Buccal swabs as an effective alternative to traditional tissue sampling methods for DNA analyses in Chamaeleonidae

Abstract

Conservation of wildlife often depends on high quality molecular data to establish reliable species identification. Traditional approaches in extracting material (DNA) for phylogenetic studies on chameleons have relied on removed, euthanized or preserved/museum specimens, while field sampling usually takes the form of tail clippings from living individuals and their subsequent release. In this article, we propose an alternative to these approaches for field sampling, towards isolation of nuclear and mitochondrial DNA with oral (buccal) swabs, a methodology already been demonstrated as effective in other taxa. Options of sampling, storage, transport, extraction of DNA are presented and the quality and quantity of extracted material (using venipuncture as a positive control) was demonstrated as sufficient for downstream applications, including sequencing thereby presenting a practical field alternative. The advantages and limitations of this minimally invasive and non‐destructive method applied to Chamaeleo africanus are further discussed.

The pros and cons of buccal swabbing and tail clipping for monitoring reptilian biodiversity

“…entire specimen collection and biopsy of organs, tissue biopsy with animal release, blood collection through venipuncture). 8,13,14 A common practice for collecting tissue samples from reptiles is to remove a small section (ca 1-3 mm) from the tip of the tail. 7,13 This approach may have little effect on squamates that have tail autotomy and regeneration as a predator defence mechanism.…”

“…22,23 One alternative method sometimes proposed for DNA sampling of large to moderately sized lizards is buccal swabbing. 13,14,27 This process includes insertion of a sterile swab into the mouth of the live animal, followed by moderate rotation of the swab to sample epithelial cells from the oral environment. This technique has led to successful DNA retrieval in lizards previously 28 and has been presented as a viable alternative to tissue sampling via tail clipping for DNA extraction 29 .…”

“…Therefore, swabbing is thought to be a less disruptive alternative to tail clipping in reptiles with nonautotomous tail-regeneration and studies have shown reliable retrieval of sufficiently high-quality DNA with the use of buccal swabs for some reptiles. 14,27,29 In larger animals, buccal swabbing presumably causes no direct tissue damage and little distress. 14,29,30 In smaller animals, the tissue damage and/or stress levels from the handling during buccal swabbing are not known, but some bleeding of the buccal epithelium has been noted in amphibians 31 , suggesting that in some cases there could be tissue damage despite the method being considered minimally disruptive.…”

“…14,27,29 In larger animals, buccal swabbing presumably causes no direct tissue damage and little distress. 14,29,30 In smaller animals, the tissue damage and/or stress levels from the handling during buccal swabbing are not known, but some bleeding of the buccal epithelium has been noted in amphibians 31 , suggesting that in some cases there could be tissue damage despite the method being considered minimally disruptive. It appears that the efficacy of buccal swabbing is subject to the size of the buccal cavity of the organism relative to the size of the swab.…”