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Barcoding Whitebait

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?

YES

I have read and agree to the Crowdicity Terms of Use, the Conservation Innovation Awards 2016 Supplemental Terms and Conditions, and the Crowdicity Community Guidelines

YES

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.

edited on Oct 15, 2016 by Stéphane Boyer

DonGraves 5 months ago

In the Nelson, Tasman, & Golden Bay districts there are now many overseas tourists who are whitebaiting to supplement their travel costs. Alongside these tourists there are many more locals who are financially reliant on minimum wages in seasonal work in orchards, vineyards & potentially 'lucrative' self-employed & non-taxed whitebaiting. There is indeed a large scale problem of fishing for the juveniles of endangered native species. Imagine if Kiwi eggs or chicks were also market commodiies, ... KFK anyone? or whitebait in Kiwi egg fritters? Perhaps not eh? !!!
Q1 you proposing to test individual whitebait, or how will you be able to determine what % of whitebait catches contain the most rare & or endangered species.
Q2 How will high-tech tools like DNA screening be able to affordably & logistically collect enough data throughout the season, from the many whiebaitng streams & rivers that attract so many keen fishers?

Reply

StephaneBoyer 5 months ago

I share some of your concerns.

R1: I propose to do both. Starting from identifying individual fish to deveop the protocol. For example, if you analyse 20 or 30 fish at random from a batch you can have an idea of the species composition. But you may be missing some species if they are very rare. So a second step will be to analyse the water/mucus in which the fish are and run some quantitative PCRs to detect all species present and get an idea of the relative amounts of DNA for each species. This would be more cost-effective since a whole batch of fish could be analysed at once.

R2: There are several ways DNA analyses/results can be made available to professionals, keen fishers and the general public.
1. Large scale collection and DNA analysis of waterways could be organised at regional/national scale. This would lead to the establishment of a map of streams that are preferentially used by threatened or declining species. But you are right in that it is difficult to imagine a fully comprehensive map. And this would require significant effort and funding.
2. Individual water and fish samples could be collected and sent to a laboratory for testing. The latter will not be extremely expensive once the protocol is fully developed.


However, the current project is really about developing a protocol that works and that could be applied to these two solutions. Turning it into a mass produced and widely available test is another step I think.

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Dave_West 5 months ago

Kia ora Stéphane, Dave West here, one of your innovation ambassadors. Great idea attempting to solve a hole in documenting whitebait catches freshwater fish folk such as myself have discussed for some years. From my experience the collection method of DNA from whitebait themselves will be quite different from collecting their DNA from water, will you try both or concentrate on one collection method? If it is from the fish themselves then there are some research programs collecting whitebait that you could ask for samples from. The extraction of sufficient quantities of whitebait DNA from water will be more difficult but might be easier to apply more widely once developed.... Looking forward to chatting more. EDIT, sorry I missed your reply to Don's points but will leave my questions in although you may have partly answered them.

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StephaneBoyer 5 months ago

Hi Dave,
Yes. I want to start with fish samples to establish a protocol that works before moving to water samples, which will be more complicated. An intermediate step will be working on the residual water/mucus in whitebait catch.
Ideally, I need to get samples from all five species to fully test the protocol. I have been reaching out to few people and I think I can easily get samples for four of the five species. The rarer shortjaw kokopu is probably the one that is going to be more difficult to get. If anyone has a lead on that, please let me know. I need a well preserved sample (ideally frozen), or live fish from which I could get a fin clip. But the fish needs to have been accurately identified.

Reply

The Forest Bridge Trust 5 months ago

Hi Stephane - great idea!
I see you say that the identification of juvenile whitebait using their DNA is relatively cheap - and could be made into a portable test that could be used by school children.
As I'm involved in the CatchIT Schools project (also on this site) I thought perhaps that your tool could be used as part of an add on to our programme. Children could investigate their environment this way and get involved in more citizen science.
The Kaipara, especially the Hoteo river is part of The Forest Bridge Trust's rohe, so we certainly have whitebait spawning areas. These were recently pinpointed by Kim Jones from the Whitebait Connection - and we are doing pest control along these riparian margins to ensure eggs don't end up a feast for a rodent or two!.

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StephaneBoyer 5 months ago

Thanks for the comment. Yes, once the portable test is operational, it could be used by school children. There is plenty to discuss and to learn from this activity and my aim is to make the test as cheap as possible so it could be distributed to as many as possible. A network of schools monitoring whitebait species across the country with this test would be amazing.

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Glenn Aguilar 5 months ago

Great idea Stephane. I would also suggest mapping your results so that an intuitive presentation of where the different identitifed species are located is available to both the data collectors and eventual public users.

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StephaneBoyer 5 months ago

Thanks Glenn,
Yes of course, mapping the distribution of each species over a large scale would be possible. All you need is little hands to either collect water samples or run the test. As mentioned before, schools could do this. It would offer a nice opportunity to discuss DNA and genetics in school classes. A great outcome would be to have a network of schools, communities and members of the public participating byrunning analyses every year to follow trends. With a test that is easy to use and cheap, I think this is absolutely doable.

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Michele frank 5 months ago

Hi Stephane don't forget to complete the next step of the process

You must answer two more questions in your idea submission form to pass this last milestone:

List five other ideas posted in the challenge that excite you. Why?
How could you improve your idea?
Click on the "Edit your idea" button in the milestones window above your challenge to access your original post and answer the additional questions. You can also click on "Edit" in the "Author's tools" bar above your idea to edit your submission.

Make sure you make it through to final judging.

Cheers
Michele

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StephaneBoyer 5 months ago

Working on it...

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Christopher Wingate 5 months ago

Love kiwi whitebait :-) Great idea- you have my support.

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