This blog post was written by postgraduate student Jonathan Ridden as part of the course, Research Methods in Ecology (Ecol608). Jonathan revisits a Lincoln University research area that looks at using DNA to identify invasive species (fish in this case) published in 2012 and 2013.
These carp were accidentally introduced to New Zealand in the 1960's as part of a goldfish consignment from Asia and Europe (the carp’s native continents). The multiple impacts these fish have on waterways in general is very bad. They stir up the pond bottom, muddying the water and destroying other aquatic organisms’ habitat. Of course, this leads to further degradation of water quality and eventual decline of associated waterfowl populations. On a good day in Centennial Park, you can still find ducks, but much fewer than when I was young, to feed some bread. This example just goes to show the impact something like an exotic and highly invasive fish species can have on waterways in New Zealand.
|Group of ducks floating on a pond. Now you can only imagine whats going beneath the surface! Fancy a swim? Photo by Thom Quine|
New Zealand has a reputation for having a very strict and stern view on biosecurity and bio-protection. The impacts of invasive species to New Zealand ecosystems can have detrimental impacts on the native flora and fauna. Fish are a major threat, as there are other species that are just as invasive as the koi carp (e.g. perch, rudd and catfish). One potential avenue for invasion of fish species into New Zealand is via the ornamental aquaculture trade. When bringing fish into New Zealand for sale and commercial ventures, many different types of fish with highly variable morphology (fish with different colours, sizes and shapes) cross our borders.
These two fish look similar, but are different
species based on DNA analysis.
Species A is Puntius filamentosus,while
species B is P.assimilis.
(Adapted from Collins et al 2012)
Many different methods can be used to distinguish the species of fish. This includes morphological identification of specimens using keys. However, this process can be difficult and requires highly trained individuals to work quickly and efficiently at the border to identify risk species. An alternative, rapidly improving method to identify organisms is to use DNA barcoding. This is done by taking a sample of DNA from a specimen to the laboratory and using molecular methods, producing a unique barcode attributed to that specimen. Water in which fish has been living in during transport between countries, can be used to get DNA sequences from, rather than clipping a part of the fish off (See this paper). Rupert Collins and colleagues from Lincoln University completed a study which used a suite of techniques centered on DNA barcoding, in order to accurately identify incoming ornamental cyprinid fish species at the border. This involved developing a reference library of fish specimens and their associated DNA sequences, using the common mitochondrial barcoding gene region cytochrome c oxidase subunit I (or CO1 for short). There are several benefits to producing a physical library of specimens for concurrent use with molecular data. It makes it faster to reinforce the accuracy of the identification of a specimen, which is of vital importance from a biosecurity point of view. Also, having a good database or library of specimens and DNA sequences will help future identification of species be quick and accurate.
|Is this Nemo?, it doesn't look like him but DNA |
Barcoding could help determine whether or not it is
Photo by Harsha K R
As a practicing molecular ecologist I have a strong appreciation of the value of good genetic data, when used appropriately. I should be clear that, it is vitality important that we have an accurate and efficient tool for identifying fish so we can manage incoming fish specimens that may present a risk to our waterways and biota. DNA barcoding can be complimented with multiple methods to ensure we have the best toolbox for managing potential biosecurity threats and giving our fish front-line protection. Because you never know when you may end up finding Nemo!
If you want to find out more about DNA barcoding for biosecurity of ornamental fish check out the paper at this link http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028381
Collins RA, Armstrong KF, Meier R, Yi Y, Brown SDJ, Cruickshank RH, Keeling S, Johnston C 2012. Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade. PLoS One 7(1).
Collins RA, Armstrong KF, Holyoake AJ, Keeling S 2013. Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA. Biological Invasions 15(6): 1209-1215.