The aim of this project is to develop a DNA-based diagnostic test to identify the different species of whitebait and to detect the presence of threatened or declining species in whitebait catch and in streams.
Whitebait are the juveniles of five New Zealand native species of galaxiid fish that migrate from the sea upstream in spring. Three of these species are considered to be declining, a fourth is classified as threatened and only one is of least conservation concern. However, juveniles cannot be differenciated morphologically and all five species are caught and sold under the name whitebait. Because of this ‘larval blackbox’, whitebait are being harvested without appropriate data to ensure sustainable management.
Using a DNA barcoding approach, it is possible to identify animals based only on the DNA sequences of their COI gene. This region of the genome is similar within species but different between species, and can therefore be used for species identification and detection.
What conservation problem are you trying to solve?
New Zealand’s whitebait consists of the young of five migratory galaxiid species. Three species are ranked as 'declining' (inanga, koaro, giant kokopu) and one is ranked as 'threatened' (shortjaw kokopu). Overharvesting of juveniles has been recognised as a main cause of decline and threat for galaxiid fish for more than 10 years. There is a need for a convenient and accurate tool to identify juveniles in the fishing industry and to map the distribution the different species in streams
How are you going to solve this conservation problem?
We will use species-specific primers for each of the five species of whitebait to develop a DNA-based diagnostic test. Such primers only recognise and amplify the DNA of one particular species. A positive DNA amplification from a particular primer set indicates the presence of the corresponding species. Species specific primers will be designed based on the DNA sequences of the five species of whitebait which we will obtained from analysing correctly identified adult specimens. Species-specific primers will then be used to identify the species in frozen and fresh whitebait. Water samples will also be collected during the 2017 whitebait season (mid-August to November) and tested as they are likely to contain whitebait DNA. This protocol does not require expensive DNA sequencing and the testing can be conducted in the field. We will develop a testing kit to use with the Bento Lab portable laboratory (see picture).
What makes your idea new and unique?
The identification of juvenile whitebait using their DNA is highly accurate can be relatively cheap. It can be made into a portable test that could be undertaken with minimal training by conservation officers, fishermen, environmental consultants or even schools. The detection of aquatic species based on DNA in water samples has been conducted in other countries to detect endangered or invasive aquatic species. The methodology is therefore available but it has never been applied to whitebait.
Who will use your idea, and how will they benefit?
The rapid and potentially portable DNA test we propose could be used to determine in which streams whitebaiting can be undertaken with no risk to endangered fish species. Such tool could be used by DOC to identify streams where the majority of fish are not endangered species and protect those streams that mainly harbour large population of threatened species. The test can also be used as a marketing tool for fishermen wanting to advertise their catch as being ‘endangered species free’.
What tasks or activities do you need investment for? How would you spend a $25,000 grant?
The required equipment includes DNA extraction kits and PCR kits for approximately 100 samples (50 fish samples and 50 water samples). A portable DNA laboratory (Bento Lab) will also be required for analyses in the field. Funds will also be used to purchase whitebait from as many providers as possible with the aim of acquiring a wide range of samples. Funds will also be used for transportation to sampling sites where water samples will be collected for environmental DNA analysis or postage of water samples collected by schools and other collaborators.
Are you a New Zealand citizen or resident?
List five other ideas posted in the challenge that excite you. Why?
Immersive conservation ; Pollinator wall ; E.T. find kiwi ; River snake ; Nothing is more powerful than effective legislation to save the environment.
How could you improve your idea?
The proposed PCR-based test requires samples to be shipped to a laboratory or to be analysed in the field using the Bento Lab. Although this is accessible to anybody with minimum training, and could be very attractive to schools, the cost of the Bento Lab may make this test not affordable to individuals.The Loop-Mediated Amplification technique (LAMP for short) is a recently-developped method for detection of specific DNA using a very simple device. The DNA sample is placed in a tube, the device heats the sample and after 20-30 minutes if the probes (primers) found matching DNA, the content of the tube turns fluorescent (http://www.ajtmh.org/content/82/4/591/F2.expansion). Developping a LAMP test specifically for each species of whitebait requires more work than I originally anticipated, but would make up for a much more portable, easy to use and cheap test (see new Picture). This would lead to the development of a test similar to the BioRanger (http://shop.diagenetix.com/category-s/100.htm/). I am working at developping a protocol for this with help from a colleague a Massey University. The first stages of my project are unchanged, but the development of the final testing protocol will vary and lead to a BioRanger-like test.