Abstract
Fin clipping of live fish under anesthesia is widely used to collect samples for DNA extraction. An alternative, potentially less invasive, approach involves obtaining samples by swabbing the skin of nonanesthetized fish. However, this method has yet to be widely adopted for use in laboratory studies in the biological and biomedical sciences. Here, we compare DNA samples from zebrafish Danio rerio and three-spined sticklebacks Gasterosteus aculeatus collected via fin clipping and skin swabbing techniques, and test a range of DNA extraction methods, including commercially available kits and a lower-cost, in-house method. We verify the method for polymerase chain reaction analysis, and examine the potential risk of cross contamination between individual fish that are netted together. We show that swabbing, which may not require the use of anesthesia or analgesics, offers a reliable alternative to fin clipping. Further work is now required to determine the relative effects of fin clipping and swabbing on the stress responses and subsequent health of fish, and hence the potential of swabbing as a refinement to existing DNA sampling procedures.
Highlights
The number of fish used in research has risen steadily over recent years, due to their ease of maintenance in the laboratory and similarities to other vertebrate species that make them useful alternatives for mammals in accordance with the principles of the ‘‘3Rs’’—replacement, reduction, and refinement of animals in research.[1,2,3,4,5] In 2015, 14% of all regulated animal procedures in Britain were undertaken on fish.[6]
In this article we provide a detailed protocol for using skin swabbing for the collection of DNA samples from small bodied, laboratory fish, and validate the technique for use with zebrafish and sticklebacks
Our results suggest that skin swabbing, combined with the low-cost recovery method, can yield DNA concentrations and purities that are comparable to those obtained from fin clips and commercially available DNA extraction kits
Summary
The number of fish used in research has risen steadily over recent years, due to their ease of maintenance in the laboratory and similarities to other vertebrate species that make them useful alternatives for mammals in accordance with the principles of the ‘‘3Rs’’—replacement, reduction, and refinement of animals in research.[1,2,3,4,5] In 2015, 14% of all regulated animal procedures in Britain were undertaken on fish.[6]. Swabbing skin mucus to collect DNA samples has been adopted for use in ecological studies of larger fish,[13,14,15,16] and potentially represents a less invasive alternative to fin clipping. Our data suggest that the swab technique is a viable and reproducible alternative for the collection of DNA samples from small laboratory fish
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