Ducks of the corn

Our research shows that there are many scary things lurking in the cornfields. (The Mallard head source, under a CC BY 2.0 license; rearranged by M. Wille).

Our research shows that there are many scary things lurking in the cornfields. (The Mallard head source under a CC BY 2.0 license; rearranged by M. Wille).

By Jonas Waldenström

The Mallard is the most widespread and abundant duck in the world. It inhabits almost any type of water body, from the shores of great open lakes, to the smallest ponds. Most people don’t really notice them; they are just there. (One exception here on the eco-evolutionary dynamics’ blog).

Our negligence of Mallards should not be taken as they are unimportant. On the contrary, they are important parts of the food web, as consumers of invertebrates and seeds, and providers of juicy dinners for aerial raptors such as Peregrine falcons and White-tailed Sea-eagles. They make good food for mammals too – many a fox has dined on Mallards eggs, and we ourselves shoot them in large numbers. Very large numbers.

In our research we are interested in Mallards as hosts for diseases, especially the influenza A virus. We have studied virus carriage in great detail over the last 12 years and are now trying to connect the various pieces to a coherent epidemiological picture. However, one part of the puzzle has been largely neglected until now: their stopover ecology.

Yes, Mallards are migratory, especially the populations that live on northern latitudes . The ducks we trap at our field site originate from the Baltic states, Finland and Russia, and migrate predominately to southern Denmark and northern Germany. Daniel Bengtsson in my lab works on Mallard ecology, focusing on what the ducks do when they are on stopovers during migration.

Mallards are relatively heavy birds, with an average body mass of just below one kilogram. Migration is taxing and requires a lot of energy, and with the heavy bulk the Mallards don’t fly the whole distance at once; rather they make several bouts of migration interspersed with longer stays at suitable stopover sites.

So what do the ducks do all day, and all night? A seemingly straightforward question. During daytime we can watch them with binoculars and note their behaviors. But it turns out they don’t do very much. A typical Mallard in an autumn day in November does pretty much nothing more than sleeps, poops, and preens its plumage. Pretty dull. Occasionally it may dabble a little in the murky water, but on average they are just chilling.

This makes sense from a prey perspective: if you are a juicy meal you should stay in groups and divide the predator scouting among individuals. The talons, beaks and jaws are always ready to take a piece of you. However, at the same time a duck needs to replenish the energy stores in order to finish migration. So if you don’t feed much at day, you have to do it at night.

Together with colleagues in Germany and Sweden we have started to tap into the whereabouts and behaviors of Mallards during migration. At our aid we have modern telemetry gadgets that help us track the birds remotely. Last week we published a paper in PLOS ONE with the latest results.

A Mallard ready for departure (Photo D. Bengtsson)

A Mallard ready for departure (Photo D. Bengtsson)

We equipped wild-caught Mallards with small GPS-transmitters, fastened on the back of the birds as little rucksacks. These devices took a GPS fix every 15 minutes, thereby allowing us to see where the birds moved, and when. However, in order to get the data we first needed to find the birds in the field and then download the data with a receiver on a radio link. The best way of doing this was to make daily flights in a light airplane, gently soaring amidst the clouds until the receiver made a ‘beep’, signaling that it located a duck. On days with bad weather the plane could not be used; instead we trudged through kilometers of shoreline on foot.

In the paper we analyzed movement patterns and habitat use of 16 individuals followed across a couple of weeks. During daytime the ducks behaved just as I said before – they didn’t move much at all. But when dusk fell all birds got on their wings and flew inland, sometimes quite long distances. Each duck seemed to follow its own nightly routines, but it was also evident that some ducks followed other ducks around. A typical night would consist of a first flight from the coast to an agricultural field, most often harvested cornfields. In the fields they would settle for a short while, often less than an hour, likely stuffing their crops full of leftover corn, before embarking on another flight out to various inland water bodies. In these ponds and wetlands they spent the reminder of the night. Just before dawn, the flight would go in the opposite direction, including a short stay in the cornfield, before settling down on the coast again.

An airial view of the study site. Ducks chill by the coast at day and fly out in the agricultural landscape at night (Photo D. Bengtsson)

An airial view of the study site. Ducks chill by the coast at day and fly out in the agricultural landscape at night (Photo D. Bengtsson)

Example of typical mallard movements between frequently used sites on southeast Öland, Sweden, October – December 2010. Inset A: Orange ovals = coastal meadows; yellow ovals = maize fields; red ovals = flooded areas; blue ovals = coastal day-roosts; green ovals = coastal reefs used as day-roosts; grey circle = duck trap location. Inset B: Yellow oval (1) = maize field visited during dawn and dusk; red ovals (2) = various small (flooded) wetlands on alvar steppe (the upper one reaching into a maize field), visited at night; green oval (3) = coastal reef used as day-roost. Inset C: Yellow oval (1) = two maize fields frequently visited, mostly during dawn and dusk; red oval (2) = flooded area (stream) visited most nights; light purple oval (3) = flooded pasture visited during two consecutive nights (probably for feeding); blue oval (4) = most frequented day-roost. From the article in PLOS ONE, under CC Attribution License.

Example of typical mallard movements between frequently used sites on southeast Öland, Sweden, October – December 2010. Inset A: Orange ovals = coastal meadows; yellow ovals = maize fields; red ovals = flooded areas; blue ovals = coastal day-roosts; green ovals = coastal reefs used as day-roosts; grey circle = duck trap location. Inset B: Yellow oval (1) = maize field visited during dawn and dusk; red ovals (2) = various small (flooded) wetlands on alvar steppe (the upper one reaching into a maize field), visited at night; green oval (3) = coastal reef used as day-roost. Inset C: Yellow oval (1) = two maize fields frequently visited, mostly during dawn and dusk; red oval (2) = flooded area (stream) visited most nights; light purple oval (3) = flooded pasture visited during two consecutive nights (probably for feeding); blue oval (4) = most frequented day-roost. From the article in PLOS ONE, under CC Attribution License.

A postdoc in our lab summarized this study as “ducks like water, and food”. Although correct, I think we could say a number of other things. Firstly, we could estimate how large home ranges the ducks were utilizing, and that they very selectively chose cornfields (which comprised only a minority of the arable land in the study area). Secondly, we could show that the omnivorous Mallard is flexible in diet selection, as corn (intended for winter fodder for cattle) is a new crop in the area, and that this happens already in inexperienced juveniles during first migration – in fact, corn isn’t a much grown crop in the recruitment areas. Thirdly, our data suggests that the ducks balanced intake of corn with predation risk, trying to minimize the time spent in open fields. Knowing these things adds to our understanding of the connection between wildlife and agriculture, especially important for the Mallard,  a prime reservoir for influenza A virus that can infect domestic poultry.

Link to the article:

Bengtsson, D., Avril, A., Gunnarsson, G., Elmberg, J., Söderquist, P., Norevik, G., Tolf, C., Safi, K., Fiedler, W., Wikelski, M., Olsen, B. & Waldenström, J. 2014. Movements, Home-Range Size and Habitat Selection of Mallards during Autumn Migration. PLOS ONE 10.1371/journal.pone.0100764

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Two new doctors – and some notes on the procedures at a Swedish PhD defense

Dr Griekspoor Berglund and Dr Stedt. In the background is the department's coffee machine - a vital instrument for the completion of a thesis.

Dr Griekspoor Berglund and Dr Stedt. In the background is the department’s coffee machine – a vital instrument for the completion of a thesis.

By Jonas Waldenström

Last Friday, my student Johan Stedt* defended his thesis. And three weeks ago, Petra Griekspoor Berglund** did likewise. Two great students – now Dr Stedt and Dr Griekspoor Berglund! – each with an excellent thesis and a great final performance at the dissertation.

Listening to your student’s PhD defense is a great moment in a supervisor’s academic life. You can’t do anything – actually you are forbidden to even open your mouth – you just have to sit down, relax and enjoy the show. Of course, most of the suspense, the bottled-up anxiety lies with the student, but it is also nerve-wracking for the supervisor(s). You want the student to have a great show, so that they can really show the world how skilled they are in their subject field.

Each graduation system is different. In Sweden it is a public event. The auditorium consists of both family and colleagues, sometimes numbering up to a hundred. It is like a mini rock concert, with the student and the opponent on stage.

Typically, the student starts with a short introduction to his/hers studies, giving some backgrounds, aims and a glimpse on how the stuff was actually done. Then comes the faculty opponent, who should be an authority on the subject, and summarizes the content of the thesis in the light of the research field as a whole. So far so good – but then the questioning starts…

The opponent can ask all the questions he or she likes, from the broad strokes to the tiniest details in Table S12 in the appendixes. When it is good it is an enlightened discussion among peers, but when it is bad it is a pain that has to be endured. Usually it is somewhere in between. For Johan and Petra it was good, really good – a real pleasure to listen!

In the Swedish system the opponent is not part of the formal examination. This is instead done by a board of three academics, associate professors or full professors chosen to represent the width of the research field. When the opponent is satisfied with the questioning (after an hour or two), the committee is free to pepper away with a new set of questions. Sometimes it is only a question per panel member, but at times it can be a new fairly long session. Once they are finished the audience can also chip in with questions or comments.

Once everyone is happy, the chairman closes the session and the panel convene and discuss whether the thesis will pass or fail. And in fairness, they nibble on fruits and drink coffee too. Meanwhile the student perspires and waits.

Once the verdict has been delivered it is time for the party – the best part of it all! If it wasn’t for the headaches the day after…

A great shout out for Dr Griekspoor and Dr Stedt! You were amazing – as I knew you would!

The exhausted supervisor after two PhD defenses in three weeks' time-

The exhausted supervisor after two PhD defenses in three weeks’ time.

* Johan’s thesis was focused on antibiotic resistant bacteria in free-living gulls, where he investigated to what extent gulls can be used as sentinels for dissemination of resistant bacteria into the environment from human and food animal sources. Examples from his research can be found here and here in previous posts.

**Petra’s thesis was on host ecology and evolution of the zoonotic bacterium Campylobacter jejuni. Humans primarily acquire infections from contaminated food, in particular poultry products. However, wild birds – such as thrushes, gulls, shorebirds and ducks – are carriers too. By investigating the genetic relationships between isolates from different sources, Petra could show remarkable patterns of host associations in C. jejuni from wild birds. An example of her research can be found here.

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Front or back – which end of the duck should you swab?

By Jonas Waldenström

Simple questions can have simple or advanced answers. The question in the title – which end of a bird you should sample for flu – will be answered in due time, but first I need to take you on an odyssey of duck flu history. Let’s start in Italy:

A Blue rock thrush view of Colloseum (Photo from Flickr, T. van Ardenne under a CC BY-NC-ND 2.0 license)

A Blue rock thrush view of Colloseum (Photo from Flickr, T. van Ardenne under a CC BY-NC-ND 2.0 license)

It was a beautiful day in Rome. The sun poured down on Colloseum and the hordes of tourists that meandered through the old remnants of the Roman empire. A Blue rock thrush fluted melodiously from the ruins, ignorant of the people below.

Meanwhile, in a concrete slab on the other side of Forum Romanum, the world’s leading experts on influenza A virus had gathered at the OIE headquarters. The acronym stands for Office International des Epizooties, but as no one could remember that name it has since been renamed the World Organization for Animal Health, a UN body devoted to fight disease in food production animals.

This was back in 2006, and the reason we were all there was the looming threat of highly pathogenic avian influenza H5N1 – or the bird flu as it was called in the media. This particular virus had crossed species barriers from the wild waterfowl reservoir into poultry and mutated into a highly pathogenic form that spread rapidly in southern China. This is in itself wasn’t too worrying – as outbreaks of highly pathogenic avian influenza emerge from time to time in poultry – but the unprecedented events were that H5N1 also spilled back into wild birds and that it infected and killed humans. Thus, it was a virus of substantial concern for the poultry industry and one which also had the potential to become a new human pandemic virus. The spread had been slow at start, with outbreaks mainly regionally in Asia but then the virus took a sudden leap across Russia into Turkey, and then further into Europe and Africa. People were scared, authorities had no proper preparedness plans, and research on avian flu was still limited.

Inside the big hearing room sat a mix of researchers, health care professionals, vets, and officials from various governments (and yours truly, in the back row, perplexed and overwhelmed of it all). The atmosphere was tense. What did we know? How could we learn more? What did we need to know to stop it? Questions without answers at the time.

A particular problem was the elusive nature of the virus. If it infected a poultry farm we would see it – it was easily detected due to its high mortality in chickens. If your chickens were dying in heaps, chances were that H5N1 had made a visit. But unlike most other previous poultry outbreaks of highly pathogenic avian influenza it also popped up in wild birds. The most covered outbreak in Europe was the dead swans on the shores of Rügen in Germany, but swans and diving ducks were found dead in several other places too, including Sweden during the winter 2005/2006. At the same time, no one found any infected dabbling ducks, despite thousands of samples being tested. Where was this bloody virus?

And it was then Ron Fouchier, a virologist from the Erasmus Medical Center in Rotterdam, dropped the bomb. In his talk he showed data from infection experiments showing that H5N1 was not primarily a gastrointestinal virus in ducks (as they usually are). Rather, the highest titers of virus were found in samples from the upper airways, suggesting an all-together different epidemiology. He had a punch line in his PowerPoint presentation that said (if I remember correctly) “Are we sampling the wrong end of the bird?” It was a deafening silence while it sank in, and then a forest of hands was raised for questions. These results, later repeated by other laboratories, changed the recommendations for wild bird H5N1 sampling more or less over night.

Let’s get back to 2014 again. We know more today than we did in 2006, but still the influenza A virus research field is full of surprises. Adding the sampling of the respiratory tract (or rather the oropharyngeal cavity or the pharynx) did not yield many H5N1 positive samples from wild birds in the EU – most found cases were still from dead birds, especially swans. The virus disappeared from Europe, and the interest from European authorities and media vaned with time. However, the question regarding front or rear remained among researchers. Not so for highly pathogenic forms of influenza A virus – which at least for H5N1 is clearly different in pathogenesis – but for the more normal, waterfowl-adapted low pathogenic precursor viruses.

The old dogma was that the low pathogenic viruses primarily infected the lower gastrointestinal tract, but that it could be found at lower frequency also in the respiratory tract. Indeed, this is often what you find in field studies; at our sampling location oropharyngeal swabs normally peak at 2-5% prevalence, compared to up to 30-40% in fecal/cloacal samples. But detection is not the same as infection, as the viruses detected there may be contaminants from feces or water. In infection experiments with low pathogenic viruses, replicating virus is sometimes found in the respiratory tract, but this may be an aberrant result due to large infection doses and mode of inoculation, where some virus may be washed down where it normally would not go.

Paraffin-embedded Mallard tissue samples waiting to be analyzed. Photo by Michelle Wille

Paraffin-embedded Mallard tissue samples waiting to be analyzed. Photo by Michelle Wille

A week ago we published a paper in Veterinary Research that aimed to test the ‘to be, or not to be’-hypothesis of natural respiratory infections. During November, the peak the flu season in ducks, we trapped and sampled roughly 125 Mallards at our field site. Instead of letting the birds go, we kept them in the trap a couple of hours until the test results were back from the lab. Four birds with positive RRT-PCR results from the oropharyngeal swab, and one which was negative, were sacrificed for assessing presence, or absence of virus infection in different body tissues; all other birds were released. The decision to kill a bird for science isn’t one to take lightly, but in this case we believed the benefit of mapping the pathogenesis of the virus justified the study (and procedures, sample size etc. were assessed by an ethical committee and approved by different authorities).

The method we used to look for replicating virus particles is called immunohistochemistry. Fresh tissue specimens are preserved in formalin, and then embedded in paraffin. Very thin slides of tissue (3 micrometer thick) are then mounted on glass slides and treated in such a way that cells infected with influenza A virus will appear red under the microscope. We (Michelle Wille from my lab, and Peter van Run and Thijs Kuiken from the Erasmus Medical Centre in Rotterdam) screened a large number of slides from the full lengths of the respiratory and gastrointestinal tracts. None of the slides from respiratory tract were positive, in contrast to several from the intestinal tract.

Figure 1 from the paper. Selected tissues of the respiratory and gastrointestinal tracts of Mallard following immunohistochemical staining to detect nucleoprotein of influenza A virus. Tissues from the respiratory tract did not show virus antigen expression, such as (A) the respiratory epithelium of the nasal cavity and (B) air sac epithelium. In contrast, some tissues from the gastrointestinal tract such as (C) the epithelium lining the jejunal villi of the gastrointestinal tract, and (D) surface epithelium of the cloacal bursa did show virus antigen expression. Virus antigen expression is visible as diffuse to granular red staining, which is usually darker in the nucleus than in the cytoplasm. The tissues are counterstained blue with hematoxylin. Arrows have been included to illustrate positive cells.  [Used under a CC 2.0 license]

Figure 1 from the paper. Selected tissues of the respiratory and gastrointestinal tracts of Mallard following immunohistochemical staining to detect nucleoprotein of influenza A virus. Tissues from the respiratory tract did not show virus antigen expression, such as (A) the respiratory epithelium of the nasal cavity and (B) air sac epithelium. In contrast, some tissues from the gastrointestinal tract such as (C) the epithelium lining the jejunal villi of the gastrointestinal tract, and (D) surface epithelium of the cloacal bursa did show virus antigen expression. Virus antigen expression is visible as diffuse to granular red staining, which is usually darker in the nucleus than in the cytoplasm. The tissues are counterstained blue with hematoxylin. Arrows have been included to illustrate positive cells. [Used under a CC 2.0 license]

Immunohistochemistry is a very sensitive method for assessing infections. While PCR-based methods are extremely sensitive for detecting presence of virus RNA, they do not say which cells that are infected, and whether they are associated with pathological changes. In our study, the Mallards were positive for influenza A virus in the oropharyngeal cavity by RRT-PCR, and in some cases we were even able to culture the virus, but none of them had any infected cells in the respiratory tract. If we cant find it in these birds (which belong to the main reservoir species), during the peak of infection in autumn, I think it is unlikely that respiratory infections are commonplace. The fact that you may find PCR-positive samples from the front end of the duck is then not due to infection in this site, but from virus received through feeding, drinking or preening.

And this is important, as the pathogenesis of a pathogen is the basis for transmission. Without knowing which parts of an animal that are infected we cannot fully understand the epidemiology and make informed decisions. Thus, if you sample for low pathogenic avian influenza in wild waterfowl go for the rear end of the bird.

And in Colloseum, the Blue rock thrush continues to sing, regardless.

Link to the paper:

Wille, M., van Run, P., Waldenström, J. & Kuiken, T. 2014. Infected or not: are PCR-positive oropharyngeal swabs indicative of low pathogenic influenza A virus infection in the respiratory tract of Mallard Anas platyrhynchos? Veterinary Research 45: 53.

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39 pages of boredom

By Jonas Waldenström

What do the academics do all day in their ivory towers? Thinking grand thoughts? Plotting the end of civilization? Mixing noxious and explosive chemicals to see what happens? Sleep?

This is Mr Burns. Not really related to this post at all, but he is such a charming gentleman. Nicked from the Simpsons.

This is Mr Burns. Not really related to this post at all, but he is such a charming gentleman. Nicked from the Simpsons.

No, sadly none of the above. Chances are we polish our ever-growing CVs. Sometime in the transition between student and postdoc I started to realize just how widespread the obsessiveness of academic bookkeeping was. Like a disease of academics. All stuff that possibly could be scribbled down as an achievement, even if incredible small, would directly go on someone’s CV.

I tried to stay out of it as much as I could, but after a while I too started to get my credentials in better order. Of course, keeping track of what papers you have written is easy – and fun – but then there is a gradual decline into bookkeeping disease. Held a presentation at a conference? Write that down. Had a poster on a conference? Write that down. Went to a conference? Write that down. Considered going to a conference? Write that down. Did your student present a poster on a conference? Et cetera, et cetera, et cetera.

In a way it is unavoidable. An inherent part of academia is the perpetual evaluations of performance. If you want to get a grant you have to face the fact that a score of other scientists also wants it, and that it is your CV as well as your project that is evaluated (in varying order…). And if you apply for a position, again your CV is scrutinized and measured.

Last week I hope I reached my peak CV writing. My current position is coming to an end and I am to be evaluated for a permanent position on the faculty. At the same time I will be evalutated for professorship. The resulting application ended on 39 pages. Thirty nine pages that some poor fellow now needs to read. Not only was I supposed to list my publications, there were also sections on outreach, administration, education, pedagogic views, achievements, awards, referee assignments, editor assignments, artistic talent, collaborations, teaching, memberships and whatnots. The most inspiring part was to write two pages about research visions and five pages on scientific breakthroughs – the remaining 32 pages were more or less bullet points on various aspects of performance.

An example of a neatly kept CV? Actually this is "Nådiga luntan"  (which Googles translates into 'gracious tome'), or simply the 2013 Budget from the Swedish Minstry of Finance. Photo from Finansdepartmentet under a CC BY 2.0 license.

An example of a neatly kept CV? Actually this is “Nådiga luntan” (which Google translates into ‘gracious tome’), or simply the 2013 Budget from the Swedish Minstry of Finance. [Photo from Finansdepartmentet under a CC BY 2.0 license.]

Don’t misunderstand me – I do think it is good to have a meritocratic system, but sometimes I feel so tired of writing text on how splendid and wonderful I am. After a month with two major grant applications, one annual report to the faculty, and now the professorship application I am pretty damn tired of myself. Especially of writing about myself, instead of writing science. Thumbs crossed, I may become professor in the autumn, and as that is the last career leap in academia I could perhaps avoid future CV opuses of this magnitude.

A final word of advice. If you pursue an academic career, there is one aspect that you should not forget to keep track on: your teaching! In which courses did you teach? At what level? Did you develop the lectures yourself? What kind of examination forms have you tried? Ask your dean (or equivalent) for a written letter on your performance when you leave an institute – it will be very hard to get one 5 years later.

Thus, keep your bookkeeping up, but don’t forget what academia is relly all about: SCIENCE! Go write those papers, otherwise no one will ask for your CV.

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