Publication: Tiny terminological disagreements with far reaching consequences for global bird trends

In February, the second chapter of my PhD was published in Ecological Indicators. This paper looks at how sensitive our understanding of global bird trends is to how we classify bird groups.

It’s common practice to use composite indices to try and understand global biodiversity trends. The European Bird Census Council is just one institution that does this, calculating an index of temporal trends in farmland and forest bird species. These bird groups (farmland and forest/woodland) are studied by many researchers and institutions, though in each case different combinations of species are assigned to the different groups.

In this paper I looked at how sensitive the trends in composite bird indices of farmland, forest/woodland and generalist birds are to which species are included in each group. We find that the trends we calculate in these bird groups can change drastically depending on which species are included (using actual, published lists of species assigned to these groups). In some cases, this effect is severe enough that under some definitions a positive trend is seen and under others the trend appears to be negative.

Our results question the current practice of idiosyncratically classifying indicators in scientific research and conservation. This inconsistency is making it more difficult to infer whether and when to preserve bird groups, potentially leading to sub-optimal conservation outcomes.

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Publication: The value of virtual conferencing for ecology and conservation

I am ecstatic to say that the final version of my recent publication is now available at Conservation Biology. Some co-authors and I from the Centre of Excellence for Biosecurity Risk Analysis and the Quantitative and Applied Ecology group got together a couple of years ago to write about the value of virtual conferencing for ecology and conservation. I’ve written a bit about this process in the past under my old name Hannah Pearson. It was a fantastic experience working with Matthew Malishev, Kylie Soanes, Stuart Jones and Chris Jones on the project.

In a nutshell

Ecologists and conservation researchers often research and express concern about climate change. These same researchers travel long distances to conferences contributing substantively to global carbon emissions that cause climate change.

Many of the world’s biodiversity hotspots and most pressing conservation problems happen in the developing world but the financial cost of travelling to conferences means that many of these researchers are unable to communicate their research or learn from recent research at international conferences.

Holding virtual conferences have the potential to overcome both problems: reducing researchers’ carbon footprint and increasing the accessibility of conferences from more poorly funded institutions such as those in developing countries.

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America Trip: UC Riverside

My last stop before I returned home was UC Riverside where I stayed with Helen Regan and her husband Kurt Anderson and visited their labs. Of course, due to the time of year most of the academics were away but I was able to meet with many of their fantastic students.

Helen Regan

Helen is the sister of one of the academics in my lab, Tracy which gave me an in to contact her. Unrelatedly, I’ve been curious to meet her for a while because one of her publications (Regan, H.M., Colyvan, M. & Burgman, M. (2002). A taxonomy and treatment of uncertainty for ecology and conservation biology. Ecological Applications, 12, 618–628) has been really influential in formulating my work on inconsistent use of terms. Obviously that work was done a while ago and she has largely moved on from there – her work now focuses on more applied questions relating to quantitative conservation, risk assessment and decision science.

Kurt Anderson

Kurt researches a variety of things including community dynamics (where he works on terrestrial, aquatic, microbial and theoretical communities), plant defences (where he works with field and simulated data) and environmental change in California.

Pamela Rueda

Pamela studies population viability analyses. A number of different methods of PVA are commonly used but it is unclear whether any of these are better or worse than others. She works with simulated data to determine whether matrix or scalar models give better approximations of the actual (as simulated) population dynamics.

Sara Freitas

Sara works on metapopulation dynamics of birds but has also been conducting a meta-analysis about how species interactions change based on climate change. I think she will have a pretty diverse PhD

Sean Hayes

Sean is studying how system stability relates to network structure. Like me, he has had trouble with terminology – stability is probably one of the worst defined terms in the field. For the purposes of his work, he considers a stable community to be one that does not go extinct. He works in simulated and real world (well- a whole lot of bottles connected by tubes with two bacteria in them) space to work out what kind of network of ‘patches’ of habitat is able to sustain a two species predator/prey system.

Katie Johnson

Katie studies hummingbird song – they evolved song separately from passerine birds and very little is known about how their song develops. She’s experimenting with playing fledglings different calls as they are developing and seeing how this affects their song. She’s also found that the terms used to describe different aspects of bird song (‘phrase’, ‘sound’, noise’ are not always used consistently which is interesting.

Daniel Goldberg

Daniel is a masters student and currently studies sexual selection in guppies but is interested in coming to Australia to work with fairy wrens. His dream is to work in a system where understanding breeding selection and behaviour can be linked with conservation outcomes. I think he’s unlikely to find a space for this with wrens because they’re hardy little guys but their behaviour is very interesting a complex so they might be worth studying anyway.

Sean Wilcox

Sean also studies hummingbirds and is particularly interested in studying determinants of hummingbird ‘quality’. He’s a bit like a hummingbird personal trainer: setting them tasks like navigating a string maze, weight lifting and flying in a wind tunnel to test their strength, agility and endurance.

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America Trip: ESA in Baltimore

Ecological Society of America centennial conference

It was my first time attending ESA (America) and this year it was in Baltimore. The conference itself was an experience; they really turned it on for the centenary. There was a personal message from President Obama, a celebratory/promotional video, an animated version of Dan Simberloff’s work on island biogeography and an incredibly depressing performance which combined a string quartet, narration and images to paint a bleak picture of our impact on the environment.

There was content between 8:30 and 5 with around 20 concurrent sessions at any given time plus poster sessions and trade displays and workshops. There was no lunch break and the whole thing was very fully on because they wanted to fit the most possible content into the days they had available.

All that aside, the talks I went to were fantastic and covered everything from education to community engagement to nutrient cycling. I went to so many fantastic talks that I couldn’t possibly describe them all I’ll detail a few of my favourites below.


How basic ecology has and will continue to shape conservation science

Each speaker in the symposium discussed how a basic research has impacted conservation – something I’m particularly interested in. A few of the talks that most interested me in this symposium were

Joshua Lawler discussed how niche theory relates to species distribution models which are now extensively used in conservation, particularly in reserve design

James Estes discussed how studying food webs gives us insights into species interactions and the nature of top down and bottom up control. This was all related to the classic Sea Otter, Urchin, Kelp problem.

Lenore Fahrig talked about how we have been misinterpreting the concept of habitat fragmentation. Habitat fragmentation literature often confounds the amount and fragmentation of the habitat (looking at patch size or distance to nearest patch etc). In fact, when you look at fragmentation independent of the amount of habitat available the effect is usually either neutral or beneficial.

Beyond Invasional Meltdown: Implications and Impacts of Co-Occurring Invasive Species and Assessing Future Research Needs

The speakers here were focussing on Dan Simberloff’s concept of invasional meltdown and more broadly how invasive species interact with eachother and native species

Dan Simberloff opened the proceedings by discussing the original concept of invasional meltdown and how it has been used/misused since its inception. The original concept of invasional meltdown was of a system where invasive species facilitated the spread of other invasives.

Carla di Antonio talked about how removing one invader in a Hawaiian system just made room for another invader to become more prevalent- it didn’t result in any improvements for the native species community.

Sara Kuebbing looked at how frequently different types of interactions occurred with invasive species and talked about how we can avoid the ‘invasion treadmill’ where one invasive species is replaces with another as Carla discussed.

Individual talks

Jane Catford is actually also part of the QAECO lab but only spends about a third of her time there and the rest in Canberra or Minnesota. Somehow, without collaborating, we have ended up working on very similar questions. Jane presented her work on the term ‘invasive species’ and the different interpretations of that term. She showed that there most classifications rely on some combination of four biogeographic criteria (local abundance, geographic range size, environmental range size, spread rate), plus impact. These can be combined to create 15 different ways of being invasive, all of which are used in the invasive literature.

Joshua Drew talked about how the density of human habitation (and consequent pollution and erosion) and fishing pressure was influencing fish assemblages in Papua New Guinea. Most of his work was using a space for time substitution, looking at areas with different human populations and relating this to their fish diversity. However, he did some nice stuff with historical data to verify that increasing human density (rather than other factors) caused the reduction of biodiversity.

Emily Farrer looked at how anthropogenic factors influence the invasion of species into suitable and marginal habitat. Road density was (unsurprisingly) very important and helped invasive species access and persist in marginal habitats. I found this particularly interesting because of the difficulty of defining what a marginal vs suitable habitat was. I believe she did this using SDM methods and calling areas with over 50% likelihood of occurrence ‘suitable’ and those with a lower likelihood ‘unsuitable’ but if these terms are widely used I suspect they are defined very differently in different studies.

Fantastic people I met

Our lab was underrepresented this year (possibly because ICCB was in such an idyllic location) so I attended on my own which was uncomfortable but ultimately probably very beneficial. Because I didn’t know anyone, it was a case of make friends or be lonely and as a result I met many more people and got to know those people much better than if I had have attended in a group of people – though there were also a few lonely times. I met so many fantastic people at ESA that I couldn’t describe them all so I’ll just tell you about the people I got to know the best

Joshua Drew

Josh (@Drew_Lab) is a lecturer at Columbia University studying biogeography and fish. He knows my supervisor Mick McCarthy (@mickresearch) through twitter. Mick recommended that we meet up at ESA and I really enjoyed hearing all about Josh’s research and teaching experiences. It sounds like he’d be a great person to study under because he puts a lot of thought and effort into his students.

Pamela Reynolds and Marissa Lee

Marissa presented in the same session as me about some work that she and Pamela (and colleagues) have been working on. They’d done a systematic review on how people are researching functional diversity. They found that most people who study functional traits collect their own information rather than using trait databases which is likely to be because people treat and measure traits very differently – so there isn’t much trust in the consistency of the trait databases. This has some strong similarities to my work on woodland birds and they use a very similar method to what I used to form the foundation for my research on woodland birds so it was interesting to hear about the pitfalls they faced during the process.

Laura Ferguson

Laura is a Masters student at Oregon State University and presented a talk about scientist-stakeholder engagement in the “Climate Change and Water Sustainability – Willamette Water 2100” project. She showed that having a facilitator, sharing a common goal and including diverse opinions in discussions resulted in more successful science-driven stakeholder engagement. Hey work is primarily in watery systems rather than terrestrial ones but she’s most interested in improving science and management through stakeholder collaboration. I think she’d be a great fit for CEED or CEBRA if she would be willing to move to Australia.

Chanda Littles

I organised to share a room with Chanda (who I’d never met before) through the ESA roomshare website and it was the best decision I could have made. She’s a really great woman who does very interesting work and hopefully will be a friend for life. She works on Manatee behaviour and deals with some fairly sophisticated modelling techniques. She presented her work on the tradeoff Manatees in her system make between feeding in the cold waters of the bay (where they need to expend extra energy to stay warm) and resting in the estuary which is fed by thermal springs. Her interest is in understanding how complex ecological and behavioural mechanisms are influencing the persistence of threatened species.

Bianca Reo/Charbonneau

Bianca studies dunes: their morphology, ecology, stability and erosion and how all of these things influenced the destruction caused by Superstorm Sandy. Natural sand dunes were able to very successfully mitigate storm damage but they tend to be under-rated. Bianca has just written an article after my own heart on dune terminology. It turns out there is disagreement about what terms like ‘blow out’ mean which is impeding communication between researchers and with the public. That article will come out some time next month and you should all read it: A REVIEW OF DUNES IN TODAY’S SOCIETY

Dan Simberloff

Dan Simberloff is a pretty famous ecologist. So much so that his paper on island biogeography (where he killed all the insects on mangrove ‘islands’ and monitored how they recolonised) was turned into a cartoon for ESA – not by his request. I’ve admired his work for years. He was at the conference presenting work on invasional meltdown where (among other things) he touched on how inconsistently the term was being used. I contacted him before the conference and he agreed to meet with me and discuss my ideas about terminological consistency! He turned out to be a lovely, humble, soft spoken man who gave me a lot of time and consideration. He heard out my ideas and thought they were interesting though he doesn’t believe that it is possible to change the way people use terms. As much as I would like to prove him wrong, I think he’s probably right (at least in most circumstances)

Lenore Fahrig

I have admired Lenore’s work for a long time too. Her research focuses on the effects of habitat fragmentation but from time to time she has published an article commenting on the use of terms in that field such as ‘fragmentation’ and ‘connectivity. She was at ESA presenting her recent review of the fragmentation literature where she found (much to her horror I imagine) that, in cases where habitat fragmentation had a significant impact on diversity, it usually increased diversity (rather than decreasing it as expected and proposed in many of her own papers). I always admire someone who finds results that contradict their previous assertions and publishes and publicises them. It shows a high level of scientific integrity. I managed to organise to meet Lenore during ESA and found her to be an excellent and insightful conversationalist. Despite my nerves she was able to draw out details of my work and we found a lot of common ground in talking about inconsistencies in terminology. Like Dan, she is dubious about the possibility of changing the way people use terms like ‘fragmentation’ because the field includes so many researchers and it would be very hard to reach and convince them all. However, she thought there might be hope for my Australian ‘woodland bird’ example because it’s a smaller, more contained system. So I’ve got my fingers crossed that she’s right.

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Structured Decision Making Course

As part of the EDG/CEED Leadership Program, CEED was kind enough to give each represented node $3000 to host an event that would help us improve our leadership skills. This is a broader brief than it sounds as the concept of ‘leadership’ as defined on the course includes everything from self leadership, to networking, to influencing others (see blogs from the leadership cohort who explore this more). Therefore, after much deliberation we decided to run a workshop on Structured Decision Making. Now this usually costs you tens of thousands of dollars but the University of Melbourne is lucky to have three resident experts in structured decision making; Libby Rumpff, Kelly de Bie and Prue Addison and they were willing to teach us. I should say that $3000 did not nearly cover their wages for the time they put in to preparing and running the two day workshop but they saw this as an opportunity to refine their skills (I hear that they may consider offering similar Structured Decision Making Courses in the future). Around 30 students, post docs and government and NGO employees attended the course. Most of these people attended in person at the University of Melbourne but we also streamed the lecture components of the workshop live to a number of interstate and overseas participants.

The workshop was designed to progress in the same way that you would approach a structured decision making problem. Structured Decision Making is made up of 6 steps (although some steps may be done multiple times depending on the concept: 1) creating a problem statement, 2) delineating objectives, 3) cataloguing alternatives, 4) determining the consequences of the alternatives, 5) comparing the different alternatives and, 6) deciding on an action. The workshop took us through each of these steps and we simultaneously learned about the steps and implemented them using a toy decision problem (deciding on a correct course of action in Victorian Mountain Ash forests).

Throughout the workshop our facilitators gave us examples of how they have used structured decision making for everything from choosing a house to protecting the Great Barrier Reef. By the end of the workshop I felt like I had the knowledge and skills to implement a Structured Decision Making process, though it might be easier to implement Structured Decision Making in a group context after some facilitation training.

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My Epic Trip to America

I just recently returned from my first solo overseas conference trip and want to chronicle all of the amazing places I saw and people I met so that the details wont get lost in the sand of time. Feel free to read on if you want to hear about some amazing people and a little bit about my adventure.

I am not a big traveller so I tried not to think of all the scary possibilities when I submitted and abstract to attend the ESA (America). After I was accepted I resorted to denial and avoidance and finally I spent the last month or so freaking out about it and obsessively organising every single detail. I decided that I wanted to make the very most of the experience and get as much bang for my carbon buck as I could. So I searched online for people who might be able to give me insights into my research. Unfortunately, my research is a little hard to describe so my success was a little bit hit and miss. Regardless, I think I made a lot of connections which will be very valuable.

Here’s the plan I came up with:

Fly to New York, see some of New York city and meet with Justin Bledin, a linguist from Johns Hopkins University

Catch the train to Princeton University meet with Matthieu Barbie, Simon Levin and the other ecologists at Princeton

Catch the train to Baltimore to attend ESA and network with the people there

Fly to LAX and travel to Riverside to meet with Helen Regan and visit UC Riverside

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America Trip: Princeton

After the chaos of New York I cant even begin to describe how relieved I was to be in Princeton. It felt like Stars Hollow (from Gilmore Girls… which I totally dont watch) except that everyone was rich and well educated. Trees lined the streets, squirrels and birds abounded and it was a critical 5 degrees cooler than New York which had felt like being inside an oven. I imagine the Princeton is a little less idyllic when it isn’t holidays, what with drunken students stumbling around everywhere but I’d still go back.

When I got into town I dropped my bags off at the AirBnB place I was staying at (which was completely lovely and reasonably priced) and headed in to Princeton University to meet Matthieu Barbier who had graciously organised a schedule of meetings for me during my stay. I’ll briefly describe each of the people I met.

Matthieu Barbier

Matthieu is a bit of an enigma, he works in the Levin Lab which focuses broadly in ecology and evolution but his expertise is in linguistics and physics. He was my point of contact at Princeton (because of his cross disciplinary expertise and the possibility that he could advise me on linguistic grounds). He is interested in introducing more qualitative methods to hard sciences and more quantitative methods to fields like linguistics. The main project he is working on at the moment is to do with bringing a qualitative emphasis to ecology by studying generalisable rules about how people make ecological choices.

Simon Levin

Simon Levin has been one of my research heroes for a long time so it was fantastic to get some career advice from him. He says that for your first post-doc you should look for a job where you can

  • Do something new
  • Take ownership over a project
  • Diversify your skills and expertise
  • Work in large labs where you can benefit from collaboration

Some funding schemes that he suggested for me and might be relevant for other QAECOlogists and allies are:

SESYNC: The National Socio-Environmental Synthesis Centre, where they use science to inform conservation policy. They have lots of post-doc opportunities but usually you dont work in a large groups so it might be a bit isolating

NatureNet Fellowships: These are run by The Nature Conservancy and you apply at one of their partner universities: Columbia, Cornell, Princeton, Stanford, the University of

Pennsylvania, and Yale.  According to the NatureNet site they are looking for outstanding early-career scientists who seek to improve and expand their research skills while directing their efforts toward problems at the interface of conservation, business and technology.

Henry Horn

Henry is a Renaissance Man who is a naturalist, statistician, historian, artist and musician. He had some really interesting stories about debates and conflicts in ecology and has been involved in some himself. His insights on these conflicts were interesting. He observed that in a lot of cases, debating ecological concepts seems to cause people to abandon their original moderate views and become polarised such that both sides end up unreasonable. Listening to his stories I resolved not to fall into this trap whenever I take part in an ecological debate. During our conversation he also showed me a song he has composed about statistics called ‘The Kuhn and Popper Knee-jerk Philosophy of Science Blues’ which features memorable lines such as “If you publish random papers, with your students working in teams, 5% of what you say will be statistical truth or so it seems. And if anyone says you’re a Fisherian liar, you can rescue yourself with a Bayesian Prior”.

Aneike Van Leeuwen

Aneike studies size structured population dynamic models which take into account energy flows in the system. We bonded over terminological difficulties. I told her about my woodland bird problem and she told me about how people tend to generalise between age structured population dynamic models and size structured ones. Both terms are used to refer to models will a vast range of complexity only some of which take into account feedback loops between size, resource availability, population size and growth. Apparently this often leads to miscommunication between researchers. We talked about how these misunderstandings could be ameliorated but didn’t come to any good conclusions.

Lyndon Estes

Lyndon has a wide range of interests but it seemed that his passion lies in examining land use change in Africa. We talked primarily about my work on ecological terms and how that related to stuff he’s come across over the years. He spoke about:

  • taxonomic change in birds where sometimes the divisions between species are based on the most minor characteristics.
  • The species concept: he studied Mountain Bongo antelope which is a subspecies with extremely limited distribution where the other subspecies is widespread – depending on whether you are interested in species or subspecies level protection these animals may or may not get protection
  • A recent article by Holly Gibbs found some surprising results about land degradation, particularly in tropical forests which has prompted a review of how consistently tropical forest is being classified, particularly how it is distinguished from tropical savannah.

David Wilcove

David is the head of his own lab at Princeton which focuses on protecting biodiversity particularly in Asia and the Americas (and often with a focus on birds). He’s an extremely engaging guy and he had some interesting insights into my current work.

At the moment I’m working with Martine Maron, Alex Kutt, Jeremy Simmonds, and my supervisors to try and get Australia’s woodland bird community listed as a Threatened Ecological Community under the EPBC Act. David suggested that I should identify which species are threatened and declining and the processes that are threatening them as a way of prioritising which species should be protected. This is definitely something that I will consider as we approach this problem in the coming months. David was also kind enough to set me up to meet a number of his lab members who I will describe next.

Fangyuan Hua

Fangyuan is studying how the current reforestation efforts in China are affecting regional economies and biodiversity (with an emphasis on birds). She’s using a whole swathe of indices to measure biodiversity including species richness, community composition, changes in abundance and beta diversity. As part of her research she studies forest dependent and open dependent species because it’s a necessary simplification but believes that studying resource/habitat preference on continuous scales (creating a n-dimensional hyper-volume resource niche) would be a more rigorous approach in many cases.

Janice Ser Huay Lee

Janice studies agricultural intensification in Sumatra and how (and why) various farmers make decisions about how to use their land. She simulates these changes across the landscapes and looks at the social, economic and environmental consequences these decisions and (perhaps) how to influence them. She was interested in my topic and suggested that I write a review article about the influence of ecological terms to broaden the emphasis of my current research which is fairly firmly grounded in one example. I think this is something I will pursue… once I’ve written my thesis.

Umesh Srinivasan

Umesh studies the effect of landuse change on bird demography and how species turnover on an elevation gradient relates to community level metrics. One of the metrics he is particularly interested in at the moment is body size. I don’t know much about this but it appears that there is a trend towards larger species having smaller population sizes. Therefore the population size of these larger species can be used as a measure of how well a community is doing.

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