Big Bio Quiz 2013

On June 4th we will be holding the annual Bio Biology Quiz at Lincoln University where Canterbury Schools compete to see who knows the most biological trivia. One of the set of questions this year is on information found on this blog! The answers to the 10 questions can be found in the blog stories going back to Danger UXB! What happens to poison in pest carcasses? from January. Welcome if you are a secondary student new to this site. Just to get you going, the answer to the first question is 'Darwin'.

Field tripping coast to coast

Rifleman in matagouri at Glentanner
Photo by Jon Sullivan

Mid-semester break was field trip season for our undergraduate ecology classes this year. Our second year biological diversity course, Ecol202, did their annual three day biodiversity coast-to-coast between Lincoln and Punakaiki. Our third year applied ecology and conservation course, Ecol302, did their annual three day trip down to Glentanner on the shores of Lake Pukaki beneath mighty Mount Cook/Aoraki.

Since last year's field trip season, NatureWatch NZ was launched. NatureWatch NZ is a website for online sharing of observations of nature. We've been making use of it in some of our assignments this year (see my blog post here on using it for our second year nature journal assignments). This way, all the observations that students make in their assignments don't go into spreadsheets that get lost or buried in staff hard-drives but instead become part of a long-term, public archive of New Zealand nature. That's a good thing.

This year, our Ecol202 class has been entering all of their field trip data directly onto NatureWatch NZ. That includes all shrub and tree species in their group 10 m by 10 m plant plots, all the birds they saw and heard in their five minute bird counts, and all the types of stream invertebrate they found in their stream kick sampling. The online community of NatureWatch NZ has helped us get our identifications correct, for all the observations with attached photos.
Noting down the species you find can yield some surprises. In last year's Ecol302 field trip, we found a barberry species in Geraldine's Talbot Bush that had not been recorded wild in New Zealand before (here's the observation now on NatureWatch NZ). This year's Ecol302 surprise find was the pretty little native plant, the tarn speedwell Parahebe canescens in full flower in Tekapo Scientific Reserve.

You can see all of the species we saw on our field trips this year in the NatureWatch NZ projects for each course. Click the "More..." button to see a live feed from NatureWatch NZ of the latest observations in those projects.
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View more observations from Ecol202: Biodiversity Coast to Coast on NatureWatch NZ »

View more observations from Ecol302: Applied ecology in the Mackenzie Basin on NatureWatch NZ »

Of genes, genus and genitalia

Can you judge a book by its cover? Does the external appearance (or morphology) of an individual tell you something about what's happening inside? Does knowing where an individual is physically found tell you something about what's happening inside? We're often told not to judge a book by its cover but is this good advice?

Each year in my first year evolution course I run a game theory lab where the students use the principles of game theory to try and collect the most points in a series of exercises. Basically, they can choose when to cooperate or not cooperate with other players. I have run this lab for 10 years now and very early on I noticed that the winner of the one-off games always seemed to sit in the same part of the lab room (4 rows back and 2 in). This was the case in 9 out of 10 of the years. I'm not sure why this is the case but there you go. Additionally, I started picking three students in the lab prior to the game theory lab who I thought would win the game theory competition. It is not clear to me what traits I use for this but it seems that the covers did say a lot about what was inside and also that where the individual was also counted. For 5 years in a row I was right. This year my main choice sat at the back... what would win out? The individual or the position. Well the individual did win the game but the student in the position (4 back and 2 in) was second! So the cover judging seems to work (at least some of the time).

In biology we often judge the content from the cover. If we look at two closely related species then we will use their slightly different morphology to identify which species they are in. If we find individuals that have bits of both species morphology then that suggests that the individual might be a hybrid. One example of this is with a butterfly genus found in New Zealand. Zizana has an almost worldwide distribution and there is some debate about how many species there are, although most agreement is that there are four. In New Zealand there are two species, Zizana labradus, the common blue, which is found in the North Island and parts of the South Island, and Zizana oxleyi, the southern blue, which is found in the South Island. The southern blue is assumed to be a native species while the common blue is found throughout Australia, Melanesia and Polynesia. The two species have virtually identical behaviour and habitat prefences and both use Fabacea plants as hosts. Visually, however, there are differences in the patterns on the respective species wings. Within the area between Blenhiem and Christchurch both species are found and a number of individuals that share mixtures of these patterns from both species. So the covers of these butterflies would suggest that there are two good species here with some hybrids being produced where the two species overlap in space.
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Ecologists at Lincoln University, Steve Wratten, Mark Gillespie, Rob Cruickshank and Ben Wiseman, have joined forces with the extremely experienced lepidoperist George Gibbs, from Victoria University, in order to explore the species boundaries of Zizana. They recently published their results in Systematic Entomology. They recorded variations in wing colouration and male genitalia. Why the fascination with male naughty bits? Often with insects a key difference between species, that are often morphologically similar, are their genitalia. If you think of the male genitalia being a key and the female genitalia as being a lock then only the right key, i.e. a member of your species, can use the lock. Therefore, mistakes in breeding between species are minimised. The team also looked at a group of mitochondrial and nuclear gene regions to examine genetic boundaries. Samples were collected from around New Zealand. Individuals with 'hybrid' genitalia and wing patterns were mainly concentrated around Kaikoura (north east South Island) which suggested that this was the boundary between species. However, mitochondrial DNA, which found a distinct difference between the two species suggested that the boundary was in the north west of the South Island. The nuclear genes found no significant difference between individuals in either species at all! So there is conflict among the data sets. Maybe the book shouldn't be judged by its cover? How to resolve this?

The difference in pattern between the mitochondrial and nuclear genes is not uncommon. Mitochondrial genes change at a faster rate and so this result might represent a recent origin of the southern blue or that hybrid matings only occur between female southern blues and male common blues (mitochondrial DNA is only passed down the maternal lineage whereas nuclear DNA comes from both parents). Therefore, there will be no difference in nuclear DNA, as it constantly mixed between the species, but a clear difference for mitochondrial DNA. For similar reasons butterflies that look like common blues may have mitochondrial genomes of southern blues. What does it all mean? Are there two species of Zizana in New Zealand? The morphology and mitochondrial genes say yes whereas the nuclear genes say no. What would lead to this pattern? Either very recent speciation of the southern blue or a long period of hybridisation. What would help? If samples were obtained from Australian Zizana then this would shed light on whether Zizana had been hybridising for a long period of time. Can you judge a book by its cover? For Zizana you can in most of New Zealand but not in the northern South Island.

The beaten track: panning panbiogeography



A track (but not a panbiogeography one)

I am an apostate. I've always wanted to say that but, of course, there are only certain situations in which you can say this. How did this come about? Well.... way back in the late 80s and early 90s when hair was big and ties were small I was a keen postgrad student at University of Otago. I was into evolutionary biology and the most exciting game in town at the time was biogeography (hey it still is!). Biogeography is the science of explaining the distribution of species - why a species is found in one place and not another. Species can either move themselves around through dispersal or they can be moved around by earth processes like continental drift or have their range split by things like mountain uplift - what is generally called vicariance. At the time vicariance was in the ascendency and dispersal was a dirty word to use. Hitting the top of the ecology and evolution charts at the time was a concept which we might think of as ultra-vicariance. Panbiogeography was the idea of Leon Croizat, a European biogeographer who had lived much of his life in the New World. He wrote some enormous books in the 1950s and 60s on his idea that life is the uppermost geological layer, and like other layers, the distribution of this layers is basically down to geological processes. Dispersal was seen as something that didn't have any real biogeographical meaning. By drawing lines, called 'tracks', between different populations of a species or close relatives you could reconstruct the history of the former wider distribution of a taxon which had been split apart over time. Quite what these tracks represented was a little hazy but that just added to the mystique. Croizat's ideas had mostly come and gone but a bunch of mainly New Zealand biologists had championed the idea of panbiogeography during the 1980s and it was again popular.

It was a great time to be a biogeography student. There was a whiff of revolution in the air and many of the main players would pass through University of Otago. Mike Heads lived in Dunedin at the time (and continues to be a major proponent of panbiogeography), my supervisor Russell Gray published in the area, Robin Craw, a leading disciple also lived locally, and Rod Page, who examined my PhD thesis, would visit from time to time. At the time a special issue of the New Zealand Journal of Zoology was published on panbiogeography which showcased this new method. So I was well-trained in this field, exposed to all the main players and could explain the methodology and philosophy of panbiogeography when I found myself at conferences in the States. I could tell my tracks from my main massings, my ocean baselines from my minimum spanning tree. I was a panbiogeography cheerleader! So what happened?

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For me DNA happened. As our understanding of what DNA can tell us increased we were better able to understand the timing of evolutionary events. In study after study that my postgrads and I did, in moths, spiders, penguins, beetles, bats and mites we found that species distributions were just too young to have been derived from geological processes. This meant that dispersal was a dominant factor. This was also found in most New Zealand studies in most other labs. So a panbiogeographical explanation just didn't seem to fit with the timing of the patterns that we observed in taxa; lineages in New Zealand are just too young to have been here since the Gondwanan breakup and must have successfully dispersed here on their own. This idea of the importance of dispersal has been a constant theme on this blog, e.g. here, here, here, here, here, and here. And there panbiogeography languished for a time. For the last decade or so I have found my research turning more and more to looking at measuring the impact of dispersal on biogeography. However, their has also been a recent resurgence in panbiogeography papers that seem to have as a central theme the fact that we should not trust molecular studies in general and the molecular clock in particular.


(Adrian, a young and keen panbiogeographer, sitting on a track in the late 1980s)
The continued promulgation  of an idea that seems to ignore the last 30 years of progress in evolutionary theory, molecular biology, computational biology and geology seems staggering. Jon Waters (University of Otago), Steve Trewick (Massey University) and I decided that enough was enough and that we needed to question how such an outmoded idea was still getting published in quite respectable journals. We recruited a few colleagues to help and have now published a Point of View in Systematic Biology. We focussed on one of the main tools of panbiogeography, the track. The track connects different parts of a taxon's distribution and has been defined as giving 'shape to or expression to the space and time that necessarily intervenes between disjunct localities' which does not actually tell you how and where to put your lines on a map (which seems to be arbitrary to a particular scenario). Often the tracks are in disagreement to phylogenetic reconstructions for a group and it is not clear then what a track is showing. Finally, as new data is collected, especially fossils outside the current known distribution, track networks will radically change. We conclude that given the lack of utility of panbiogeography, its lack of hard methodology, its lack of quantitativeness and the amount of evidence against the interpretations that it generates, that the only reason that panbiogeographers continue to publish is through some kind of feeling of being fair on the part of editors. However, science is not about giving 'equal time' to all hypotheses otherwise I would have to teach a lot more creation science. If hypothese are repeatedly shown to fail or lack usefulness then they should be put to one side until someone works out how to make the idea useful and successful. We feel that panbiogeography is in this situation and it is currently distracting a number of researchers from using methods that explain the world better.

King of the rock! Founder populations on islands

One of the downsides of your children moving to the teenage phase is that you tend to miss out on the latest movies for kids. Many of these movies that I watched with younger versions of my sons have become personal favourites. Recently, I happened to see what I consider to be the best of the Disney films of the modern era - Mulan. I like the story, I like Eddie Murphy as the dragon, I like the songs and I especially like that Mulan isn't a princess! I came across it on the telly last week and enjoyed catching up with the characters after a few years. One scene that always made me laugh was when the soldiers decide to go skinnydipping while Mulan is bathing (for those of you that haven't had the pleasure, Mulan pretends to be a man so that she can join the Emperor's army to save China as well her father's honour). Particularly amusing is when the soldiers play king of the rock with one of them sitting on a rock in midstream and knocking allcomers back into the water. I recall playing a similar game in my youth. In the game the king has an advantage because the challenger is coming out of the water whereas the king is on solid footing on the rock with gravity on their side. This time while watching the movie the scene also reminded me of a paper that has just been published by my colleagues Rob Cruickshank, Hannah Buckley and me in the journal Trends in Ecology and Evolution. What?

All of us are interested in how populations form in new habitats. Rob and I tend to be more interested in the long term evolutionary patterns whereas Hannah is more interested in the ecological processes. Over the last few years we have learned how to speak to each other so that the evolutionary biologists can understand the ecologists and vice versa. There are several areas in which this seems to help. One of the puzzles of looking at populations that have established in new habitats, such as islands, recently glaciated terrain, volcanic areas and so on, is that, despite a constant 'rain' of colonisers carrying different genes, most populations have a reduced genetic diversity. There are several ideas as to why this is the case. Recently, Jon Waters from University of Otago and his colleagues speculated that the 'founder (first established population) takes all'. There may be several explanations for why this happens but Jon and his team favoured what is termed 'space pre-emption'. In other words the first established population is king of the rock and newly arriving individuals with different genetic haplotypes will find it physically difficult to find the space they need to survive and establish and then to push the king off his rock. So the order of arrival of different populations is crucially important, a population arriving second to an island A will struggle to establish whereas it will find it easy if it is first to island B.


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We followed on from Jon's paper by suggesting other reasons by which this phenomenon could play out. First, certain populations may have a competitive advantage (a useful behaviour or physical trait) that allows that group to be successful. An individual is more likely to become king of the rock if they are strong, large or agile. Second, niche specialisation to the particular area could help the established population. The more that you have played king of the rock in one area, the more you learn about best places to stand to anchor yourself to the rock. Third, incoming populations may be genetically incompatible with the established population which will affect their chance of mating. Those that turn up at the swimming hole just to relax will not end up as the king of the rock. Fourth, there may not have been enough time for new populations to have arrived on the island. You may be king of the rock simply because there are no or few challengers. There are no doubt other possibilities to explain this phenomenon and the most important thing is that all of these factors could be at work.

What is most important about this debate is that we are dealing with a biological process that falls a little between two major types of study. Ecological studies tend to be interested in what is happening over a few generations. Evolutionary studies tend to be interested in what is happening over thousands of generations. As such, historically ecologists and evolutionary biologists have not worked together that closely and even have different languages for similar concepts. Processes like species establishing on islands take place somewhere between these ranges in the tens to hundreds of generations. As most founding events take place over the intermediate range of generations our understanding has often been slowed by misunderstandings between the different types of research. The upside of the Waters paper and our response is that scientists from ecology and evolution backgrounds are finding ways to communicate and understand one another. Now that I think about it, that's one of the messages of Mulan as well.

What's wrong with DNA barcoding?

In many sci fi tv series or movies there is a point at which a starship arrives at a new planet. The captain usually says something like "Scan for life forms" and the science officer is able to push a few buttons and give a nice report on the life on the planet, ecosystems to be found and so on. Sometimes this makes me smile wistfully and think about how great it would be to be able to do this. Sometimes I get a little annoyed that an endeavour that currently takes thousands of people huge amounts of time and resources every year just to get a little closer to knowing this information for Earth is being treated so cavalierly. The idea that we could quickly identify and measure biodiversity is a powerful one and there are many innovations that are certainly helping to speed the process up. One of these is DNA barcoding. The basic idea of DNA barcoding relies on different regions of our DNA changing at different rates over time. Some regions change slowly, taking hundreds of millions of years, others change from generation to generation. DNA barcoding relies on the fact that some DNA regions change fast enough that different species have a unique pattern within gene regions but slow enough that different populations within that species share the same pattern or 'barcode'. This approach has now been around for a decade and has become useful for two related but different tasks: specimen identification and species discovery. Specimen identification occurs when we have a sample from an individual, say fruit fly eggs in some bananas, and need to know which existing species they belong to or which country they have come from. Species discovery occurs when we have a bunch of samples, say a bunch of big, black forest beetles from throughout the South Island, some of which we already know and others that look a little different, and we see if the different looking group are significantly different from the known species DNA and might warrant be species themselves.

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DNA barcoding has had some fierce opposition over the last ten years. Many researchers have felt that species identification is more complicated than just simply finding whether an individual possesses a particular chunk of DNA and there have been debates about whether one gene region, usually CO1, is reliable enough. However, many of these issues have been dealt with or acknowledged and DNA barcoding is becoming a useful tool in the ecologist toolkit. Rupert Collins and Rob Cruickshank have put together a review paper in Molecular Ecology Resources that looks at the 'seven deadly sins of DNA barcoding' where they examine common mistakes made in DNA barcoding research (which become just the sort of thing that annoys other researchers about this method). The first is a failure to present clear hypotheses, which is not unique to this type of research. Second, DNA barcoding relies on starting with DNA sequences from identified species and often this is a source of human error which invalidates the rest of the research. Third, often the term 'species identification' is used which is a conflation of species discovery and specimen identification which have very different goals and methods. Sins four to six are to do with inappropriate use of different statistical methods and the seventh focuses on how researchers often do not correctly interpret the genetic variation that they find between their specimens. Despite these issues, Rupert and Rob are optimistic about the future of DNA barcoding as it has become an accepted tool and more time is spent on fine-tuning the method. Who knows, maybe starship captains of the future may be able to get that quick survey of a new planet's biology after all.

Danger UXB! What happens to poison in pest carcasses?

Lincoln University has a special link to the German University of Goettingen. We run a joint Master of International Nature Conservation. Students who enrol in this degree spend a semester at each university doing papers. So each year we have about 15, mainly European, post grad students in our classes from Germany. When our Lincoln students ask about doing this degree they usually focus on what it will be like in Goettingen. There is one potential hazard that I only read about last week, unexploded bombs. It took me back to a favourite TV programme of my younger years 'Danger UXB!' where a British unit went around England diffusing UneXploded Bombs dropped during the Blitz. During the second world war the allies also dropped millions of bombs on Germany. A small percentage of these bombs did not explode and are still buried in various parts of Germany, including Goettingen. Unfortunately, these bombs were not made to last for long periods and most are reaching the stage where corrosion is liable to set them off. There is (and has been) a major effort to neutralise these dangerous items before they cause casualties.

This problem of weapons working longer than intended is also an issue when it comes to wildlife pest management. A common control method for reducing numbers of rodents, possums and mustelids in New Zealand is to use poison baits. The target animal eats the bait, ingests a lethal dose of poison and dies. This has been an incredibly effective tool for reducing the impact of pest species in conservation areas. There are also a lot of people who are uncomfortable with putting poison out into the environment. What happens to the poison over time, are we creating some UXBs that may cause problems at a later date? If a possum dies from ingesting poison then what happens to the poison in the body? If a scavenger, say a pig or dog, comes along and eats the carcass then will it too be poisoned?

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Charlie Eason and James Ross from the Centre for Wildlife Management and Conservation based at Lincoln University have joined with Aroha Miller, a colleague based in Sweden, to look at this phenomenon, known as secondary poisoning, with the most commonly used toxin in New Zealand pest control, sodium fluroacetate (1080). The group looked at decades of research and their findings have been published in the New Zealand Journal of Zoology. 1080 breaks down through normal metabolism in just a few hours, so if an animal takes a sublethal dose and then is later eaten by a predator there are no particular problems. If an animal takes a lethal dose then metabolism stops at the time of death and the toxin remains.

Eason and co found that for most organisms, such as birds and invertebrates, there was little risk of secondary poisoning killing the scavenger. With mammals the risks increased although notable scavengers like pigs are more likely to become ill rather than die. Of most concern are mammalian predators. Cats and mustelids (stoats and ferrets) are likely to suffer death from secondary poisoning (although these species are often the targets of control operations in wild areas anyway). Most vulnerable are dogs that require only a very small dose of 1080 to be lethal. It was found that poisoned carcasses can remain dangerous for dogs for up to 75 days, although this is determined by how cool and dry the climate is.

So are there masses of UXBs in our native bush waiting for the unwary? For a toxin like 1080 this is not a problem for the long term. For dogs there are some problems that might extend for a couple of months. Other toxins may have more scope for UXBs. In a follow-up paper soon to be published in the same journal, Eason and Ross and several other authors look at another group of toxins, the anticoagulants like diphacinone, and find that they potentially persist for several months. So toxins are not like allied bombs that can cause problems many decades later but their effects do linger on for some weeks after the poisoning period.