DNA barcodes earn their stripes – News

 

A Grass Skink (Lampropholis guichenoti) or maybe a new species?

A Grass Skink (Lampropholis guichenoti) or maybe a new species?

GTAC's 2014 DNA barcoding results are in and they raise the prospect that students have discovered a new species.

DNA barcoding complements classical approaches to describing and identifying species. Most of us know of barcodes as the irregular zebra pattern displayed on commercial products. Scan the barcode and it identifies the product. DNA is made up of building blocks called nucleotides and a DNA barcode is a nucleotide sequence obtained for a short, conserved region of an organism’s genome. In principle, the DNA barcode sequence uniquely identifies the species.

Traditional taxonomy often relies on the expertise of trained specialists who have invested their scientific careers on understanding the subtle differences between species of a particular group of organisms. By contrast, the expertise required for DNA barcoding reduces to a few fundamental protocols in biotechnology: DNA amplification by polymerase chain reaction (PCR), gel electrophoresis for assessing the PCR product, and DNA sequencing. This makes DNA barcoding an ideal theme for students of Unit 4 VCE Biology.

GTAC has partnered with Museum Victoria (MV) and the Australian Genome Research Facility (AGRF) to generate DNA barcodes for Victorian reptiles. For the 2014 program, the collaboration extended to over 250 VCE Biology students representing 10 Victorian schools. Reptile specimens were collected at the Alpine National Park by MV herpetologists and curated at the Museum. Liver subsamples were cut from 33 specimens and sent to GTAC where students extracted the genomic DNA from the subsamples, copied the CO1 gene of the mitochondrial DNA using PCR, and assessed the PCR products by gel electrophoresis. The PCR fragments were then sent to the AGRF for sequencing.

The aim was to have two or more consistent DNA barcodes generated for each reptile specimen by different students from different schools in different labs on different days. Consistency under these circumstances provides confidence that the DNA barcode for any given animal is authentic. This criterion was achieved for 23 of the reptiles with sequences obtained for another seven that remain to be cross-checked.

What did the data generated by the students reveal? The data showed that, at the level of their DNA, dragon species grouped together and skink species grouped together, reflecting the traditional classification schemes.

Each reptile species represented by multiple specimens also showed small variations in DNA sequences within the species. These are point mutations recognised as substitutions in which one nucleotide has been swapped for another. In a gene of some 664 nucleotides, it is reasonable to expect a few nucleotides differ between individuals of the same species. After all, that’s what alleles are.

What came as a surprise was that the specimens named as grass skinks (Lampropholis guichenoti) fractured into two separate groups according to their DNA barcodes. Barcodes showed just a couple of nucleotide differences between each member of the same group yet there were almost 50 nucleotides different between the two groups.

Is this a case of cryptic diversity, in which a single superficial species turns out to be two different species detectable at the level of their DNA? Or is it a demonstration of the power of DNA barcoding to expose species misidentification, even if in the hands of the taxonomic specialists? At the moment we don’t know. We’re working with our collaborators at Museum Victoria to explain this finding but there is no question hanging over the value of DNA barcoding as a collaborative educational and scientific venture between students and scientists. Here at GTAC, DNA barcodes have earned their stripes.