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Rainey TA, Tryc EE, Nicholson KE. Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran ( Acris blanchardi). Biol Methods Protoc 2024; 9:bpae030. [PMID: 38818027 PMCID: PMC11139508 DOI: 10.1093/biomethods/bpae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Multiple methods for collecting genetic samples from amphibians exist, each with their own implications for study design, animal welfare, and costs. Toe clipping is one common method, but there is ongoing debate regarding its potential detriment. Less invasive methods should be implemented, if efficacious, as amphibians are a particularly vulnerable vertebrate group. Skin and buccal swabbing are less invasive methods for genetic sampling, but the potential for contamination and a lower yield of DNA may exist. To compare these methods, we gathered skin swabs, buccal swabs, and toe clips from the same individuals of a relatively small anuran species, Blanchard's Cricket Frog (Acris blanchardi). We then compared DNA yield, DNA purity, amplification success rate, and genotypic data quality among sample types. We found toe clips and buccal swabs generated similar DNA yield and purity, with skin swabs yielding significantly less DNA of significantly lower purity than the other sample types. Amplification success rate was significantly higher using toe clips compared to the other sample types, though buccal swab samples amplified more readily than skin swabs. Genotypic data from toe clips and buccal swabs did not differ significantly in quality, but skin swab data quality was significantly lowest among sample types. Thus, skin swabbing could produce erroneous data in some situations, but buccal swabbing is likely an effective substitute to toe clipping, even for small species. Our results can help future researchers select which genetic sampling method might best suit their research needs.
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Affiliation(s)
- Travis A Rainey
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Emily E Tryc
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
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2
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Vickers E, Kerney R. Screening Salamanders for Symbionts. Methods Mol Biol 2023; 2562:425-442. [PMID: 36272092 DOI: 10.1007/978-1-0716-2659-7_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial symbionts are broadly categorized by their impacts on host fitness: commensals, pathogens, and mutualists. However, recent investigations into the physiological basis of these impacts have revealed nuanced microbial influences on a wide range of host developmental, immunological, and physiological processes, including regeneration. Exploring these impacts begins with knowing which microbes are present. This methodological pipeline contains both targeted assays using PCR and culturing, as well as culture-independent approaches, to survey host salamander tissues for common and unknown microbial symbionts.
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Affiliation(s)
- Elli Vickers
- Gettysburg College, Department of Biology, Gettysburg, PA, USA
| | - Ryan Kerney
- Gettysburg College, Department of Biology, Gettysburg, PA, USA.
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3
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Reyne M, Helyar S, Aubry A, Emmerson M, Marnell F, Reid N. Combining spawn egg counts, individual photo-ID and genetic fingerprinting to estimate the population size and sex ratio of an endangered amphibian. Integr Zool 2020; 16:240-254. [PMID: 33137231 DOI: 10.1111/1749-4877.12497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
According to the International Union for Conservation of Nature Red List, 41% of the world's amphibian species are threatened with extinction, making them more threatened than any other vertebrate group nowadays. Given the global amphibian crisis, comprehensive understanding of demographics and population trends of declining and threatened species is essential for effective management and conservation strategies. Counting egg spawns is widely used to assess population abundance in pond breeding anurans. However, it is unknown how such counts translate into robust population size estimations. We monitored the breeding activity of the Natterjack toad (Epidalea calamita), combining egg string counts and individual photo-identification with Capture-Mark-Recapture population size and operational sex ratio estimation. Male Natterjack toads were identified by the pattern of natural markings with repeated ID of the same individual confirmed for 10% of the samples using genetic fingerprinting. We identified 647 unique individuals within a closed study population at Caherdaniel, Co Kerry. Population estimates derived from egg string counts estimated a breeding population of 368 females (95% CI 353-384) and Capture-Mark-Recapture estimated a breeding population of 1698 males (95% CI 1000-2397). The female:male sex ratio was conservatively estimated at 1:5 (95% CI 1:3-1:6) where 62% ± 6% of females were assumed to spawn. These substantially departed from any priori assumption of 1:1 which could have underestimated the breeding population by up to 72%. Where amphibian absolute population size estimation is necessary, methods should include empirical survey data on operational sex ratios and not rely on assumptions or those derived from the literature which may be highly population and/or context-dependent.
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Affiliation(s)
- Marina Reyne
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Sarah Helyar
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Aurélie Aubry
- Agri-Food & Biosciences Institute (AFBI), Hillsborough, UK
| | - Mark Emmerson
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Ferdia Marnell
- National Parks & Wildlife Service (NPWS), Dublin, Ireland
| | - Neil Reid
- School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
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4
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Thomas S, LeBlanc L, Perez-Umphrey A, Williams ST, Nevarez JG, Taylor SS. DNA Yield and Turtle Handling Time: Buccal Swabs Versus Blood Samples from Red-Eared Sliders and Eastern Musk Turtles. SOUTHEAST NAT 2020. [DOI: 10.1656/058.019.0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Sarah Thomas
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA 70803
| | - Layni LeBlanc
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA 70803
| | - Anna Perez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA 70803
| | - Steven Tyler Williams
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA 70803
| | - Javier G. Nevarez
- School of Veterinary Medicine, Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Sabrina S. Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA 70803
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Ward A, Hide G, Jehle R. Skin swabs with FTA® cards as a dry storage source for amphibian DNA. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-018-1018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Kroska AC, Wolf N, Dial R, Harris BP. Exploring sample cross-contamination in fish epidermal mucus. JOURNAL OF FISH BIOLOGY 2019; 95:647-650. [PMID: 30963579 DOI: 10.1111/jfb.13979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Cross-contamination of epidermal mucus was assessed at three sampling locations on the bodies of Pacific halibut Hippoglossus stenolepis by inducing contact between fish coated with labelled synthetic mucus and non-treated fish. Results indicate a positive relationship between sampling site exposure and sample contamination and that mucous sample cross-contamination can be mitigated by sampling in a location protected from external contact.
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Affiliation(s)
- Anita C Kroska
- Fisheries, Aquatic Science and Technology Laboratory, Alaska Pacific University, Anchorage, Alaska, USA
| | - Nathan Wolf
- Fisheries, Aquatic Science and Technology Laboratory, Alaska Pacific University, Anchorage, Alaska, USA
| | - Roman Dial
- Marine and Environmental Sciences, Alaska Pacific University, Anchorage, Alaska, USA
| | - Bradley P Harris
- Fisheries, Aquatic Science and Technology Laboratory, Alaska Pacific University, Anchorage, Alaska, USA
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Abstract
Skin swabbing, a minimally invasive DNA sampling method recently proposed for adult amphibians, was tested on the dendrobatid frog Allobates femoralis. I compared DNA yield from skin swabs and toe clips by evaluating obtained DNA concentrations and purity of extracts, as well as amplification success using eleven polymorphic microsatellite loci. I also tested whether storing skin swabs for two months at −20°C affected the properties of the extract or microsatellite analysis. Results show that skin swabs of adult A. femoralis suffered from high contamination and yielded significantly lower DNA quality and quantity, resulting in insufficient genotyping success, than DNA obtained from toe clips. The relatively dry skin in dendrobatid frogs may have impeded the collection of sufficient viable cells, and the presence of skin alkaloids and microbiota in the frog mucus may lead to high contamination load of skin swabs.
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Affiliation(s)
- Eva Ringler
- Department of Integrative Biology and Physiology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA.,Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.,Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, University of Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
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8
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Lenhardt PP, Brühl CA, Leeb C, Theissinger K. Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog ( Rana temporaria)? PeerJ 2017; 5:e3520. [PMID: 28713651 PMCID: PMC5508807 DOI: 10.7717/peerj.3520] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/08/2017] [Indexed: 01/22/2023] Open
Abstract
Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity) on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria) populations in Southern Palatinate (Germany). We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance) than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance). Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat, inhibiting genetic exchange and causing genetic differentiation of pond populations in agricultural areas. In viniculture, pesticides could be a driving factor for the observed genetic impoverishment, since pesticides are more frequently applied than any other management measure and can be highly toxic for terrestrial life stages of amphibians.
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Affiliation(s)
- Patrick P Lenhardt
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
| | - Carsten A Brühl
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
| | - Christoph Leeb
- Institute for Environmental Science, Universität Koblenz-Landau, Germany
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Hudson CM, Brown GP, Shine R. Effects of Toe-Clipping on Growth, Body Condition, and Locomotion of Cane Toads (Rhinella marina). COPEIA 2017. [DOI: 10.1643/ce-16-564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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Espinosa‐de Aquino W, Olvera‐Ramírez A, Arellano‐Carbajal F, Lanz‐Mendoza H, Villagrán‐Herrera E, Acevedo‐Whitehouse K. Protein and
RNA
extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wendy Espinosa‐de Aquino
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Andrea Olvera‐Ramírez
- Department of Veterinary Medicine School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Fausto Arellano‐Carbajal
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Humberto Lanz‐Mendoza
- Center for Infectious Diseases National Institute of Public Health Cuernavaca Morelos 62100 Mexico
| | - Elena Villagrán‐Herrera
- School of Medicine Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
| | - Karina Acevedo‐Whitehouse
- Unit for Basic and Applied Microbiology School of Natural Sciences Autonomous University of Queretaro Santiago de Querétaro Queretaro 76230 Mexico
- The Marine Mammal Center 2000 Bunker Road Sausalito CA 94965 USA
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