GENETICS: REPTILES
CROCODILES
Velo-Anton G., Godinho R., Campos J. C., Brito J. C. (2014): Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles. Plos One 9: e94626.
FULL TEXT
Abstract
The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.
LIZARDS
Miller H. C. (2006): Cloacal and buccal swabs are a reliable source of DNA for microsatellite genotyping of reptiles. Conservation Genetics 7: 1001–1003.
FULL TEXT
Abstract
In this study, a minimally invasive method for DNA sampling of reptiles and amphibians using cloacal and buccal swabs is described. High molecular weight DNA was isolated from the swabs, which were collected from tuatara (Sphenodon punctatus), and stored in 70% ethanol at room temperature for approximately 1 week. Amplification of mitochondrial and microsatellite DNA loci was successful from both cloacal and buccal swabs, and in all cases the genotypes matched those obtained from blood samples. These results show that cloacal and/or buccal swabbing is a useful alternative to blood sampling and toe clipping for genetic studies on reptiles. This method is rapid, inexpensive and easy to implement in field situations.
Schulte U., Gebhard F., Heinz L., Veith M., Hochkirch A. (2011): Buccal swabs as a reliable non-invasive tissue sampling method for DNA analysis in the lacertid lizard Podarcis muralis. North-Western Journal of Zoology 7: 325-328.
FULL TEXT
Abstract
We tested the performance of buccal swabs for microsatellite analysis in an introduced population of the Common Wall Lizard (P. muralis) in Germany. The quantity and quality of the isolated DNA collected by buccal swabbing and by screwing a tail tip of the same individuals was compared. Although the DNA yield from buccal swabs was much lower than from tissue, it was sufficient for a successful amplification. We genotyped the individuals at two microsatellite loci. Buccal swabs generated genotypes just as well as tissue samples. We could not find a lower threshold of DNA quantity that increased genotyping errors. In contrast, very high DNA yields (>10 ng/ml), as found in some tissue samples, produced a higher number of unspecific peaks. These results show that buccal swabs are a simple and efficient non-invasive sampling method for DNA analysis in adult lacertid lizards. Carefully applied, the technique does not harm the specimens in their locomotor performance and energy reserves. An additional advantage of buccal swabbing is the time-saving DNA extraction, since there is no need to remove scales, chop up the tissue, nor for a long digestion step.
Williams D. A., Leach C., Hale A. M., Karsten K. B., Mujica E., Barber D., Linam L. A., Rains N. (2012): Development of tetranucleotide microsatellite loci and a non-invasive DNA sampling method for Texas horned lizards (Phrynosoma cornutum). Conservation Genetics Resources 4: 43-45.
FULL TEXT
Abstract
We developed a non-invasive DNA sampling method and 15 tetranucleotide microsatellite markers for Texas horned lizards (Phrynosoma cornutum). Swabbing the cloaca with a small cotton swab and preserving the cells in lysis buffer was an effective method to obtain tissue for DNA extraction. Loci were highly polymorphic with 8–25 alleles and observed heterozygosity was high (0.71–0.96). Some of these loci can also be used for round-tailed horned lizards (P. modestum).
Horreo J. L., Peláez M. L., Fitze P. S. (2015): Skin sheds as a useful DNA source for lizard conservation. Phyllomedusa: Journal of Herpetology 14: 73-77.
FULL TEXT
Excerpt
In this work, skin sheds were obtained from the European common lizard, Zootoca vivipara (Lichtenstein, 1823) (Lacertidae), during population sampling. To date, almost all DNA studies carried out in lizards have sampled a small piece of the tail, toes, or blood. Thus, the DNA source tested here will provide a new, currently unused, method of non-invasive DNA sampling. We extracted and PCR-amplified DNA from ten individuals from three different populations (two in France and one in Spain).
Pearson S. K., Tobe S. S., Fusco D. A., Bull C. M., Gardner M. G. (2015): Piles of scats for piles of DNA: deriving DNA of lizards from their faeces. Australian Journal of Zoology 62: 507-514.
FULL TEXT
Abstract
Non-invasive genetic sampling using scats has a well established role in conservation biology, but has rarely been applied to reptiles. Using scats from captive and wild Egernia stokesii (Squamata, Scincidae) we evaluated two storage and six DNA-extraction methods and the reliability of subsequent genotype and sequence data. Accurate genotype and sequence data were obtained from frozen and dried captive lizard scat DNA extracted using a QIAamp® DNA Stool Mini Kit and a modified Gentra® Puregene® method, but success rates were reduced for wild lizard scats. Wild E. stokesii eat more plants than their captive counterparts, possibly resulting in scat DNA extracts containing plant compounds that inhibit PCR-amplifications. Notably, reliable genotypes and sequences were obtained from wild E. stokesii scat DNA extracted using a Qiagen DNeasy® Plant Mini Kit, a method designed to remove plant inhibitory compounds. Results highlight the opportunity for using scat-derived DNA in lizard studies, particularly for species that deposit scats in piles.
Statham M. J., Woollett D. A., Fresquez S., Pfeiffer J., Richmond J., Whitelaw A., Richards N. L., Westphal M. F., Sacks B. N. (2020): Noninvasive identification of herpetofauna: pairing conservation dogs and genetic analysis. The Journal of Wildlife Management 84: 66-74.
FULL TEXT
Abstract
Noninvasive fecal sampling combined with genetic analysis is a technique allowing the study of elusive or otherwise difficult to monitor species without the need for direct contact. Although this method is widely used in birds and mammals, it has never been successfully applied on a large scale in reptiles. The blunt‐nosed leopard lizard (Gambelia sila) is an endangered species endemic to the San Joaquin Desert, California, USA. Presently, acquiring data on the species for research and management involves more traditional methods such as live capture or visual surveys, the latter of which are required for regulatory monitoring in accordance with wildlife agency protocols. We used an approach for gathering additional information that combines conservation detection dogs trained to locate blunt‐nosed leopard lizard scat samples with genetic analysis for identifying and distinguishing among sympatric lizard species. We developed 2 polymerase chain reaction assays that produce fluorescently labelled amplicons of species‐specific fragment length for 6 lizard species in the study area. Using these assays, we genetically identified to species 78% (255 of 327) of samples collected by dog‐handler teams across 4 years. The majority of the genetically identified samples (82.4%; 210 of 255) were confirmed as originating from blunt‐nosed leopard lizards. Although an assessment of the viability of detection dogs in regulatory monitoring efforts is required, our ability to recover usable DNA and to differentiate among a diverse group of lizards highlights the broad potential of our methodology for noninvasive sampling in reptiles.
Koutsokali M., Dianni C., Valahas M. (2023): Buccal swabs as an effective alternative to traditional tissue sampling methods for DNA analyses in Chamaeleonidae. Wildlife Biology: e01052.
FULL TEXT
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.
SNAKES
Beebee T. J. (2008): Buccal swabbing as a source of DNA from squamate reptiles. Conservation Genetics 9: 1087-1088.
FULL TEXT
Abstract
Buccal swabbing was compared with other tissues as a source of DNA for microsatellite genotyping from two squamate reptiles. For both species, the lizard Lacerta agilis and the snake Coronella austriaca, buccal swabbing proved more reliable than tissues including tail tips, toe clips and ventral scale clips.
Jones R., Cable J., Bruford M. W. (2008): An evaluation of non-invasive sampling for genetic analysis in northern European reptiles. The Herpetological Journal 18: 32-39.
FULL TEXT
Abstract
Genetic studies of native herpetofauna populations are important for the conservation of European biodiversity, but previous studies have been largely dependent on invasive sample collection. Here we explore the efficiency of noninvasive sampling (NIS) for molecular studies and review the various potential sources of such samples. Snakes produce a multitude of by-products, such as sloughed skin, faeces and eggs or embryos, that, along with road kills, predated specimens and museum samples, could potentially be used in molecular studies. We describe a new method for obtaining snake faeces in the field and, using mitochondrial cytochrome b primers, we successfully amplified 500 and 758 bp sequences from a variety of tissues collected by NIS. The availability and degradation of such material differed greatly, and both DNA extraction and PCR success appeared dependent upon sample origin and storage. Nevertheless, for the first time we demonstrate that faecal, egg and foetal tissues, as well as sloughed skin and carcasses, represent valuable NIS source material permitting genetic studies with minimal disturbance to the individual and its population.
Ford B., Govindarajulu P., Larsen K., Russello M. (2017): Evaluating the efficacy of non-invasive genetic sampling of the Northern Pacific rattlesnake with implications for other venomous squamates. Conservation Genetics Resources 9: 13-15.
FULL TEXT
Abstract
A common challenge for conservation genetic studies is finding minimally invasive sampling methods that maximize the quantity and quality of data produced. Conventional approaches rely on tissue or blood sampling, which typically require lengthy handling times, and can be hazardous for high-risk species, such as venomous snakes. Finding alternative, less invasive techniques is imperative in such circumstances. We compared DNA quantity and genotyping success of blood samples to those from buccal swabs, cloacal swabs, and scale clippings in the Northern Pacific rattlesnake (Crotalus oreganus oreganus). Buccal swabs and scales yielded significantly less DNA compared to blood, whereas cloacal samples were not significantly different. Cloacal swabs produced the highest PCR success and lowest genotyping errors commensurate to the blood samples, but differences were not significant between sample types. Our findings suggest cloacal swabbing as an efficient, less invasive alternative for providing high quality genotypic data for squamate reptiles (venomous or nonvenomous).
Maigret T. A. (2019): Snake scale clips as a source of high quality DNA suitable for RAD sequencing. Conservation Genetics Resources 11: 373-375.
FULL TEXT
Abstract
Restriction site associated DNA sequencing (RADseq) methods are growing in popularity, yet require large starting amounts of high quality DNA. I examined the utility of scale clips, a minimally invasive method of tissue collection for live snakes, as a source of high quality DNA suitable for RADseq. I compared DNA extracted from muscular tissue obtained from roadkilled copperheads (Agkistrodon contortrix) and ventral scale clips obtained from live A. contortrix. Much less DNA was extracted from scale clips than from muscular tissue, yet molecular weight and number of sequence reads were not different. Amount of DNA extracted from scale clips was not affected by the size of the animal. My findings suggest that high quality DNA can likely be obtained from ventral scale clips for most species of snakes. The high molecular weight also allows the lower DNA yields accessible via scale clips to be amplified using whole genome amplification.
Brekke T. D., Shier L., Hegarty M. J., Mulley J. F. (2019): Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles. bioRxiv: 658989.
FULL TEXT
Abstract
Association and genetic mapping studies aimed at linking genotype to phenotype are powerful tools that require large numbers of samples, complicating their use in long-lived species with low fecundity. Shed skins of snakes and other reptiles contain DNA; are a safe and ethical way of non-invasively sampling large numbers of individuals; and provide a simple mechanism by which to involve the public in scientific research. Here we test whether the DNA in dried shed skins mailed to us from citizen scientists is suitable for reduced representation sequencing approaches, specifically genotyping-by-sequencing (GBS). We find that shed skin samples provide DNA of sufficient quality and quantity for GBS, although libraries from shed skin resulted in fewer sequenced reads than libraries from snap-frozen muscle, and contained slightly fewer variants (70,685 SNPs versus 97,724). This issue is a direct result of lower read counts of the shed skin samples, and can be rectified quite simply with deeper sequencing. Skin-derived libraries also have a very slight (but significantly different) profile of transitions and transversions, suggesting that DNA damage occurs but is minimal. We conclude that shed skin-derived DNA is a good source of genomic DNA for a variety of genetic studies, and use it to identify sex-linked scaffolds in the corn snake genome.
Auliya M., Hofmann S., Segniagbeto G. H., Assou D., Ronfot D., Astrin J. J., Forat S., Ketoh G. K. K., D’Cruze N. (2020): The first genetic assessment of wild and farmed ball pythons (Reptilia, Serpentes, Pythonidae) in southern Togo. Nature Conservation 38: 37-59.
FULL TEXT
Abstract
The ball python (Python regius) is the world’s most commonly traded python species for the “exotic” pet industry. The majority of these live snakes are produced via a number of python farms in West Africa that have been in operation since the 1960s and involved with “ranching” operations since the 1990s. However, to date no thorough taxonomic review or genetic studies have been conducted within its range, despite the fact that the evaluation of a species’ genetic variability is generally considered mandatory for effective management. We used mtDNA sequence data and eight polymorphic microsatellite markers to assess the underlying population genetic structure and to test the potential of the nuclear markers to assign farm individuals to wild reference populations in southern Togo. Despite the relatively large distances between sample locations, no significant genetic population structure was found, either in mtDNA sequence data or in the microsatellite data. Instead, our data indicate considerable gene flow among the locations. The absence of a distinct population subdivision may have resulted from an anthropogenic driven admixture of populations associated with commercial wildlife trade activity in recent decades. Given the ongoing largely unregulated nature of the commercial ranching of ball pythons in West Africa, should a wild release component continue, as a first measure we recommend that the Management Authorities should develop an action plan with specific release protocols for python farms to minimise any potential negative conservation impacts resulting from admixture (genetic pollution) between farmed and wild individuals.
Schmidt D. A., Campbell N. R., Govindarajulu P., Larsen K. W., Russello M. A. (2020): Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology. Molecular Ecology Resources 20: 114-124.
FULL TEXT
Abstract
Minimally invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping‐by‐sequencing approaches, which have been traditionally developed for high‐quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping‐in‐Thousands by sequencing (GT‐seq), a multiplex amplicon sequencing approach, to effectively genotype minimally invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT‐seq from a de novo restriction site‐associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT‐seq for the same individuals found low rates of genotyping error (GT‐seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT‐seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT‐seq and RADseq data sets, as were inferred patterns of population structure. Overall, GT‐seq can be effectively applied to low‐quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
Brekke T. D., Shier L., Hegarty M. J., Mulley J. F. (2023): Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles. Conservation Genetics Resources 15: 117-124.
FULL TEXT
Abstract
Over a fifth of reptile species are classified as ‘Threatened’ and conservation efforts, especially those aimed at recovery of isolated or fragmented populations, will require genetic and genomic data and resources. Shed skins of snakes and other reptiles contain DNA; are a safe and ethical way of non-invasively sampling large numbers of individuals; and provide a simple mechanism by which to involve the public in scientific research. Here we test whether the DNA in dried shed skin is suitable for reduced representation sequencing approaches, specifically genotyping-by-sequencing (GBS). Shed skin-derived libraries resulted in fewer sequenced reads than those from snap-frozen muscle samples, and contained slightly fewer variants (70,685 SNPs versus 97,724), but this issue can easily be rectified with deeper sequencing of shed skin-derived libraries. Skin-derived libraries also have a very slight (but significantly different) profile of transitions and transversions, most likely as a result of DNA damage, but the impact of this is minimal given the large number of single nucleotide polymorphisms (SNPs) involved. SNP density tends to scale with chromosome length, and microchromosomes have a significantly higher SNP density than macrochromosomes, most likely because of their higher GC content. Overall, shed skin provides DNA of sufficient quality and quantity for the identification of large number of SNPs, but requires greater sequencing depth, and consideration of the GC richness of microchromosomes when selecting restriction enzymes.
TURTLES
Shamblin B. M., Dodd M. G., Williams K. L., Frick M. G., Bell R., Nairn C. J. (2011): Loggerhead turtle eggshells as a source of maternal nuclear genomic DNA for population genetic studies. Molecular Ecology Resources 11: 110-115.
FULL TEXT
Abstract
Tagging studies on nesting beaches are commonly used to estimate nesting frequency, remigration interval and nesting population size for marine turtle rookeries. Estimates of these demographic parameters from tagging projects may be biased because of the small scale of tagging efforts relative to female nest site fidelity and the logistical difficulty of intercepting all nesting females. Therefore, alternative and supplemental means of individual identification of nesting females are required. We demonstrate that maternal nuclear microsatellite DNA can be isolated from unincubated eggshells of the loggerhead sea turtle (Caretta caretta) through comparison of DNA extracted from 59 eggs collected within 15 h of oviposition and DNA derived from skin samples from respective nesting females. Scorable microsatellite genotypes were produced in 897 of 994 (90.2%) single‐locus egg amplifications attempted. Among eggs from known females, 730 of 748 (97.6%) single‐locus, egg‐derived genotypes matched the respective skin‐derived genotypes. Allelic dropout was the most common type of error, followed by the presence of nonmaternal, presumably paternal, alleles. Genotypes derived from unincubated eggshells permit individual assignment of nests and therefore demographic parameter estimates for loggerhead turtle nesting populations, despite genotyping errors that require further optimization. Although sampling unincubated eggs is destructive, this technique is noninvasive to nesting females and is applicable in marine turtle population genetics studies when individual resolution is required but direct interception of nesting females is undesirable or logistically infeasible.
Lanci A. K., Roden S. E., Bowman A., LaCasella E. L., Frey A., Dutton P. H. (2012): Evaluating buccal and cloacal swabs for ease of collection and use in genetic analyses of marine turtles. Chelonian Conservation and Biology 11: 144-148.
FULL TEXT
Abstract
Buccal and cloacal swabs have been used for genetic sampling for a variety of reptiles but not for marine turtles to date. We evaluated whether this method offers a simple and quick way to sample cells from live marine turtles in the wild when it is not feasible to obtain blood or skin. Good-quality DNA was obtained for genetic analyses from both buccal and cloacal swabs. Although we recommend blood and skin sampling whenever possible to collect the highest quality DNA, buccal and cloacal swabs do represent a useful alternative for genetic sampling when these preferred methods are not feasible.
Mucci N., Mengoni C., Berti E., Randi E. (2014): Cloacal swab sampling is a reliable and harmless source of DNA for population and forensic genetics in tortoises. Conservation Genetics Resources 6: 845-847.
FULL TEXT
Abstract
Testudo graeca, Testudo hermanni and Testudo marginata are endangered species listed in the IUCN Red List and Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Correct identification of species and distinct population units can support sound conservation projects and forensic applications. However, the collection of biological samples is not always easy or harmless. Blood sampling is usually invasive and risky. Salivary swab sampling is commonly used in other reptiles but can be unsafe for tortoises by the reason of their head retraction escape response. Cloacal swab sampling should be easier and less risky. In this study, we genotyped 37 tortoises at eight microsatellite loci and compared the reliability of individual genotypes obtained from blood, cloacal and buccal swabs. Results showed that performances of cloacal samples are comparable with those of buccal and blood samples, and proved that cloacal sampling is an alternative and reliable source of DNA for tortoise genotyping.
Mitelberg A., Vandergast A. G., Nussear K. E., Dutcher K., Esque T. C. (2019): Development of a genotyping protocol for Mojave Desert tortoise scat. Chelonian Conservation and Biology 18: 123-132.
FULL TEXT
Abstract
Noninvasive fecal genotyping can be a useful tool for population monitoring of elusive species. We tested extraction protocols on scat samples from the threatened Mojave Desert tortoise, Gopherus agassizii, to evaluate whether scat-based mark–recapture and population genetic monitoring studies are feasible. We extracted DNA from G. agassizii scat samples collected in California and Nevada using several extraction protocols and evaluated the reliability of resulting genotypes using quality scores, maximum likelihood reliability estimates, and paired scat and blood genotypes from the same individuals. Finally, we assessed probabilities of identity and sibship, and locus amplification quality, and calculated genotyping error rates for 19 microsatellite loci to determine the best set of loci to use with G. agassizii scat extractions. We found that genotype quality depended more on the sample quality than on the extraction method, and that the Qiagen DNeasy Plant Mini extraction kit is an efficient method for extracting tortoise DNA from tortoise scat. We identified 6 G. agassizii microsatellite loci that can be used to generate a unique molecular tag for individual tortoises. We characterized the reliability of an additional 13 microsatellite loci for use in population genetic analyses where additional power at the expense of some increase in error may be advantageous. As proof of concept, with very low error rates, we matched 3 opportunistically collected scat samples to blood genotypes from animals captured during population surveys within the study area and discovered at least 3 new individuals, even after 2 years of extensive survey work. These results suggest that genotyping of field-collected scat can complement existing methods used in long-term demographic and movement studies of G. agassizii and other, closely related, tortoise species.
Manning J. A., Edwards T., Clemons J., Leavitt D. J., Goldberg C. S., Culver M. (2022): Scat as a source of DNA for population monitoring. Ecology and Evolution 12: e9415.
FULL TEXT
Abstract
Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz’s desert tortoise, Gopherus agassizii, California, US, and Morafka’s desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz’s desert tortoise and for the study of 42% Morafka’s desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non-invasive samples.