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Ripa A, Díaz-Caballero JA, Palacios-González MJ, Espinosa A, García-Zapata JL, Fernández-Garcia JL. Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples. Mol Biol Rep 2024; 51:76. [PMID: 38180618 PMCID: PMC10770224 DOI: 10.1007/s11033-023-09010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. METHODS AND RESULTS The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. CONCLUSIONS We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.
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Affiliation(s)
- Adriana Ripa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
| | - José A Díaz-Caballero
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
- Área del Medio Natural, Sociedad de Gestión Pública de Extremadura (GPEX), Junta de Extremadura, Mérida, España
| | - María Jesús Palacios-González
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
| | - Antonio Espinosa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
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Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs. CONSERV GENET RESOUR 2022; 14:203-213. [PMID: 35673611 PMCID: PMC9162989 DOI: 10.1007/s12686-022-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.
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Identifying individual ungulates from fecal DNA: a comparison of field collection methods to maximize efficiency, ease, and success. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00176-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractNon-invasive genetic sampling can facilitate the identification of individual animals across a landscape, with applications to management and conservation. Fecal material is a readily available source of DNA, and various methods exist for collecting fecal samples for DNA preservation. In particular, swab methods offer considerable promise, but their utility in real-world field contexts remains relatively untested. We systematically compared multiple genetic fecal sampling methods across all stages of data collection and analysis, including sampling in the field, DNA extraction in the lab, and identification of individuals using microsatellite genotyping. We collected 112 fecal samples from black-tailed deer (Odocoileus hemionus columbianus) in the field in Mendocino County, California, across a range of sample conditions of unknown age. We systematically compared the efficiency, ease, and genotyping success of three methods for field collection and storage of ungulate fecal samples: whole pellets in ethanol, whole dry pellets in paper envelopes, and cotton swabs in buffer. Storage method, sample condition, and their interaction predicted genotyping success in the top binomial GLMMs. We found that swabbing pellets resulted in the greatest percentage of individually identifiable genotypes (81%, compared to 60% for dry samples and 56% for ethanol), despite lower DNA concentrations. While swabbing pellets requires a greater time investment in the field, the samples are easier and safer to store and transport, and subsequent labwork is more efficient as compared to whole-pellet collection methods. We, therefore, recommend the swab method for most contexts. We provide additional recommendations and field protocols based on subsequent collection of 2284 swab samples for a larger monitoring study of the deer population, given that this large number of samples spanned a range of sample conditions and time spent in storage.
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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Davis AJ, Keiter DA, Kierepka EM, Slootmaker C, Piaggio AJ, Beasley JC, Pepin KM. A comparison of cost and quality of three methods for estimating density for wild pig (Sus scrofa). Sci Rep 2020; 10:2047. [PMID: 32029837 PMCID: PMC7004977 DOI: 10.1038/s41598-020-58937-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/13/2020] [Indexed: 12/02/2022] Open
Abstract
A critical element in effective wildlife management is monitoring the status of wildlife populations; however, resources to monitor wildlife populations are typically limited. We compared cost effectiveness of three common population estimation methods (i.e. non-invasive DNA sampling, camera sampling, and sampling from trapping) by applying them to wild pigs (Sus scrofa) across three habitats in South Carolina, U.S.A where they are invasive. We used mark-recapture analyses for fecal DNA sampling data, spatially-explicit capture-recapture analyses for camera sampling data, and a removal analysis for removal sampling from trap data. Density estimates were similar across methods. Camera sampling was the least expensive, but had large variances. Fecal DNA sampling was the most expensive, although this technique generally performed well. We examined how reductions in effort by method related to increases in relative bias or imprecision. For removal sampling, the largest cost savings while maintaining unbiased density estimates was from reducing the number of traps. For fecal DNA sampling, a reduction in effort only minimally reduced costs due to the need for increased lab replicates while maintaining high quality estimates. For camera sampling, effort could only be marginally reduced before inducing bias. We provide a decision tree for researchers to help make monitoring decisions.
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Affiliation(s)
- Amy J Davis
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA.
| | - David A Keiter
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- University of Nebraska, School of Natural Resources, Hardin Hall, 3310 Holdrege St., Lincoln, NE, 68583-0961, USA
| | - Elizabeth M Kierepka
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Chris Slootmaker
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
- Mountain Data Group, 115 N. College Ave. Suite 220, Fort Collins, CO, 80524, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
| | - James C Beasley
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
| | - Kim M Pepin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
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Animal Visitation to Wild Pig ( Sus scrofa) Wallows and Implications for Disease Transmission. J Wildl Dis 2018; 55:488-493. [PMID: 30311547 DOI: 10.7589/2018-05-143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Knowledge of animal visitation to locations where species aggregate is valuable for evaluating potential pathways of inter- and intraspecific transmission of infectious diseases. There is no research evaluating the potential of wallows created by invasive wild pigs ( Sus scrofa) as locations of transmission of infectious diseases. We monitored wild pig wallows by using trail cameras to determine the frequency with which wild pigs and native vertebrate species visited wallows and to characterize these interactions for their potential for disease transmission. We placed cameras from 20 June 2016 to 21 September 2016 at 16 individual wallows within 10 wallowing sites. Wild pigs of both sexes visited wallows frequently (115 total visits) for varying durations and exhibited wallowing and drinking behavior. We also observed 12 native mammalian and avian wildlife species using wallows at various frequencies (165 total visits). Of particular interest, nine of these species were observed drinking from wallows. Given the high frequency of wild pig visits to wallows and the drinking behavior they and native wildlife species exhibited, these locations might have an important role in transmission of diseases.
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Robeson MS, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ. Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig ( Sus scrofa). Ecol Evol 2017; 8:185-196. [PMID: 29321862 PMCID: PMC5756863 DOI: 10.1002/ece3.3638] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.
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Affiliation(s)
- Michael S Robeson
- Fish and Wildlife Conservation Biology Colorado State University Fort Collins CO USA.,USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA.,Present address: Department of Biomedical Informatics College of Medicine University of Arkansas for Medical Sciences Little Rock AR USA
| | - Kamil Khanipov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - George Golovko
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Samantha M Wisely
- Department of Wildlife Ecology and Conservation USA 5 USDA, Wildlife Services University of Florida Gainesville FL USA
| | | | | | - Timothy J Smyser
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
| | - Yuriy Fofanov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
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