From mothers to eggs – maternal anti-influenza antibody transfer in Mallards

A Mallard nest. Photo by Flickr user nottsexminer, used under a CC BY-SA 2.0 license.

A Mallard nest. Photo by Flickr user nottsexminer, used under a CC BY-SA 2.0 license.

By Jonas Waldenström

I have spent the last two days at home nursing one of my offspring that has been down with a cold. Actually, since this is the oldest daughter, nursing generally involves providing her with unlimited access to her mother’s iPad and all the sandwiches she cares to eat.

The added benefit is that I have had more time to read and think than I usually have, far away from the office turmoil. So while I have time, I thought I could toss in yet another blog post.

A few months ago I served as an external examiner on Jacintha van Dijk’s PhD thesis in the Netherlands. That was an enjoyable experience – because of the quality of the thesis, and the unfamiliar and ancient procedures of a Dutch defense. I got to wear a funny hat and toga, there was a whole lot of ceremonial ‘all rise’, some marching in and out of rooms in predetermined processions, and other strange things that we don’t do in Sweden.

Anyway, most of Dr van Dijk’s papers are now published, and today I reread a story on maternal antibodies against avian influenza virus in Mallards, published in PLOS ONE this November.

For animals, the energy put into rearing offspring is a substantial investment. Generally, the more you invest the better chances the offspring has to reach reproductive age. However, as all things in ecology, energy isn’t endless, and animal needs to trade-off investments in one life history parameter to those of other parameters. For instance, in animals with several breeding seasons, current reproduction needs to be balanced with survival.

The last 15 years, ornithologists have looked into allocations of maternal antibodies between mothers and offspring. When an egg is laid some of the antibodies of the mother can pass over to the yolk, providing the hatching chick a kick-start of antibodies to fight infections. Such maternal antibodies do not last more than a few weeks, but may nevertheless be important in the early stage of a chick’s life. For instance, this is seen in commercially reared chickens, where maternal antibodies against Campylobacter can protect the chicks from colonization up to two weeks. It has been argued that the mother can choose how much antibodies different eggs receive, thereby modifying the future prospects of her offspring.

In this paper, the Dutch team investigated deposition of anti-influenza antibodies in Mallard eggs. They collected eggs from free-living Mallard nests – which is quite an achievement, since the nests are often tucked away and camouflaged. They also investigated eggs from captive ducks, more conveniently situated in a pen just outside the research institute.

Antibody concentrations were determined in both egg yolk and in the blood of the mothers, and they controlled for egg size, embryo sex, egg laying order, and female body condition. However, first they needed to check whether the incubating female indeed was mother to all the eggs in the clutch, since mallards are notorious egg dumpers.

Association between the AIV antibody concentration in egg yolk and female serum from (A) the field study and (B) the captive study. Note: axes are minuslog10-scaled. (From the original publication doi:10.1371/journal.pone.0112595.g001)

Association between the AIV antibody concentration in egg yolk and female serum from (A) the field study and (B) the captive study. Note: axes are minuslog10-scaled.
(From the original publication doi:10.1371/journal.pone.0112595.g001)

Indeed, maternal anti-influenza antibodies were found in Mallard eggs from antibody positive females, similar to earlier studies conducted on gulls. There was a positive correlation between antibody concentrations in the eggs and the concentration in the females, but there was no effect of any of the other investigated factors, including the body condition of the female. One more thing, though: there seemed to be an increasing concentration of antibodies with egg laying order; thus, later laid eggs had higher concentrations of antibodies than the early eggs in the clutch.

It remains to show whether this maternal transfer confers protection against influenza virus infections in young mallards, but it is an interesting finding. If maternal antibodies do protect, that could potentially affect local perpetuation patterns of flu, by temporarily reducing the general number of susceptible animals. Or if the antibodies are specific to only those subtypes that infected the mother (which is likely), it could potentially affect subtype distributions in the population, favoring subtypes that are antigenically different. However, if maternal antibodies wane after a few weeks, these effects, if any, should be transient.

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Inside the PLOS ONE Academic Editor studio, part 1.

How did you end up being an Academic Editor at PLOS ONE?

Well, I was asked, then pondered on it for a day, and said yes. Quite simple, actually. And apparently, this is how it is usually done: another editor recommends you, you get an invitation from the journal office, submit your CV for perusal, and then you’re either in or out.

That’s all good, but why did you choose to become and editor?

I am an editor for two smaller societal journals, one aimed for amateur ornithologists and one on infection ecology and epidemiology, so I knew what was expected of me. However, the main reasons were academic solidarity and promotion open access publishing. That may sounds a bit presumptuous and aloft, but I think it is important to see science as something that is different from other lines of business. In my case, I have published >100 papers. If we assume that 1-6 reviewers have read each paper, depending on whether they were accepted in the first journal or passed on to other journals, this means several hundred peers have been evaluating my work. That is quite a work load, done by unpaid peers – and without that commitment science wouldn’t work. I have always tried to do as many referee assignments as possible, but now I am in a position to also contribute to the editor role more widely.

I heard the word ‘open access’ there, is that an important concept for you?

Yes, it is. Good science should be accessible for everyone, especially when based on taxpayers’ money. However, open access is not a religion, and I think it is important that we acknowledge that there are pros and cons with this way of publishing, including the balance on how much auxiliary data that need to go with a publication, for instance. In any case, the plus side is way larger than the down side, and I sincerely believe that open access journals are the future of scholarly publishing.

Why PLOS ONE, and not any of the other journals out there?

Well, PLOS ONE was first to ask, he he he. But flattery aside, I also have a very good publishing history with the journal, and its sister journals. My first paper in PLOS ONE was published in 2007, back when it was a very new journal. In fact, we hadn’t really figured out how the journal worked, and thought it was the most selected of the PLOS’ journals. That paper on avian malaria speciation was first submitted to Science, where it was out on review, but rejected in the second round. Anyway, it found a good home in PLOS ONE and has to date been viewed more than 7000 times and cited 44 times. I am pleased.

After that I have submitted many articles to PLOS ONE, sometimes as the first choice, sometimes after being turned down in general societal journals. My experience has been very positive, and we have nearly always got constructive critique from reviewers. What I really, really like is that the articles are accessible directly after publication, and that figures and other materials can be shared – for instance, on our blog. Collectively, this has made me very positive to the journal, and I am happy to now serve as an Academic Editor.

Thank you very much, Jonas. I think we need to stop here for a commercial break, but when we return I would like to ask you more of what you do as an editor, and what authors that submit articles should think about.

You’re welcome. I’d love to chat about that.

TO BE CONTINUED… (at a later date)

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The rise and fall of avian flu research

By Jonas Waldenström

You’d be surprised how much of science that goes in and out of fashion. A certain topic may become hot for a time, go through a burst of development and then either stagnate, branch out in a new direction, or just vane into oblivion. These trends can be broad and slow, as say for instance a shift from behavior ecology to conservation biology, or very narrow from one bacterial protein to the next. Examples of recent trends in biology include epigenetics and CRIPRs, that currently seem to grow exponentially.

The figure below is a good illustration to a thought that has lingered with me for some time: have we reached peak avian flu? It comes from a recent PLOS ONE paper by Sarah Olson et al that investigate sampling strategies and biodiversity patterns in avian influenza viruses. It is a very nice paper, and I hope to return to it in a future post. But for now I stick with this single figure (actually it was hidden in the supplementary files), as I find it highly interesting.

Decline in subtyped AIV sequence submissions to GenBank in both poultry and wild birds. From Olson et al. 2014 PLOS ONE.

Decline in subtyped AIV sequence submissions to GenBank in both poultry and wild birds. From Olson et al. 2014 PLOS ONE.

So what does the figure say? It looks like a population fluctuation plot of the introduced reindeers on St. Matthew Island; a sudden increase followed by collapse (for a great comiv see here). But it is not. It is a graph that shows the variation in the number of sequences with know sample years submitted to Genebank from 1979 to 2012 divided on wild birds and poultry. As can be clearly seen, flu sequences from the early years are few. In fact, they don’t start to rise in numbers until 2004/2005. Then there is a massive peak followed by a large decline. Interestingly, these trends follow the natural history of H5N1, which is also depicted in the figure.

If you remember your flu history, you will recall that H5N1 hit Europe in 2005, making a very swift journey from SE Asia through Russia to Europe, and then south to Africa. But it didn’t start then – the first cases occurred in Hong Kong already in 1997, but for the first couple of years it was an all Asian affair, that didn’t involved western research labs. Our mallard study started in 2002, quite timely if you look at it in retrospect: before the big boom, so to speak. In the first years our research on low-pathogenic avian influenza viruses (the milder cousins to H5N1) mainly interested those already in the field, but after 2005 the interest exploded. Avian flu was hot, and our research was highly warranted – not only by researchers, but more so from policymakers, governmental bodies, and media. It was a raving storm for a time.

At that time many labs jumped onto the bandwagon and for some years many things happened at once. The European Union funded surveillance schemes in all member countries, the US and Canada launched big schemes as well, and even Africa became involved, with sampling in several sub-Saharan countries orchestred through the French research body CIRAD. Everyone was looking for H5N1, but few found it. Fortunately, they found a lot of low-pathogenic viruses and some great studies were made (and some less great, too) but as time passed the bars for publication became higher, funding agencies were more reluctant to give out money, and many scientists left for greener pastures elsewhere.

Having spent time in different research fields, such as ecology, parasitology and virology, it is striking how often the virology field jumps from one virus to the next. During my time we have seen SARS, H5N1, Bluetongue, Schmallenberg, Ebola, MERS, and Chikungunya. It remains to see what happens in the years to come. H5N1 is not gone – it is endemic in parts of Asia and in Egypt – but not at present occurring in the EU or the Americas. And during the last two years new avian influenza viruses have caused human infections in Asia, and it is clear that there is much more we need to understand regarding this extremely important zoonotic pathogen. And especially, we need to study the viruses before they pop up in the human population.

Link to the article: Olson SH, Parmley J, Soos C, Gilbert M, Latorre-Margalef N, et al. (2014) Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds. PLoS ONE 9(3): e90826. doi:10.1371/journal.pone.0090826

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Looking back on 2013 (part I): A dozen publications, some zombies, but no pandemics

By Jonas Waldenström

Post-apocalyptic dawn will have to wait some time more

Post-apocalyptic dawn will have to wait some time more

A year goes by so fast, and soon it is time to close the book on 2013. One thing we can conclude, at least, is that there was no apocalypse, and no end-of-humanity pandemic. However, there have been some worrying notes on new emerging pathogens in 2013. On top of the list of concern we find the MERS coronavirus in the Middle East, and the H7N9 low-pathogenic influenza virus in China. Neither of them has caused many human casualties, nor are they common or widespread. No, it is not what they do, but what they potentially could do that worries the disease world. The MERS virus is related to SARS – a deadly viral pathogen that in 1997 jumped from bats, to civets, and further to humans, and which was on the brink of causing a pandemic before it was fortunately contained and stopped. The other bad guy, the H7N9 influenza virus, carries novel antigenic properties to which the human population lacks immunity; thus, if it becomes adapted to spread between people (and not as today, between infected poultry and humans) it could turn into pandemic flu. Both viruses face strong guilt by association, you can say. These pathogens, and others, are like butterflies, fluttering in and out of detection. Worrisome echoes on the radar screens at WHO and CDC. They are also good examples to why field biology is needed in medicine: we need to track reservoirs of diseases, new and old, and we need to understand how diseases evolve. And that’s exactly what we try to do in ZEE. (In sale pitch jargon: we are the good guys!)

So what happened in ZEE during 2013? In this and other posts we will give you a hint of what we did, and how things went.

Publications. 2013 has been a productive year for the ZEE group! More than a dozen publications were published from Linnaeus University (plus a bunch from Uppsala). Most of these are available freely and you can reach them by following the links below. This year was also the year when this blog was launched! A motto we have is to provide popular accounts on the science we do. Thus, for some of the publications there is a link to a blog post in the list below. Read them – lots of fun!

  1. Tolf, C., Wille, M., Haidar, A-K., Avril, A., Zohari, S. & Waldenström, J. Prevalence of avian paramyxovirus type 1 in Mallards during autumn migration in the western Baltic Sea region. Virology Journal 10: 285  [Ebola, Chikungunya and Newcastle – of places, names and Mallard viruses] http://bit.ly/IToOVG
  1. Gillman, A., Muradrasoli, S., Söderström, H., Nordh, J., Bröjer, C., Lindberg, R.H., Latorre-Margalef, N., Waldenström, J., Olsen, B. & Järhult, J. 2013. Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected Mallards to low levels of oseltamivir. PLoS ONE 8(8): e71230. [This flu, that flu, and Tamiflu®] http://bit.ly/1gw2roa
  1. Safi, K., Kranstauber, B., Weinzierl, R., Griffin, L., Rees, E., Cabot, D., Cruz, S., Proaño, C., Takekawa, J. Y., Waldenström, J., Bengtsson, D., Kays, R., Wikelski, M. & Bohrer, G. Flying with the wind: scale dependency of speed and direction measurements in modelling wind support in avian flight. Movement Ecology 1: 4. [As the Mallard flies] http://bit.ly/19mFVtC
  1. Wille, M., Tolf, C., Avril, A., Latorre-Margalef, N., Bengtsson, D., Wallerström, S., Olsen, B. & Waldenström, J. 2013. Frequency and direction of reassortment in natural influenza A virus infection in a reservoir host. Virology 443: 150-160. [How do you do, the things that you do, Mr Flu?] http://bit.ly/18JpZkp
  1. Latorre-Margalef, N., Grosbois, V., Wahlgren, J., Munster, V.J., Tolf, C., Fouchier, R.A.M., Osterhaus, A.D.M.E., Olsen, B. & Waldenström, J. Heterosubtypic immunity to influenza A virus infections in Mallards may explain existence of multiple virus subtypes. PLoS Pathogens 9(6):  e1003443. [Why are there so many flu viruses?] http://bit.ly/IUiwoM
  1. van Toor, M. L., Hedenström, A., Waldenström, J., Fiedler, W., Holland, R.A., Thorup, K. & Wikelski, M. Flexibility of continental navigation and migration in European mallards. PLoS ONE 8(8): e72629. [Perdeck revisited – or how does a Mallard know its way?] http://bit.ly/1904O0h
  1. Tolf, C., Latorre-Margalef, N., Wille, M., Bengtsson, D., Gunnarsson, G., Grosbois, V., Hasselquist, D., Olsen, B., Elmberg, J. & Waldenström, J. 2013. Individual variation in influenza A virus infection histories and long-term immune responses in Mallards. PLoS ONE 8(4): e61201. [Disease is a property of the individual] http://bit.ly/1ebcGOz
  1. Hellgren, O., Wood, M. J., Waldenström, J., Hasselquist, D., Ottosson, U., Stervander, M. & Bensch, S. 2013. Circannual variation in blood parasitism in a sub-Saharan migrant passerine bird, the garden warbler. Journal of Evolutionary Biology 26: 1047-1059.
  1. Griekspoor, P., Colles, F.M., McCarthy, N.D., Hansbro, P.M., Ashhurst-Smith, C., Olsen, B., Hasselquist, D., Maiden, M.C.J. & Waldenström, J. 2013. Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds. Molecular Ecology 22: 1463-1472. [Of chickens, wild birds and men – host specificity in Campylobacter jejuni] http://bit.ly/1bCcFeu
  1. Griekspoor, P., Olofsson, J., Axelsson-Olsson, D., Waldenström, J. & Olsen, B. 2013. Multilocus Sequence Typing and FlaA sequencing reveal the genetic stability of Campylobacter jejuni enrichment during coculture with Acanthamoeba polyphaga. Applied and Environmental Microbiology 79: 2477-2479.
  1. Hernandez, J., Johansson, A., Stedt, J., Bengtsson, S., Porczak, A., Granholm, S., Gonzalez-Acuna, D., Olsen, B., Bonnedahl, J. & Drobni, M. 2013. Characterization and comparison of Extended-Spectrum β-Lactamase (ESBL) resistance genotypes and population structure of Escherichia coli isolated from Franklin’s gulls (Leucophaeus pipixcan) and humans in Chile. PLoS ONE 8(9): e76150. [Travel the world – can antibiotic resistant bacteria hitchhike with migratory birds?] http://bit.ly/19mF2kV
  1. Olofsson, J., Axelsson-Olsson, D., Brudin, L., Olsen, B. & Ellström, P. 2013. Campylobacter jejuni actively invades the amoeba Acanthamoeba polyphaga and survives within non-digestive vacuoles. PLoS ONE 8(11): e78873. [doi:10.1371/journal.pone.0078873]. [Good morning Mr Amoeba, may I come in?] http://bit.ly/1cqPybs
We study ducks, and they study us.

We study ducks, and they study us.

Staff and students. A year is also a quarter of a PhD time span, and half of a master student’s time. This means that there are many comings and goings in a research group over time. This year, one PhD left the nest and graduated, and four are due in 2014. No new PhD student started, but there were three babies born, thereby boosting the current ZEE children count to more than 10, enough for a football team!

Two former PhD students got a flying start: Dr Neus Latorre-Margalef is on a postdoc in Athens, Georgia, funded from the Swedish Research Council (VR), and Dr Josef Järhult in Uppsala got a huge researcher grant from VR to build up his own group! Fantastic news!

After finishing her MSc last year, Anna Schager got a PhD position in Italy in the spring. Olivia Borg and Anu Helin made their honors’ degree in the lab and then moved to Uppsala for MSc studies, while Johanna Carlbrand and Andras Turai stayed on with MScs at Linnaeus University.

With no real apocalypse in sight, 2013 instead became the zombie year, a trend that culminated with the WWZ movie. If you want to prepare for the coming zombie apocalypse, the author and blogger Colin M. Drysdale has a range of tips for you, including how to make projectile weapons with toilet brushes. You never know, such a skill may come in handy one day when the undead are going for your entrails. Next week we will get back on the-end-of-year-theme and present the best and the worst links/papers/topics of 2013! Cheers!

Smell the roses –how does the fecal aroma differ between infected and uninfected Mallards?

By Jonas Waldenström

Dogs do it, mice do it, and probably a bunch of other mammals do it too! Do what? Use their noses to sniff the disease status of conspecifics. Chances are, you do it too – certain diseases give an odor taint, a recognizable miasma, suggesting us to keep our distance. For a dog, the world is made up of fragrances, and a sniff in the but is a social call and a way of catching up on the latest developments (e.g. what you ate, which reproductive state you currently are at, and your disease status). However (unfortunately?), humans very rarely smell each other’s bottoms – it is simply not socially acceptable, and we are not very bendy animals. Even though our noses are better than we give them credit for.

A social call of fragrances that tells the receiver all the things she/he needs to know

A social call of fragrances that tells the receiver all the things she/he needs to know

But what about ducks? How and what do they smell? In the rear end? After infection? These questions are about to finally get an answer through the very recent publication of Dr Kimball and his USDA and Chicago State University colleagues in the journal PLOS One! Read it, it has already gone viral on the internet – some studies are just so unexpected that they flutter into the limelight for a while. But similar to IgNoble prizewinning studies, it does tell you some things worth remembering.

Ever wondered how a duck's rear end smells?

Ever wondered how a duck’s rear end smells?

So lets tease this study apart and look at the rationales and the results. First of all, influenza A virus infection in Mallards is a gastrointestinal infection, with viruses primarily replicating in the cells of the smaller intestine. Virus progeny is released in huge amounts with feces out into the environment. These well-known facts make the rear end a good starting point for studies on the possible olfactory difference between infected and uninfected birds. Mallards are fairly gregarious, although not extremely social birds, and the viruses released from the behind of one individual need to find its way to the front of the next individual. Mallards spend a large part of their lives dabbling – a behavior where surface water is taken into the mouth, the beak closes and the tongue presses upward, forcing the water through thin lamellae on the side of the beak. The yummy stuff, and perhaps viruses too, are stuck on the lamellae and is swallowed down. This behavior is thought to be one reason why Mallards (and other dabbling ducks) are especially frequent influenza A virus hosts.

Given this, it would actually be beneficial for a duck to be able to tell if the duck ‘over there’ is excreting viruses or not. Kimball et al. took this to heart and infected six domestic Mallards with an H5N2 low-pathogenic avian influenza virus. The researchers collected Mallard feces (the fancy word for bird shit) before experimental infection, and up till 10 days post infection. These fecal samples were then used to train mice – yes, you read it right: MICE – to differentiate between duck feces from infected and uninfected individuals. In the training sessions, mice were rewarded if they went to the right fecal sample (i.e. the infected one), and this was later tested in a double-blind test where both the mice and the operator had no clue where the different samples went in.

The tests showed that mice were actually quite good at learning to differentiate which birds that had been positive. The remainder of the paper examines which volatile compounds that were present in the feces and that may have given the results. For those of you that are keen chemists, I suggest you read the original article. For the rest of us, let’s just settle with that there were differences in the chemical spectra of the two groups. Particularly, acetoin (3-hydroxy-2-butanone) was more prevalent in the fecal samples from the infected birds.

Let us pause here and summarize. Mice can be trained to distinguish the smell of fecal samples from an influenza-infected duck. End of story. But a rather fun story. And not too far-fetched. The volatiles associated with infections are coming more and more in medicine, all the way from dogs trained at sniffing out cancers, to breath test to diagnose Helicobacter pylori infections. Smell is the future. However, the results of the current publication are not strong enough to say much on the use of olfactory cues among Mallards. Unfortunately, the paper is very thin in the material and methods section and the scant information on the infection protocol, the methods used for detecting influenza A virus in the samples, and for how long individual birds where shedding virus aren’t very helpful. If we are to believe the results we also need to be able to read all relevant information. For instance, the sex of each bird, whether control birds (if they indeed where controls) were housed together with the others, or separately, whether the diet and husbandry was the same for all birds etc. Many small questions, but where answers are important for interpretation.

And the bigger question, of course, is whether ducks themselves can distinguish the fragrance of infection. And whether that translates into a modified behavior. My personal feeling is that a duck with its bill spooning up water with muck and filth like a boss probably doesn’t take the time to smell the roses.

Don't forget to stop and smell the roses!

Don’t forget to stop and smell the roses!

Citation: Kimball BA, Yamazaki K, Kohler D, Bowen RA, Muth JP, et al. (2013) Avian Influenza Infection Alters Fecal Odor in Mallards. PLoS ONE 8(10): e75411. doi:10.1371/journal.pone.0075411

As the Mallard flies

By Jonas Waldenström

Migratory animals are per definition mobile, performing regular movements between areas. Sometimes such movements are small, as in up or down a mountain. Other times they involve crossing 11,000 km over open sea, as the Bar-tailed Godwits do on their migration from Siberia to New Zealand.

Not exactly a rocket

Not exactly a rocket

Our model species is the Mallard. It is not exactly a rocket or a Godwit. No, it is a bulky and rather heavy bird, not designed for enduring intercontinental flight. But it does fly, and fairly decent distances. From band recoveries and analyses of stable isotope contents in feathers, we know that the breeding areas are for Mallards passing Ottenby in autumn can be roughly outlined as the Baltic States, Finland and parts of Eurasian Russia. Winter areas are more easily depicted, as a lot of ducks are harvested by hunters and the number of bands reported back during non-breeding is high.

But a dead duck is an endpoint, and doesn’t tell us much about its behavior before (or after) it was shot. As Mallards are an important reservoir host for influenza A viruses we want to know more about what movements actually mean for the epidemiology of disease. Does infection impair movements? Can infected birds transport viruses along migration to other sites? How does that affect local and global transmission?

A few years ago we started to collaborate with Martin Wikelski and his research group at Max Plank Institute of Ornithology in southern Germany. His group is a leading group on research in movement ecology, experts in animal movements. It is really a cutting-edge discipline, as new techniques for following animals are constantly developed. A lot of new cool gadgets!

Together with our German colleagues, we have carried out a number of studies with tagged Mallards, equipped either with satellite transmitters or with GPS loggers. There are a few articles in the tube, and Daniel Bengtsson, one of my PhD students, has Mallard movements as his subject area. The very first article on Ottenby Mallards appeared recently in Movement Ecology. Actually in the very first issue of the journal!

In this study, Kamran Safi gathered movement data from nine different species of birds (including our Mallards) and used it to analyze how the effect of wind support during migration best should be modeled. Completely still air is rare, and migrating birds need to adjust migration to wind strength and wind direction. A tail wind component can be extremely beneficial, and headwinds detrimental. With the modern tags birds can be followed at high sampling frequencies (at the scale of minutes and hours) during active flight, and their heading and speed can be examined in conjunction with global weather databases. But it is crucial that you used the right models, otherwise you may end up with the wrong conclusions.

2051-3933-1-4-1

Schematic representation of the calculated measures, where α represents the vector of a bird’s movement relative to the ground. Its length is vg. Wind support (ws) is the length of the wind vector in the direction of c and cross-wind (wc) the length of the perpendicular component. Finally, airspeed (va) is the speed of the bird relative to the wind and can be calculated as given above, or modeled as the intercept of a model with vg as a function of ws and wc.

Perhaps not surprising, Safi et al found that wind was a strong predictor of bird ground speed, but with variation among species. However: determining flight direction and speed from successive locations, even at short intervals, was inferior to using instantaneous GPS-based measures of speed and direction. Use of successive location data significantly underestimated the birds’ ground and airspeed, and also resulted in mistaken associations between cross-winds, wind support, and their interactive effects, in relation to the birds’ onward flight.

It is rather complex paper if you are not into the field, but it feels good that our flu-carrying little duckies can contribute with some pieces of the puzzle in the making of next generation migration models. We will return to Mallards and movements in this blog in the future, as the Mallard flies and the papers become published.

Links to the papers:

Safi et al 2013 Movement Ecology

Gunnarsson et al 2012 PLoS ONE

Bubbles and dots – novel ways of perceiving scientific impact

winner-takes-all-2012-07_3

Science is a very competitive business. We compete with our colleagues for positions, grants and tenures. The main currency is publications – the more the better, and in as good journals as possible. (Teaching is often portrayed as being important for your career, but in most cases that are simply not true – just lip service from the system). But how can we measure quality?

Quantity – the number of articles – is one way to show it. This is probably most important in the early part of your career, where each and every publication counts and competition for postdoc money is fierce. But for established scientists this is not as relevant; really, is a scientist with 60 publications better than one with 50? And of course the number of publications is a function of time too, and the old silverback will always win in such comparisons.

Everyone agrees that it should be quality, not quantity that should be most important. But we can’t read everything everyone is publishing – it is simple beyond the realms of possibilities, given the enormous flow of articles in peer-reviewed fora. So how, then, can we put a quality brand on our work? For the last 10 years, the light from the journal Impact Factor has been the beacon to which scientists have set their course. This is an index on how much the average article in a specific journal is cited by other articles in the years that follow. Undoubtedly a very crude measure, and an AVERAGE measure of the journal, not a metric of the specific articles that appears in the journal. (Or in other words: just because an article is published in Nature, it doesn’t need to be a gold nugget.)

Thus science has a huge problem in measuring researcher, article and journal qualities. The quest of publishing in journals with highest possible impact factors, rather than in the journal with the best scope for your study, overloads the peer-review system with an ever-increasing number of reviews.

For individual researchers, the total number of citations, and the arithmetic H2 factor (a value of 3 means the person has 3 articles that have been cited at least 3 times; a value of 23 means the person has 23 articles that have been cited at least 23, etc.) are becoming more and more used.

But impact can also be at the societal level; how well it gets across to the public. The journal family PLOS just released a beta-version of a new article-level metric system that measure a range of factors in articles published in their journals. Quick and easy you can see the number of viewings of a particular article (and all PLOS articles are open access, by the way), the number of downloads, the number of citations in different databases, the social media impact (twitter, Facebook, Wikipedia etc.) and how all these things change over time. You can also play around and compare different articles and journals. A fun exercise, but potentially informative too.

Five hundred PLOS articles matching the keyword 'avian influenza'

Five hundred PLOS articles matching the keyword ‘avian influenza’

The graph above shows the change over time in citations for 500 articles matching the keyword avian influenza. Different journals in different colors, PLOS One in yellow, and the high impact journals PLOS Biology, PLOS Medicine and PLOS Pathogens in green and shades of purple, respectively. And, yes, over time the average article seem to do better in the ‘best’ journals, but the spread in PLOS One is more interesting – with many articles with as good, or better impact than those published in the top-notch journals.

You can also gain insights in where science is made. For instance have a look at where researchers on sexual selection have their headquarters. The dominance of Europe and America is monumental; partly of course due to historic reasons, research infrastructure, funding etc., but likely also because of language (Russians still publish a lot in Russian, Latin American researchers in Spanish, etc.).

Affiliations of researchers on 500 sexual selection papers.

Affiliations of researchers on 500 sexual selection papers.

Speaking about sexual selection. Guess which article that has had highest ALM impact? The dot in the graph below is an article that appeared in PLOS One on fellatio in bats. Perhaps not the most important paper in terms of science, but a curiosity teaser likely picked up by a lot of newspapers. This paper has been cited 6 times, but have more than 9000 shares on social media and 288,000 views at the homepage.

fellatio in batsFinally, what could PLOS do to make it better?

  • It would be awesome if this could be more in Gapminder style, where the user could use combinations of search terms to contrast the results. For instance, if I want to see how well my articles on flu are doing in relation to other articles on flu – how can I do that?
  • It would also be interesting to add journal or keyword-based regression lines.
  • The author institution map is very slow when many articles are chosen. Speed it up please!
  • And of course, it would be nice to see a similar system incorporating other journals too. But, that’s something for the future.

A good initiative!

Jonas Waldenström