How much leaf area does a tree have?

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The Bird Tree (it’s actually a cork oak, Quercus suber), Haute-Corse, France. Nominated as European Tree of the Year in 2019 but came in a disappointing 4th place.

What is the total area of leaves on a tree? On the one hand, this is a pretty obvious question to ask. Leaves are the exchange surfaces of plants, absorbing light, taking in carbon dioxide and releasing oxygen and water vapour. If we want to measure the rates at which each of these occurs for an individual tree then the area of their leaves is an essential parameter.

On the other hand, the total leaf area of a tree is an extremely difficult thing to measure, which is why for the most part we don’t bother. Up until now the only way to do so would be to pull all the leaves off a tree, measure them individually, then add the areas together. This kind of destructive sampling is generally frowned upon and makes long-term monitoring impossible.

Forest ecologists have therefore developed a range of alternative metrics which capture something of the same information. The most commonly used is Leaf Area Index (LAI), which gives the average number of leaf layers in a forest stand (strictly speaking it’s an estimate of the leaf area per unit ground area). This is very useful for modelling forests at the ecosystem level, where the overall area available for transpiration or gas exchange is important. But if you’re interested in the growth of individual trees, as I am, then it’s not much help. Likewise if you care about the foliage available as either habitat or food for herbivores, or where in the canopy those leaves actually are, LAI doesn’t provide the resolution you really need.

Terrestrial laser scanning has often been touted as a grand solution to challenges such as this. A conventional scanning laser can in theory measure at 2 mm resolution up to 50 metres away, which sounds impressive. Certainly the point clouds provide stunning visualisations which always make an impact in a presentation*.

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A 10 x 50 m reconstruction of a UK woodland as used in our paper on deer browsing impacts, surveyed by Joe Ryding.

There are a number of challenges though, and some of the over-ambitious expectations for laser-scanning derive from a few misconceptions. Dealing with these is an essential first step.

The main thing to clarify is that laser scanners don’t directly measure the amount of stuff; they measure the distance to stuff. A point cloud shows the nearest thing to the laser scanner that a beam actually struck**. That beam (you might want to think of it as a vector) is a straight line from the scanner which stops when it hits something, and everything past that point is effectively invisible. We refer to this as the occlusion problem, and it causes all sorts of issues.

To use a logical argument made famous by Donald Rumsfeld, what lies behind the first point in a laser beam’s pathway are a lot of known unknowns. We know there’s nothing until the first point (known absences), until it hits an object (a known known). After that we have no information. On top of this, coverage of laser beams is never continuous, and they spread out with distance from the scanner, so even at the highest resolution there are many things that the laser beams wouldn’t ever strike anyway.

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A conventional scanning laser in action in the forest. The white globe in the background acts as a reference point for linking multiple scans together. What we see in our visualisations is only what the scanner can see. Photo credit Joe Ryding.

To cut a long story short, terrestrial laser scanning provides a biased sample of the amount of stuff in a habitat, not a complete picture, however seductive our visualisations appear. We know it’s biased but we don’t know how much we’re missing. If we want to use our point cloud to estimate leaf area then we need to fill in the gaps.

In our new paper we provide a proof-of-concept for doing exactly this based on a computer simulation approach. The first step was to take a set of trees for which we knew the sizes, positions and angles of every single leaf (this was a mammoth sampling effort for which credit goes to my collaborator Sylvain Pincebourde and his team). Then we reconstructed those trees using computer graphics and simulated terrestrial laser scanning in a similar fashion to what would take place in the field. The next phase, which was also relatively novel, was to develop an algorithm to convert point clouds into flat surfaces. We could then use the area of these to create a direct estimate of tree leaf area.

Why do this? Well, it allows us to quantify exactly what proportion of the true leaf area we are theoretically able to replicate, identify how much we might be missing, and work out how our coverage varies through the canopy. It varies between the five trees, unsurprisingly, but the main lesson comes from what it tells us about the effectiveness of terrestrial laser scanning overall.

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Graphical abstract from our paper. This illustrates the process of virtual scanning, conversion of points to surfaces, and comparison of different scanning approaches.

Scanning a single tree from one viewing point on the ground allows us to reconstruct only around 30% of the leaf canopy. That’s not particularly great. However, with three scanning positions around the tree, we could raise coverage to around 67% of leaf area (this scanning method matches standard recommendations). Two-thirds of leaf area might not sound amazing, but it’s better than anyone else has managed, and still much easier than pulling all the leaves off! Finally, adding an airborne scan pushes the recovery rate higher still, up to a maximum of 90%, but there are practical issues that mean this is unlikely to work with current technology, at least unless the LiDAR device is mounted on something solid like a canopy crane. All these are also theoretical maximum values; in the real world problems such as moving leaves or additional obstructions will reduce coverage.

The good news, however, is that it’s possible to get a direct estimate of tree leaf area with a laser scanner, and we have a starting point to work from. As with any new technology we’re still at the outset. Lots of people have been working on using terrestrial laser scanning to measure timber volume or tree heights but leaf area remains challenging. The next step is to see how this might integrate with hand-held mobile scanning lasers. What we have provided is a platform that at last allows us to evaluate the known unknowns and find a way to compensate for them. Eventually that means we should be able to answer the original question — what’s the area of leaves on a tree — without needing to remove a single leaf.

 

Yun T., Cao L., An F., Chen B., Xue L., Li W., Pincebourde S., Smith M.J.  and Eichhorn M.P. (2019). Simulation of multi-platform LiDAR for assessing total leaf area in tree crowns. Agricultural and Forest Meteorology, 266–277, 107610. pdf

 


* And would make a stunning addition to this blog post if I had paid for a full WordPress account which allowed me to include videos. But I haven’t. So look here instead.

** For simplicity let’s not talk about split beams or multiple-return LiDAR. That gets messy very quickly.

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Did I actually lose my faith?

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Abandoned church in Italy. Photography by Roman Robroek from a series on abandoned houses of worship in Europe. Used with permission.

It’s now more than twenty years since I left Christianity and became an atheist. There was no Damascene conversion; like many people I drifted away rather than having a sudden insight. A series of events and discoveries led me to finally break from the church, although it took moving country to finally sever the social bonds and expectations that had kept me involved long after I would otherwise have left.

It’s been a long psychological journey from growing up as a creationist in a church of Biblical literalists (not the extreme Young Earth kind, but close enough) to becoming a professional academic biologist who teaches evolution. In that time I’ve established a career, worked all over the world, started a family, lost some friends and gained many more. All the turbulence that makes up a fairly normal life. Neither the good times nor the bad have led me to reconsider my position on religion.

The last two decades were also a period during which the tension between science and religion broke into mainstream discourse. A number of prominent atheists derided what they saw as unreason; none of the arguments were new but their vehemence and prominence were unusual. Of the main figures, the most persuasive was Christopher Hitchens, a man by all accounts possessed of magnetic charisma, compelling in debate and uncompromising in his writings. Other notable contributions were Dawkins’ The God Delusion and PZ Myers’ Pharyngula, for a while the most-read science blog on the internet. None of them influenced my decision because I had already become a convinced atheist before I encountered any of them.

Times have changed as the main protagonists have died, become caricatures of themselves, or merely declined in profile. It would be nice to think that people grew tired of hearing angry old white men argue with each other. They certainly didn’t succeed in making religion disappear and were likely a symptom of declining religious belief rather than its cause. While tempers on the subject have cooled, at the same time I have matured and become more reflective, and it’s now possible to look back on this period with a degree of detachment.

One of the ways in which leaving religion is described is as ‘losing your faith’. This is worth interrogating a little further. The Apostle Paul gives the following definition of faith, the only explicit one to be found in the Christian Bible:

Now faith is confidence in what we hope for and assurance about what we do not see.*

The basic point is that faith means believing in something despite not having complete or direct evidence for doing so. This seems as good a definition as any to me; I don’t know whether other religions have similar ones in their sacred texts. Put simply, you don’t need faith if you have incontrovertible evidence.

Much of the modern rationalist case against faith in general, and the Christian religion in particular, can be traced back to this verse. It is a prima facie example of how religious belief requires the absence of evidence, in contrast to scientific rationalism, which only allows for belief in things which can be directly proven. Religious truths are obtained through divine revelation, and are hence diverse, whereas scientific truths are produced via rigorous enquiry, which means that eventually they should hone in on a single answer.

The strongest proponents of scientific rationalism declare it to be impossible to be a true scientist whilst also holding a spiritual belief. This is clearly not the case; many scientists worldwide are religious. I know a good number and think no less of them. Whether the two positions are intellectually incompatible is not something I want to get into here, although I will note that we all manage to sustain contradictory viewpoints on many things. It has been claimed that biologists are less religious than other branches of science, but the evidence for this is inconsistent, and may to some extent reveal social norms within fields rather than any link with the subject material or mode of enquiry.

Regardless of whether I might describe myself as not having a faith, I expend a lot of my time believing fervently in things for which I have no direct evidence, at least not yet. What is ‘confidence in what we hope for‘ if not the anticipated outputs section of a grant proposal? Past evidence of over-ambition has not changed my approach to these.

As for ‘assurance about what we do not see‘, there’s more to this than believing the results of papers which we can neither replicate nor access the underlying data or code. Even were we able to do so, we usually lack time and resources to check. Instead we invest our trust in institutions (journals) or authority figures (other researchers) whose work we often accept without direct scrutiny. Given that we can’t check everything, we place confidence in the peer review system to rigorously inspect claims, despite personal experience of its occasional flaws. The difference between something I could check, at least in principle, and something I will accept without further question, is semantic insofar as how I respond is unchanged in practice. Such intellectual shortcuts are standard for everyone.

Moreover, our field (like most in science) is littered with fundamental theorems which work in closed or simplified systems but come unstuck when faced with the complexities of the real world. This doesn’t mean that they’re incorrect, but rather that uncovering the evidence for them is harder than we assume. If you’re an ecologist then perhaps ask yourself how often you’ve thought to directly test the logistic model of population growth, equilibrium model of island biogeography, Tilman’s R* or any number of theories which for many of us form the cornerstones of our understanding. If you have then my guess is that it didn’t go as smoothly as you hoped.** For the most part our evidence base derives from a surprisingly small set of case studies. Other theories for which the jury remains out (e.g. Metabolic Theory of Ecology) have advocates who by very definition are basing their belief on incomplete evidence given that other critical observers remain unconvinced.*** Is believing something because logically you feel it must be true that much better than accepting something without direct evidence?

A few weeks ago I stood on a seashore and stared at a rock covered in barnacles. The patterning was inconsistent with a model of their organisation which I’d published a few years ago. What went on in my mind was not a collapse in confidence but rather a reconsideration of what other processes or factors I might have been missing. I looked at that rock still believing in some version of the model even while the evidence in front of me so obviously disagreed. If I continue to work on this system then I remain certain that the model can be recovered, and have a few ideas of how to go about it. What is this if not a form of faith?

All this comes round to a recognition that perhaps I didn’t lose my faith; I simply realigned it by investing in a different set of principles and authorities. God disappeared from my worldview but maths and the scientific method took over. I may believe that my work is in pursuit of truth and serving a higher purpose****, but this this any different to those who follow a spiritual calling? In the last twenty years I have certainly changed but perhaps not as much as I thought.


* Hebrews 11:1 in the New International Version. The remainder of the chapter goes on to give historical examples of faith in practice.

** In writing this I am in no way questioning whether any of these fundamental theories is correct. Well, maybe the equilibrium model.

*** For the record, my take on metabolic theory is that it must be correct on some level but perhaps we haven’t been able to characterise natural systems in the appropriate way. I’m planning to have a chapter on this in the next edition of my textbook (don’t start getting excited just yet).

**** If you agree with me that understanding trees and barnacles represents a higher purpose then we really should be friends.


CODA: having swum in these waters before I know that taking a conciliatory line on religion and science is likely to see me being savaged by both sides. So let me be absolutely clear about my own position before anyone assails their favourite straw man. I am a scientist, humanist and atheist. I am convinced that the scientific process, whilst sometimes flawed and inefficient, remains the best means of deriving facts about the world. I hold no spiritual beliefs of my own but respect those who choose to and do not question their personal reasons. In response to this post I welcome constructive discussion that aims to increase mutual understanding but will not allow any comments which do not meet this standard, regardless of the viewpoint they seek to advance.

Writing about writing about decolonisation

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Three privileged white men displaying the normal range of responses to calls for decolonisation of science. Still from 90s classic sitcom Friends.

Who gets to make the case for decolonisation in the sciences? One of the anticipated reactions to our recent paper on decolonising field ecology (written with Kate Baker and Mark Griffiths*, and summarised in this blog post) was that we’re just three white Europeans. What right do we have to comment? Aren’t we part of the problem?

The answer is that yes, we are the problem, and that’s why it’s our responsibility to draw attention to it. Dismissing our argument because we come from a position of privilege is like disputing evidence of a crime wave because you’ve only heard about it from the police. Why aren’t the victims making a fuss? Researchers from developing countries don’t have the same platform. We know that. We’re using our platform to make exactly that point.

Another way of phrasing the critique is: “We like what you have to say, we’d just rather it was being said by someone else.” At best this derives from an assumption that we are stealing attention which should be directed towards academics from developing countries. To which I can only agree, and point out that our main message is to point away and shout “Look over there!” We haven’t silenced or excluded anyone. If our paper opens up space for others to be heard then we will have achieved one of our goals.

We freely acknowledge that our line of argument isn’t novel; the whole point of the paper is to draw attention to how a movement originating in the social sciences hasn’t penetrated far in ecology. There have been powerful statements made in the past, some of which we cite, but it’s fair to say that their impact has been limited. Many appeared as magazine articles or were published in non-science fields, which means that a majority of researchers in ecology will simply never encounter them unless they deliberately go looking. We have instead placed a commentary in the principal journal of tropical ecology, a publication which mostly features conventional scientific papers, which is much harder to ignore.

Was it easier for us to do publish this paper than it would be for others? Yes, without a doubt. But that doesn’t mean it wasn’t worth doing. We gained our current positions through structural inequalities, but the system will only change if those in control of it make an effort to do so. We aren’t demanding action from scientists in developing countries, although we strongly advocate listening to them. The walls aren’t going to fall down just because someone’s shouting outside. We need to start dismantling them ourselves.

At its worst, criticising the profile of the authors instead of the message is a means of deflecting responsibility to act. Throughout history, most movements for social justice have foundered at some stage because those in positions of authority grumble that no-one affected has complained to them directly. It always takes calls from within the establishment to provoke a response.

Also, who’s asking? If your response to the paper is that you agree with the message, but that we’re not the right people to be saying it, then who is? Who gets to judge? This turns out to be another means by which established authorities control participation in discourse. I will gladly accept, and try to learn from, any criticism from those adversely affected by the colonial aspects of science. It’s notable that all the push-back I’ve had so far is from other white people complaining that white people are telling them what to do.

We have been asked why we didn’t invite a developing world author onto the paper. This is a source of regret to us as well, but we didn’t have one. The paper arose out of direct discussions between the authors which took place in the UK and determined the message and outline. Approaching someone post-hoc and asking them to stick their name on a manuscript would have been the worst form of patronising tokenism, merely serving to insulate ourselves from criticism rather than being genuinely inclusive. So no, we didn’t do that. Of course it would have been best of all to have incorporated a broad panel of authors from the start, but it would also be disingenuous to pretend that this happened. To criticise the paper on these grounds is once again dodging the message to score a moral point. I too wish that science was more inclusive and fully collaborative; that’s one of the points we’re making.

Finally, I’m happy to accept that I am not the right person to lead by example. My encounter with the decolonisation literature has come through an awareness and confession of past mistakes, most of which were made through arrogance and ignorance. By all means criticise me for what I’ve done wrong — I’m comfortable with my errors being used as instructive examples. I’m also stumbling into a new field and likely to make further blunders. This will be an iterative process and one I’m entering into with some trepidation. But I firmly believe that this is a necessary direction and hope that others will join us.


* None of my thoughts in this blog post are original; I’ve learnt everything from discussions with the other authors.

Remembering rhinos

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Is this how we will remember the rhinos? Will it be any better than Dürer’s rhinocerus?

This autumn I will be teaching a new module in Conservation Biology. There’s a lecture I’m already writing in my head, though I dread the day that it finally happens because it comes with a personal dimension. I must be among a small number of living witnesses to two species which are now on the verge of extinction.

This week we learnt that Tam, the last male Sumatran rhino in Malaysia, has died. I met Tam while working in Borneo many years ago. My home was close to an institute that was attempting to breed rhinos and I would regularly walk past the enclosure hosting these recalcitrant giants on my way into the forest.

The story of the rhinos of Sabah is tied up with political disagreements, human tragedy* and some extremely bad luck. For many years it was asserted that there were 30 left in the wild, despite a persistent absence of evidence. Now we have to admit that they are on their way out. And no, I don’t have much hope for expensive lab-based interventions. If the habitat they lived in has gone, along with the accumulated knowledge and experience that allowed herds to move and forage through the landscape, then the species can only return as a curio. Limited conservation funding is better directed elsewhere.

By coincidence I also met one of the last of the northern white rhinos while teaching on a field course in Kenya 15 years ago. Not the very last, though this hardly matters, because their trajectory was already dismal. It lumbered peaceably around a bush and came directly towards me, staring directly down the barrel of my camera lens. Sadly I have no evidence of this because the film was subsequently ruined**, but I don’t need the photograph. The moment is seared in my memory for life.

In both cases I encountered the rhinos in sad circumstances. Tam was so domesticated by human contact that he was more interested in having a belly rub than in demonstrating his physical strength. He certainly wasn’t much interested in sex with other rhinos, which was the preoccupation of his keepers. The northern white rhino I met was accompanied at all times by a pair of armed guards. In neither case could I claim to have seen the species in its full glory. They were docile, amiable memories of rhinos.

These are the only rhinos I have seen outside zoos, although their absence is tangible in the increasing abundance of Euphorbia candelabrum in African savannahs, a generally unpalatable species but one which rhinos formerly consumed. Losing such a major herbivore inevitably has impacts on plant communities as well. If you know where to look then there is a rhino-shaped hole.

Yet my world is full of rhinos at the moment. My son plays with a plush cuddly rhino, has a soft blanket with a rhino print, wears a t-shirt covered with cartoon rhinos. The same could be said of dinosaurs, and what rhinos share in common is that they are large, charismatic megafauna which he will probably never see in the wild.

Yes, I know that there are positive stories to tell in rhino conservation. Global rhino numbers across all five species are close to 30,000, mainly due to successful protection of the southern white rhino in South Africa, but still the two Asian species hover on the brink, and a new poaching epidemic threatens recent gains.

And so, later this year, I will stand in front of a classroom of students and bear witness to the losses of my generation. We knew this was happening, we watched it happen, we tried to raise the alarm but our voices were not enough. The pressure is now building through movements like Extinction Rebellion and the realisation that this is an emergency. I hope that the tide is turning. Much remains to be saved. But even if we succeed this time, one day we will be forced to look back and see how much we have lost, plants and animals alike. I hope that I never have to describe a rhino.

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Albrecht Dürer‘s famous 1515 print of a rhinocerus. It was drawn based on a written description of a rhino in Lisbon; Dürer himself never saw one. This fantastical image of a rhino nevertheless became wildly popular and shaped European imaginations of what a rhino looked like for centuries thereafter. Will our grandchildren know any better?

 


* My memories of the Sumatran rhino will also be tinged with sadness in recollection of the brilliant Dr Annelisa Kilbourn, a wildlife vet who died tragically in a plane crash in Gabon in 2002. Best known for her brave work demonstrating the link between gorillas and ebola, the rhino project was another large gap she left behind.

** At this point I might need to explain to the students that cameras used to contain film, before the arrival of digital mechanisms of capturing and storing images. This will only make me sound like even more of a dinosaur.

Where are the African ecologists in Wytham Woods?

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Are Wytham Woods really that special? Photo from https://www.flickr.com/photos/oxox/509238022

*** See end for updates and responses ***

Calls have been growing across many academic fields for the necessity of decolonising science, both as a means of addressing the legacy of imperialism and broadening the scope and inclusivity of the collective human endeavour. Yet these discussions have been slow to take root in ecology. Many ecologists complacently assume that they are above this — we work with international collaborators in countries around the world, often living and working alongside local scientists with whom we interact with as equals (or at least that’s what we tell ourselves). Can we shrug off this latest movement as the well-meaning but unnecessary moaning of pious social scientists?

No. And this ought to be glaringly obvious.

Those of us who work in the tropics are all familiar with the classic study sites: Barro Colorado Island in Panama, La Selva in Costa Rica, Danum Valley in Malaysia… the list could go on. What unites all these sites is that they were usually established, and are often still run, by white scientists from First World countries (mainly Europe, North America and Australia). They are visited by streams of researchers and students from these First World countries. While the field centres are staffed by locals and include local scientists in their research programs, the funding to support them comes primarily from overseas.

Many ecology programs in First World universities include a glamorous field trip to an exotic location where our students can learn about applied conservation. They travel to Africa, South America or Southeast Asia and spend a few weeks visiting field sites which have been made famous through the published work of mainly white First World scientists, sometimes their own instructors. Often these field courses employ local teachers and guides, but they are based at local institutions. Locals are there to support the visiting experts, not to be celebrated for their own local research programs.

We have our classic field sites in the First World too. But how many visitors from the developing world come to see them? Why are there no Africans in Wytham Woods, studying the dynamics of a temperate woodland? Where are the Brazilians in Hubbard Brook? How many Indonesian scientists make a pilgrimage to see the Daintree Forest in Australia?*

There is one obvious reason why developing world scientists don’t visit these sites for research: money. Yet this is not an insuperable barrier. If we genuinely cared about developing international science, and believed that our cherished major study sites were of international importance, then we could find a way. In the same way as a British forester could develop sufficient expertise to interpret a study site in Africa, surely a Ugandan forester would be able to shed some light on what’s happening in a forest in Oxfordshire. Has anyone thought to ask?

More important is that they probably don’t care. Our favoured locations are much less interesting than we would like to believe, and have little to say to scientists in other countries. The one-way flow of assumed expertise and insight is a glaring failure in the way our entire field operates. In short, we need to decolonise ecology.

In a new paper in Biotropica we draw attention to this problem and suggest three responsibilities that researchers from the developed world need to accept as part of a moral imperative to decolonise our field.**

The first is a recognition of objectivity; ecologists from the Global North bring a set of priorities, paradigms and assumptions that are not always shared by the people living in the countries in which we work. The solution is not to indoctrinate the locals in our way of thinking, but to learn what their own perspectives are, and fully incorporate them in our research programs.

Secondly, we can stop calling our field sites ‘remote’ just because they require a long plane flight to reach and are found in places without reliable running water. To many people they are simply ‘home’. We should recognise and respect their expertise, even though it is exhibited in different ways from our own. If we genuinely wish to support local people then we should seek to arrive as supporting collaborators in achieving their goals, not solely ours. That would be truly impactful research.

Finally, we should start reflecting on our own background and how it inflects our conduct as researchers. Positionality statements are a common starting point in the humanities literature but remain very rare in science. This isn’t just a tick-box exercise for which we need to find an appropriately contrite form of words before carrying on as before. We need to acknowledge that the neutral scientific voice is a myth, one which disguises our own agency while writing out the contributions of others, particularly the locals we rely upon. We need to reflect on and state our potential biases in the same way as we would expect a declaration of conflict of interest or funding sources.

None of these prescriptions are inherently difficult, it’s just that the structures of modern science do not currently provide incentives for achieving them. But we created the structures of science. It’s our responsibility to change them.

 


 

UPDATE (22 May): there’s been a lot of commentary on Twitter about this post but no-one has followed through by commenting on the blog itself. Instead I’ll summarise some of the objections and my responses.

A few people were upset by the original title, which turns out not to be strictly accurate (although this was anticipated this in the footnotes). It has been amended slightly but due to WordPress defaults it’s impossible to change the link title without deleting the entire post. I had no intention of ignoring or writing out the contributions of scientists from the Global South to our understanding of Wytham, of which I was unaware. These deserve recognition:

To which I can only say brilliant, and I hope his work gets published. Another one here:

This is great news, and I hope the program is successful and leads to papers. Few people have done more for capacity-building in developing countries than Yadvinder Mahli, and I’m very happy to be proven wrong. We do need much more of this.

Finally, however, this:

I hope this helps clarify where I’m coming from. It wasn’t my intention to single out Wytham Woods for special criticism (#WythamSoWhite) but rather use it to make a general point. I could have chosen to illustrate it using almost any of the classic temperate field sites. Sadly a few exceptions, which I’m still glad to have learnt about, don’t negate the overall story.


This is an updated version of an article I wrote for a newsletter a few years ago. My thinking has been greatly refined through discussions with Kate Baker and Mark Griffiths, my coauthors on our paper in Biotropica.

* To anyone reading and planning a comment saying “I took some African ecologists to Wytham, look, here’s a photo”, please stop and think about whether that either invalidates or reinforces my argument.

** In case you’re wondering how three white Europeans feel that they have a right to weigh in on this, then another blog post on this will follow, but briefly: in cases of inequality, it’s the responsibility of those in a position of privilege to take action, not to wait for someone with less of a platform to tell them that they need to.

Of otters and scurvygrass

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A dense patch of scurvygrass (Cochlearia officinalis agg.) in an area much frequented by otters based on the clear trails, spraint and crushed mollusc shells.

On a sunny February weekend I made a trip out to Bere Island (Oiléan Béarra), a short ferry-ride off the southwestern tip of Ireland, to investigate a peculiar botanical phenomenon. An old friend had called on me recently and enquired what the connection was between otters and scurvygrass (Cochlearia officinalis L.*). I confessed to knowing nothing about it and was slightly sceptical, but he was adamant that there was such an association, and wanted to show me in person. Any excuse for a field trip is welcomed so off I went.

Once there on the ground there’s no doubt about it. The otter haul-outs are very obvious, and invariably marked with scurvygrass. The plant does grow elsewhere, unsurprisingly, but never in such densities and with such luxuriant foliage as where they occur alongside otter signs. Whatever the otters are doing, the scurvygrass is enjoying it. A representative sample of rocky outcrops suggests that if you spot a patch of scurvygrass it’s clear indication that once you get up close there will be matching evidence of otters. Neighbouring outcrops lacking the plant are also devoid of otter signs.

It’s not only at the shoreline where otters leave the sea, and where their spraint or the remnants of smashed shells indicates favoured spots to hang out. Their tracks continue inland. Often after coming onshore the track leads directly to a freshwater pool, suggesting that they like to wash the salt water off their fur, then out the other side. They then wend their way through the grass and heather, apparently choosing to cross the island on foot rather than swim their way round.

This is where it gets even more interesting: in the midst of these fields, scurvygrass is only found on the otter trails. Elsewhere the sward is higher and there is no sign of the plant. Otters are clearly carrying scurvygrass inland and encouraging it to grow in places where it otherwise would not. This effect is only seen in fields which don’t contain livestock; cows and sheep have a tendency to share the same trails with otters and perhaps browse or beat down the scurvygrass. But on the old military firing range, where otters have the land to themselves, every one of their trails is peppered with patches of the plant.

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An inland otter track through a field with a dense grass sward. Scurvygrass can only be found along this trail.

On returning to the office I consulted the usual books to see whether I could find any record of this particular association, and drew a blank. Web searches, whether in the scientific literature or the internet at large, have also come up with nothing. So what is going on? I have a few hypotheses:

  1. It’s a coincidence. Any ecologist has to keep the null hypothesis in the back of their minds. Maybe this is pure chance, or else some unknown independent environmental factor dictates the combined presence of otters and scurvygrass. I haven’t done a randomised sampling design to demonstrate a statistical association, but often the evidence of your eyes is enough to tell you that there’s no need.
  2. Otter disturbance. Scurvygrass thrives in patches with frequent disturbance, and the constant to-and-fro of otters might open up denser vegetation in such a way that they allow it to enter. Perhaps scurvygrass is more tolerant of this kind of disturbance than other plants.
  3. Dispersal by otters. The seeds of scurvygrass don’t look like they are adapted for sticking to the sides of animals, which would be one mechanism. Do otters eat scurvygrass, and thereby carry the seeds with them, defacating them in freshly-disturbed areas that aid its germination? This is currently my favoured explanation, but I don’t know enough about the diet of otters to be sure.
  4. Saline environments. Perhaps all the salt water clinging to the fur of otters changes the soil at their haul-outs and along their trails, favouring the growth of a halophyte such as scurvygrass. This is possible, but not entirely plausible given the presence of patches quite a way inland and even after they’ve taken a freshwater bath. Soil samples might resolve this. There are also no other halophytes which show the same pattern.
  5. Otters go where the scurvygrass is. Maybe they like the feel of it on their paws? It’s unlikely to be that they’re feeding on it, otherwise you would expect to see less scurvygrass in the places they use most frequently, while the opposite appears to be true.

Have I missed anything? Is this a known phenomenon that my friend has independently discovered? I’d be interested to hear from anyone who knows more about this in the comments. For now it’s only a small mystery, but also an intriguing natural history observation, and a reminder that people who walk outdoors and watch the world around them carefully often spot patterns that professional ecologists in their offices would never find.

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Credit to Bere Island resident Maurice Neligan for spotting this interesting pattern.


* This is as close as I can get to an exact species identification. Stace notes (in the 3rd edition; I don’t have the latest one just yet) that C. officinalis is highly variable, an aggregate of several likely species, and also freely hybridises with C. anglica and C. danica, especially in Ireland.

UPDATES!

As ever, Twitter provides a wealth of insights from other botanists. Here are the pick of the suggestions:

The first can be summarised as ‘disturbance + fertiliser’, the second with the twist of extra salinity, which might not be important given observations elsewhere. But scurvygrass isn’t only found where spraint occurs. It’s also along trails, some of which are quite steep, and any spraint is likely to roll or blow away pretty quickly. Otters may be marking trails with urine which could have a similar effect. Scurvygrass is also found right at the point at which otters emerge from the sea. I can’t help thinking that there must be a dispersal element to the story as well. This seems to be supported by another sighting of scurvygrass associated with birds:

There’s only one thing for it — we need to do some experiments! This may not be the most important project on my list but it makes for an enjoyable distraction.

Why should anyone care about Ugandan lianas?

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The liana team surveying in 2015 (Takuji Usui, Julian Baur and first author Telma Laurentino). Bridget Ogolowa (far left) did not participate in the study. Photo by Line Holm Andersen.

Habent sua fata libelli as the Latin epithet puts it, meaning ‘little books also have their destinies’. I’d like to think that the same is true of papers. Not every scientific publication appears in a major journal, or attracts media attention, or becomes a highly-cited classic. Some, perhaps, are never read again by anyone. This doesn’t mean that publishing them wasn’t valuable. A paper represents a new piece of knowledge or insight that adds to our total understanding of the world. And in some cases its small part in the greater whole is the main reason why it matters.

As an example, our latest paper just came out in African Journal of Ecology, a minor regional journal with an impact factor so small (0.797 in 2017) that in the metric-obsessed world of Higher Education it barely registers. Some would argue that the effort of publishing in such a low-status journal is a waste of time*. Why bother?

In this case, our study — small and limited in scope as it was — adds an important point on the map. Over recent years it has been noted that the abundance of lianas is increasing in South American forests. This process, sometimes known as ‘lianification’, is troubling because lianas can impede the growth of forest trees, or the recovery of forests following disturbance (including logging). At a time when we need forests to capture carbon from the atmosphere, an increase in the abundance of lianas could be exactly what we don’t want.

The causes of this increase in lianas are unknown, and it is also uncertain how widespread the effect might be. The best evidence that it’s happening comes from neotropical forests**, but we can’t be sure whether the same process is occurring in Southeast Asia, or Sri Lanka, or Africa. If the driver is global one, for example a change in the climate (warming, higher carbon dioxide concentrations, or longer dry seasons) then we would expect the same trend to be occurring everywhere. If it’s a purely local effect within South America then it might reflect historical factors, modern disturbance or the particular composition of plant communities.

It’s not just that we don’t know whether lianas are increasing in all parts of the world simultaneously; for most forests we don’t even know how many lianas were there in the first place. We could only find evidence of four published studies of liana abundance in the entirety of Africa, of which two were in secondary or transitional forests. That means only two previous studies on the continent had measured lianas in a primary forest. If we want to monitor change then we first need a starting point.

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Location of our study in in Kanyawara, Kibale National Park, Uganda. Figure 1 in Laurentino et al. (2018).

What did we find? Actually it turns out that liana densities in our forest were quite similar to those seen elsewhere in the world. An average liana basal area of 1.21 m2/ha is well within the range observed in other forests, as are the colonisation rates, with 24% of saplings and 57% of trees having at least one liana growing on them. These figures are unexceptional.

What does this tell us about lianification? To be completely honest, nothing. Or at least not yet. A single survey can’t say anything about whether the abundance of lianas in Africa is increasing, decreasing, or not changing at all. The point is that we now have baseline data from a part of the world where no-one had looked before. On their own these data aren’t particularly interesting. But considering the global context, and the potential for future studies to compare their work with ours, means that we have placed one more small piece in the jigsaw. And for the most part, that’s what science is about.

 

CODA: There’s another story behind this paper, because it came about through the awesome work of the Tropical Biology Association, an educational charity whose aims are capacity-building for ecologists in Africa and exposing ecologists from species-poor northern countries to the diversity and particular challenges of the tropics. Basically they’re fantastic, and I can’t recommend their courses highly enough. The work published here is based on a group project from the 2015 field course in Uganda and represents the first paper by three brilliant post-graduate students, Telma Laurentino, Julian Baur and Takuji Usui, who did all the real work***. That alone justifies publishing it, and I hope it’s only the first output of their scientific careers.


 

* A colleague at a former employer once memorably stated in a staff meeting that any journal with an IF of less than 8 was ‘detritus’. This excluded all but a handful of the most prestigious journals in ecology but was conveniently mid-ranking in his own field.

** Although this might be confounded by other factors — look out for a paper on this hopefully some time in 2019.

*** I also blogged about the liana study at the time here.