples are valuable for studying endangered species, but they face challenges like poor DNA yield and increased... Simple SummaryNon-invasive genetic approaches using fecal samples are valuable for studying endangered species, but they face challenges like poor DNA yield... |
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| SubjectTerms | Defecation DNA degradation Endangered & extinct species Endangered species Ethanol Eurasian otter Feces Genetic research genotyping errors Humidity non-invasive sampling Otters PCR amplification success Success Temperature Winter |
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| Title | Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy |
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