A vertebrate-specific qPCR assay as an endogenous internal control for robust species identification

Development and validation of a universal primer pair for the taxonomic and phylogenetic studies of vertebrates

BACKGROUND

Recent studies in the field of molecular identification have described 16S rRNA gene as a highly informative fragment of mitochondrial DNA for species discrimination. This study presents a newly developed universal primer pair yielding an approximately 350 bp fragment of mitochondrial 16S rRNA, variable enough to encompass and identify all vertebrate classes.

METHODS AND RESULTS

The primers were designed by aligning and analyzing over 1500 16S rRNA sequences downloaded from the NCBI nucleotide database. A total of 93 vertebrate species, spanning 27 orders and 55 families, were PCR-amplified to validate the primers. All the target species were successfully amplified and identified when aligned with reference sequences from the NCBI nucleotide database. Using the Kimura 2-parameter model, low intra-species genetic divergence of the target region was observed - from 0 to 4.63%, whereas relatively higher inter-species genetic divergence was observed, ranging from 4.88% to 69.81%. Moreover, the newly developed primers were successfully applied to a direct PCR protocol, making the workflow very cost-effective, time-saving and less laborious in comparison to conventional PCR.

CONCLUSIONS

The short length, high variability and conserved priming sites of the target fragment across all vertebrate species make it a highly desirable marker for species identification and discrimination.

Poaching Forensics: Animal Victims in the Courtroom

Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.