Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes)

Abstract

Background: Noninvasive and nondestructive DNA sampling techniques are becoming more important in genetic studies because they can provide genetic material from wild animals with less or even without disturbance, which is particularly useful for the study of endangered species, i.e., birds. However, nondestructively and noninvasively sampled DNA may, in some cases, be inadequate in the amount and quality of the material collected, which can lead to low amplification success rates and high genotyping errors. Methods:In this study, noninvasive (eggshell swab, shed feather and feces), nondestructive (plucked feather and buccal swab) and invasive (blood) DNA samples were collected from the vulnerable Chinese Egret (Egretta eulophotes). DNA concentrations, PCR amplification success and microsatellite genotyping errors of different sample types were evaluated and compared to determine whether noninvasive and nondestructive samples performed as well as invasive samples in our experimental procedures. Results:A total of 159 samples were collected in the field. Among the different sample types, the highest DNA concentrations (154.0-385.5 ng/μL) were obtained from blood. Those extracted from fecal samples were the lowest, ranging from 1.25 to 27.5 ng/μL. Almost all of the DNA samples, i.e., 95.59 %, were successfully amplified for mtDNA (n = 152) and 92.76 % of mtDNA samples were successfully genotyped for at least five of the nine microsatellite loci tested (n = 141). Blood samples and buccal swabs produced reliable genotypes with no genotyping errors, but in feces, allelic dropouts and false alleles occurred in all nine loci, with error rates ranging from 6.67 to 38.10 % for the dropouts and from 6.06 to 15.15 % for the false alleles. Conclusions:These results indicate that both nondestructive and noninvasive samplings are suitable for avian microsatellite genotyping, save for fecal DNA. However, we should remain cautious of the appearance of genotyping errors, especially when using noninvasive material.

Zoonotic Blood-Borne Pathogens in Non-Human Primates in the Neotropical Region: A Systematic Review

“…Non-invasive genetic sampling was defined by Taberlet, et al [ 137 ] as “ the source of the DNA left behind by the animal and that can be collected without having to catch or disturb the animal ”. Non-invasive samples have been used in several studies of a wide range of vertebrates, such as birds [ 138 , 139 , 140 ], marine mammals [ 141 , 142 , 143 ], wolves [ 144 , 145 ], amphibians [ 146 , 147 ], reptiles [ 148 ], fish [ 149 , 150 ] and non-human primates. Non-invasive samples are known to have low quality and low quantity of DNA [ 151 , 152 , 153 ].…”

Blood, sweat and tears: a review of non-invasive DNA sampling

“…Some authors clearly stated the invasiveness of the different methods used (e.g. Dai et al, 2015;Yannic et al, 2016;Cullingham et al, 2016), however, most papers where mixed DNA sampling strategies were applied did not specify which of these methods were considered non-invasive.…”

Blood, sweat and tears: a review of non-invasive DNA sampling

“…Some authors clearly stated the invasiveness of the different methods used (e.g. [49][50][51]), however, most papers where mixed DNA sampling strategies were applied did not specify which of these methods were considered non-invasive. Another facet of this issue arises when tools (e.g.…”