30 August 2012

Molecular Ecology Conference at Lincoln

New Zealand Molecular Ecology Conference 2012
 The weekend after the New Zealand Ecological Society Conference at Lincoln University gel jockeys will be leaving their labs and heading along to the New Zealand Molecular Ecology Conference (30th Novemeber-2nd December). This conference has been happening for over a decade and usually takes about 50 people (mostly university lecturers and their postgrad students) to some place off the beaten track where they indulge in their passions for DNA, ecology, trivia, poor football skills and poorer beer. This year Lincoln University is hosting the conference at the Eyre Lodge in the Waimakariri District just north of Christchurch. A website for information and registration has now been set up. You can also contact Stephane Boyer for information.

29 August 2012

Let's Save our Forests, Native Species and Agricultural Industry... Nah, Let's Argue Instead

This blog post was written by postgraduate student Thomas Agnew as part of the course, Research Methods in Ecology (Ecol608). Thomas revisits a Lincoln University research area on the use of toxins for possum control published since the early 1990s.

Signs of protest against DOC controlled 1080 drops
The 1080 (Sodium Fluoroacetate) debate has reared its ugly head once again. Articles just weeks apart in common New Zealand media suggests that Kiwis are more aware than ever of the threat posed by pesticide and toxin applications in natural environments. Department of Conservation plans to aerially apply 1080 to forested land in Wainuiomata (Dominion Post, 08/05/2012) and Golden Bay (Nelson Mail 03/05/12)have been met with fierce opposition. Those opposed to controlling possums with the use of 1080 desire a highly selective, humane control method, with little effect on non-target species and domesticated animals, which they feel 1080 cannot claim. As our science and technology advances, new and improved methods for controlling possums and other introduced mammalian predators arise, some show promise, whilst others fade away. It is often difficult to tell whether we are making progress when it comes to pest management in New Zealand. Whilst the debate between supporters and disapprovers of 1080 rages on, I set out to investigate whether the turn of the century has meant improvement for our most loved and most hated toxin.

In 1992, Charles Eason of Lincoln University published a paper evaluating the appropriate alternatives to 1080 use for possum control1. It highlighted not only the need to develop a socially acceptable chemical product, but also the need to avoid bait shyness and resistance build up towards 1080. The focus fell with non-anticoagulants, such as Cholecalciferol and Nicotine. Within the article, Charlie explained how the lethal doses for both male and female possums for these substances had already been established, and that the next step in finding an alternative to 1080 was getting non-anticoagulants into palatable bait types at a cost effective price. I feel that this paper best represents the 1990’s scientific viewpoint of finding an alternative toxin to 1080. With that in mind, have we seen the advancements in possum control technology that Charlie suggested back in 1992?

20 years down the track, and we are still commonly debating the pros and cons of 1080 use in New Zealand, as shown by those articles mentioned above. It remains at the forefront of our nationwide attack on possums, and it doesn’t seem to be disappearing anytime soon. Just two years ago, Charlie Eason was again the lead author in a modern review of the toxicology and efficacy of 10802. This paper was an overall review of the modern day 1080 toxin, which compared it with other common toxins (including the aforementioned Cholecalciferol) for various aspects such as environmental persistence, ability to bioaccumulate, and effectiveness for killing possums. Compared with the other options, 1080 proved to have a relatively low half life, and an average level of bioaccumulation. It still proves to be one of the most potent (if not the most potent) chemicals for causing fatalities amongst possums, and acts at one of the lowest concentrations. Brodifacoum is the new kid on the block. This anticoagulant was absent from debate during the 1990’s, and it now opens up a whole new can of worms. It is a slow acting toxin, as it takes up to 14 days within the animal before any adverse effects begin. It is this form of pesticide that will fix our problem with bait shy and 1080 resistant possums. Off course, Brodifacoum doesn’t come without its own issues. It is less selective than 1080, remains in the environment for much longer, and has the potential to bioaccumulate.

1080 :  a poisoned possum displayed alongside a deceased tree weta

In my personal opinion, the aerial application of 1080 is not the perfect option, but it is the best one available to us at this time, and has been so for the last 20 years. Any attempt to introduce “new and improved” chemical products to control possums in this country will always be met with heavy competition (which I also believe to be healthy), and biological control seems to still be a fair way off. To expect those who protect our native species and our agricultural industry to control possums without an effective chemical product is, to me, outrageous. Our climate and terrain is such that labour intensive methods such as shooting and trapping cannot possibly be expected to make a significant enough impact. It is my opinion that those looking to improve the 1080 poison need to address the concerns of the general public and hardcore greenies, by making domestic animals, waterways and endangered species less susceptible to intoxication. Perhaps when this is achieved, both sides can work together in an attempt to eradicate what is arguably the worst pest in our forests.

For more on possums have a read of this, this, this and this.
1 Eason, C. (1992) The evaluation of alternativetoxins to sodium monofluoroacetate (1080) for possum control, Proceedings of the Fifteenth Vertebrate PestConference.
2 Eason, C., Miller, A., Ogilvie, S.,Fairweather, A. (2010) An updated review of the toxicology and ecotoxicology of sodium fluoroacetate (1080) in relation to its use as a pest control tool inNew Zealand, New Zealand Journal of Ecology, 35, 2011.

22 August 2012

Ecology Conference set for Lincoln

The New Zealand Ecological Society will have their annual meeting at Lincoln University in late November. The theme of the conference will be "Is New Zealand ecology on solid foundations". There will be a student only day on the 25th of November and the regular conference will run from the 26th - 28th with a field trip day on the 29th. Keynote speakers are Richard Hobbs, Trevor Worthy, Hamish Campbell, J. Bastow Wilson, Kerry Jayne Wilson and Lesley Hughes (winner of the Ecological Society of Australia award last year). There will also be a celebration of 50 years of ecology teaching at Lincoln. There will be the following symposia: Restoration Ecology, Microbial Ecology, Plant Functional Traits, Drylands Research, Next Generation Sequencing, Wildlife Management and Conservation, Community-led Projects, and Data Archiving.

We look forward to seeing you there! Registration and a call for abstracts can be found here.

20 August 2012

Say no to botrytized wines? Biological control of Botrytis cinerea in vines

This blog post was written by postgraduate student Wei Liu as part of the course, Research Methods in Ecology (Ecol608). Wei revisits a Lincoln University study on biological control in grapes published in 1999 and assesses the progress made since then.

If you think it’s weird to see your friends appreciate red wines with heavy bitterness and astringency, I strongly recommend you try noble rot wine, a famous wine with particular sweetness, made from botrytized grapes. Noble rot wine is a special product, but we do not want all the grapes to be botrytized!
 Botrytis (noble rot) shrivels the grapes, concentrating their
 sugar and flavour, and lends unique flavours to the wine (by stoneboatvineyards)

Winemakers don’t set out to make noble rot wine. Grapes occasionally become infected with Botrytis cinerea, a kind of fungus. The crop yield of grapes suffers as a result. Botrytis cinerea usually happens during wet weather just prior to harvest. After harvesting, the pathogen survives on rotten canes and leaves in the vineyard floor, or infected tissues of the vines. Then they become active again next season!

During the growing season, one of the key controlling methods is applications of fungicides. However, Botrytis cinerea will become resistant to fungicides over time, and pesticide residues in grapes are harmful to human healthy as well.
In 1999, S.R. Fowler and other Lincoln University staffs published an article about biological control using antagonistic fungi for the control of Botrytis cinerea. In their experiment, Epicoccum sp., Scytalidium sp. and Ulocladium sp. suppressed Botrytis cinerea effectively. The suppression was via competition for nutrients and space between antagonistic fungi and Botrytis cinerea, and production of toxic metabolites to Botrytis cinerea. There were some limitations to this research. This study was done only in two places: a vineyard of Lincoln University and one in Napier, and the only factor studied was in suppressing the sporulation of Botrytis cinerea on rachii of grapes.

How time flies! A research paper published in 2011 reported that Epicoccum is currently being developed commercially as a biological control method. Because Epicoccum produces metabolites which are toxic to Botrytis cinerea.

Another article published recently studied the infection of Botrytis cinerea on grapevine debris left on the ground of vineyard and inside the canopy in vineyards of Marlborough, New Zealand. Fowler’s method of measuring the severity of Botrytis cinerea, which was published in his article mentioned above, was used in this experiment.

The Botrytis cinerea problem in wine industry is a worldwide issue, but especially in New Zealand, which has a relative warm and wet winter that suits Botrytis cinerea. More advances in Botrytis cinerea control will benefit wine industry more. On one hand, unnecessary Botrytis cinerea infection could be better controlled. On the other hand, we would be able to make noble rot wine in New Zealand, and would not need to buy as much noble rot wine from France! We could just drop down to a local winery and enjoy the kiwi noble rot wine!

16 August 2012

Finding Name-os! Barcoding aquarium fish

These two species look extremely similar but DNA barcodes can
tell us that A is a species of barb called Puntius filamentosus
while B is Putius assimilis
 When you have a young family, a good and entertaining way to spend some time is to visit a local pet shop. Toddlers love to look at the kittens and puppies. When they tire of that there are more exotic pets to examine. One that seems endlessly fascinating is the aquarium fish. There are usually a number of species in different tanks in all shapes and sizes and colours. Not being a fish expert I am sometimes overwhelmed by the diversity, tanks with lesser spotted whatsits sitting next to blue-striped dodads and sometimes swimming with clown thingamys. Although I've never succumbed to getting fish, many obviously do. Aquarium fish account for about $20 billion in global trade each year! That's an estimated one billion fish moving mostly from tropical to temperate countries. That's a lot of fish! The fate of most of these fish is to live comfortable lives in an aquarium before going belly-up. For a few there is the prospect of liberation as they make it into the wild. Of 59 fish species colonisations into the USA, 37 of them are as a result of the aquarium trade. So there is a significant biosecurity problem here. If these fish establish then they may outcompete native species, modify habitats and so on.


New Zealand is a country that works hard to maintain its borders from entry by potential pest species. We have a fragile native fish fauna that is already under threat from previous introductions and habitat change. In order to manage the possible threat of aquarium fish the government has developed a list of species that are allowed to enter the country as they can be easily managed or are unlikely to survive in the wild. Of course this relies on being able to identify individuals coming into the country as belonging to the right species. For some species this is obvious but for most, especially if they are larval forms which haven't developed their species traits, this can be very difficult and time-consuming. You don't want to bring a pest species into the country that happens to look like a safe species. What to do?
Rupert Collins with many colleagues, mostly from Lincoln University, has thought long and hard about this. Rupert realised that using the appearance of fish, known as morphology, was not ideal as species often look very similar. One thing that always differs between species is their DNA. Even if two species look exactly the same they still differ in their DNA. Taking DNA samples from individuals would remove doubt about the species. This approach has been termed DNA barcoding (as each species has its own DNA code). Rupert checked to see whether this approach would work for aquarium fish species and his study is now published in PLOS One. Rupert collected DNA from 678 fish from 172 species entering New Zealand. Rupert was able to match over 90% of the DNA sequences with known named species. He was also able to show that there were at least 10 cryptic species (species that happened to look like another species on the safe list). From this study, Rupert was able to develop a procedure that can be used to make fast and accurate identifications of fish coming into New Zealand. So the next time a toddler asks you what that fish is you can be confident in the name written on the tank!