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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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Rothstein AP, Byrne AQ, Knapp RA, Briggs CJ, Voyles J, Richards-Zawacki CL, Rosenblum EB. Divergent regional evolutionary histories of a devastating global amphibian pathogen. Proc Biol Sci 2021; 288:20210782. [PMID: 34157877 PMCID: PMC8220259 DOI: 10.1098/rspb.2021.0782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Emerging infectious diseases are a pressing threat to global biological diversity. Increased incidence and severity of novel pathogens underscores the need for methodological advances to understand pathogen emergence and spread. Here, we use genetic epidemiology to test, and challenge, key hypotheses about a devastating zoonotic disease impacting amphibians globally. Using an amplicon-based sequencing method and non-invasive samples we retrospectively explore the history of the fungal pathogen Batrachochytrium dendrobatidis (Bd) in two emblematic amphibian systems: the Sierra Nevada of California and Central Panama. The hypothesis in both regions is the hypervirulent Global Panzootic Lineage of Bd (BdGPL) was recently introduced and spread rapidly in a wave-like pattern. Our data challenge this hypothesis by demonstrating similar epizootic signatures can have radically different underlying evolutionary histories. In Central Panama, our genetic data confirm a recent and rapid pathogen spread. However, BdGPL in the Sierra Nevada has remarkable spatial structuring, high genetic diversity and a relatively older history inferred from time-dated phylogenies. Thus, this deadly pathogen lineage may have a longer history in some regions than assumed, providing insights into its origin and spread. Overall, our results highlight the importance of integrating observed wildlife die-offs with genetic data to more accurately reconstruct pathogen outbreaks.
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Affiliation(s)
- Andrew P Rothstein
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Allison Q Byrne
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Roland A Knapp
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, CA, USA.,Earth Research Institute, University of California, Santa Barbara, CA, USA
| | - Cheryl J Briggs
- Earth Research Institute, University of California, Santa Barbara, CA, USA.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Jamie Voyles
- Department of Biology, University of Nevada, Reno, NV, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
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