Collecting in collections
A new technique developed at the Australian Museum allows us to make better use of historical insect collections for DNA barcoding.
DNA barcoding is a technique for identifying species. It works much like the barcodes on products in a supermarket: each species has a unique DNA sequence that one reads and compares to a central database to get the corresponding species name. The success of DNA barcoding depends on the accuracy and completeness of the underlying DNA sequence databases, so it is unfortunate that only a third of DNA barcode sequences in public databases are associated with species names. Our new technique provides hope for setting these records straight by more easily sequencing the degraded DNA of identified museum specimens, the bulk of which are decades old.
DNA researchers prefer to work on freshly collected specimens, with intact DNA, which allows them to use genomics-based high-throughput workflows to process their material. Curating and identifying the specimens so collected is the bottleneck in the DNA barcoding process, but neglecting this aspect has the potential to bring down the whole edifice. Museum collections, with their wealth of identified specimens, are therefore vital to the DNA barcoding movement. Our technique brings those already identified, decades-old museum specimens back onto the playing field.
The new protocol works best for specimens up to 25 years old. We were able to get DNA barcode compliant sequences (for building a reference DNA barcode database) from 70% of beetle and moth samples up to 25 years old, and we got enough data to query existing databases and get an accurate identification for 99% of these specimens. For specimens up to 50 years old, success rates fell to 50% and 67% respectively. These success rates compare favourably with previous studies but this protocol has the advantage of simplicity (a 2-step protocol versus 5- or 6-step protocols) and scalability, meaning that it can be adapted for robotic workstations in high-throughput lab workflows.
Museum collections have been built with decades or centuries of collecting and curation effort. Museum specimens are the ultimate reference points for species names, and sequencing older museum specimens allows one to connect the dots between the heritage scientific literature and the mountains of environmental DNA data resulting from next generation sequencing datasets. When an unusual insect pest is detected in a port, authorities need to establish whether it is a local or exotic species. This may be very difficult to do with our incomplete knowledge of the native fauna, and almost impossible for insect larvae. DNA barcoding provides a way to do this rapidly and our new method will make it more accurate. Collecting in a collection may provide the bridge to the future.
Dr Andrew Mitchell
Senior Research Scientist
Mitchell A (2015). Collecting in collections: A PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens. Molecular Ecology Resources (Online Early)