It seems like a simple question, right? We have all climbed a tree and know perfectly well that the branches are the bits that stick out, and the trunk is the bit in the middle. However, when it comes to giving a robust definition that holds for all types of trees, I am having some difficulties.
It seems to me that there are essentially two types of trees in theory: the ‘fractal tree’ and the ‘Christmas tree’, these correspond roughly to the idealized broadleaf and conifer. The problem is that real trees lie somewhere between these two types, which makes it more of a challenge. To make this clear I’ll need to take a step back and explain the context, so bear with me.
I work with terrestrial laser scanning (TLS) data, a relatively new technology that can produce beautiful 3D cylinder model trees . Now that we have these 3D cylinder model trees, we want to ask questions like: ‘How much of the mass is contained in the branches and how much in the trunk?’ and ‘Is the tree symmetric about the trunk?’
Clearly, to answer these kinds of questions we need to be able to reliably define which bit is the trunk. Taking this one step further, we would also like to be able to define the branching order. This is just an extension of the same problem: if the trunk has branching order 1, then the next branches have order 2 and then 3 and so on. This would allow us to explore questions about the resource use and the mechanics of the tree. As far as I can see there are two possible definitions.
As usual, Leonardo da Vinci has had his say on this matter, so we’d better put his views first. He reckons that a tree is like an upside-down river: "All the branches of a tree at every stage of its height when put together are equal in thickness to the trunk… All the branches of water at every stage of its course, if they are of equal rapidity, are equal to the body of the main stream". That’s a very compelling idea, and leads to a clear definition of branching order: The branching order increases by one at every branching event.
This definition fits very well with our fractal type tree, but it gives silly results on the ‘Christmas’ tree. If you want to see the problem with this definition just have a scroll up and look at the banner image – every time a branch comes off, the main stem increases in branching order. That means that the trunk stops at the height of the first branch! Despite this obvious limitation, this is the definition which is often used because it doesn’t require any arbitrary decisions and is completely reproducible, which is an important point if we are trying to compare the work of multiple studies.
The trunk continues right to the top of the tree. This definition was developed primarily with conifers in mind. They generally have a central axis that often extends to the very top of the tree, with all the branches coming off it in a similar way. It seems natural to call this the trunk. But if you apply this definition to the fractal tree you get strange results again – every time there is a split, one of the stems is called the trunk and the other is now a branch. That leads to the trunk taking a pretty random path to the top of the tree.
Now think back to the question we wanted to ask: how much of the mass is contained in the branches and how much in the trunk? Is the tree symmetric about the trunk? Clearly, the answers to these questions are going to depend on how we define the trunk and branching order.
Shockingly, real trees don’t look like my neat idealized trees in the diagrams above! They are messy, with branches sticking out all over the place. The ‘real trees’ I am dealing with are actually cylinder model recreations of real trees, based on terrestrial laser scanning data. These are great but the underlying assumption, that trees look like a series of cylinders, breaks down at exactly the point we are interested in - the branching point. Before and after the branching point the tree is basically cylindrical, but at that point one branch is emerging out of the stem, leading to a strange shape. This causes the cylinder fitting algorithm we use to give errors, and to sometimes put multiple cylinders right next to each other, or mistake which branch is connected to which.
This is what my cylinder model trees look like, coloured by branching order according to the two definitions. In making these plots I have deleted lots of the smaller branches to make things clearer. Nevertheless, there are still lots of small cylinders, which represent branches, poking out all over the place. Each time this happens, according to definition A, the branching order increases. This leads to the many different branching orders, represented by many different colours, in the three trees in figure 5. Now this definition may give reproducible results but it seems pretty ridiculous, especially in the case of the pine tree on the right. If we want to know how much of the mass is contained in the trunk and how much in the branches, the trunk is just the turquoise bit down at the bottom, so is tiny compared to the rest of the tree.
The three trees in figure 6 are coloured by branching order as defined by definition B. this makes a lot more sense for the pine tree, and works OK for the tree in the middle too. However, you can see the problem with this method in the first tree in figure 6. The main stem splits in a large ‘Y’ shape quite low down. Since definition B requires the trunk (branching order 1) to continue to the top of the tree, the algorithm chooses either the right or left-hand path. This leads to an asymmetry throughout the tree. You could define a rule which chooses which path to follow based on a few factors (probably size, angle etc) but this would be sensitive to the quality of the cylinder fitting procedure and would require more arbitrary decisions, making the research less reproducible.
In summary, both definitions give some strange results, and this is partly due to the fact that the data is messy and our cylinder assumptions are not ideal. However, the fact that there are different possible definitions, and the results of some pretty basic questions depends strongly on which one we choose, is pretty worrying for me still! Sorry, maybe I should’ve warned you that this blog doesn’t have a solution. Next time you look at a tree, think about this problem and ask yourself – ‘are you confident you know which bit is the trunk?’
Finally, if you came here thinking about elephants and managed to make it right through to the end, keep scrolling down or have a look at this piece by Andy Burt
Lau, et al. 2018. Quantifying Branch Architecture of Tropical Trees Using Terrestrial LiDAR and 3D Modelling. Trees. doi: 10.1007/s00468-018-1704-1
Malhi, et al. 2018. New Perspectives on the Ecology of Tree Structure and Tree Communities through Terrestrial Laser Scanning. Interface Focus 8 (2). doi:10.1098/rsfs.2017.0052.
da Vinci, Leonardo, Jean Paul Richter, and R. C. Bell. 1970. The Notebooks of Leonardo Da Vinci. New York: Dover publications.
By Anabelle W. Cardoso
We've set up a network of hidden camera traps in the central African rainforest.
Motion and heat sensitive cameras are set up along elephant paths in central Gabon. They photograph any animal (or human!) that walks past them, and to analyse these millions of images we've teamed up with www.zooniverse.org.
The aim of the study is to better understand which areas have more elephants visiting them, whether this changes throughout the year, and how this might be affecting, and affected by, the vegetation in these areas.
Finding and counting forest elephants and other animals.
Citizen scientists are helping us find and count African forest elephants. The process itself is simple: you, as a citizen scientist, are shown an image from one of the camera traps, you identify the animal in the image, and if it's an elephant you tell us how many elephants you see. It seems simple enough, but the speed and accuracy that citizen scientists can achieve in an analysis like this is incomparable and invaluable.
The most exciting part of the project though is finding the animals! We've got tons of beautiful photographs of elephants, but there's also photos of gorillas, leopards, chimpanzees, pangolins, buffalo, red river hogs, and other forest animals to find. It really is a virtual safari through the central African rainforest!
How does Citizen Science help?
We have forty different sites being monitored by camera traps, and these cameras run for at least a year, and they capture every animal that walks past... that's a lot of photographs, and we need a lot of help to analyse them! Citizen science is a great way to analyse camera trap data because nothing is better at identifying animals in photographs than people. Citizen science platforms (such as Zooniverse) bring together millions of people from across the world with a shared interest in science and unite them to reach a shared objective.
Citizen science is a partnership between researchers and interested members of the public, and both parties benefit. The citizen scientist get's to be an active participant in a large-scale scientific project, often involving quite enjoyable activities, such as searching for wild animals in camera trap photographs. The research team also benefits, and gets much needed help with analysing their data. Most of all, the opportunity to share the science from such an early stage, all the way through to the completion of the project, makes citizen science a hugely rewarding activity for everyone involved.
Join us, and go on your own virtual safari through the Central African rainforest!
The project is called Elephant Expedition and anyone who wants to be involved becomes part of a community. You can identify photos from the camera traps, you can save and share your favourite animal photos, you can discuss interesting photographs on the talk boards of the project, and you can follow and interact with the project, it's researchers, and it's citizen science community through social media.
We're always expanding the Elephant Expedition community.
Join us, we'd love to have you!
Find the project here:
Follow us on:
Twitter @ellieexpedition and
Airborne forest surveys have recently helped to find some seriously tall trees in Northern Borneo. Until late last year, the tallest tree in the tropics was thought to be in Tawau hills, a spectacular 89.5m! In November 2016 another record breaker was been found along with 49 other trees, all over 90m. https://news.mongabay.com/2016/11/worlds-tallest-tropical-tree-discovered-along-with-nearly-50-other-record-breakers/
This grove of giant trees is to be found about 10km away from Danum Valley field centre, and that’s exactly where I am right now. I just got back to the field centre after visiting the new tallest tree this morning, here it is:
This Shorea Faguetiania was estimated at 94m by airborne survey but measured at 96m by a climber just yesterday. Obviously, there is a bit of uncertainty around the exact figure but whichever way you look at it this is a very impressive discovery and it brings a few questions to mind, such as: What is the limit to tree height? Does this limit vary from place to place? How will forests respond to change in their local climate?
I don’t have the answers, but there are giant redwood trees in California that are taller still (some reaching 110m I believe). Also, trees in Borneo can grow far taller than those in the Amazon. Interestingly, the record-breaking tree in question is situated between two steep slopes, so it probably benefits from quite substantial sheltering from the wind which may otherwise have toppled it long ago.
(by Benjamin Blonder)
Lab researcher Dr. Sam Moore is currently heading up a traits campaign in central Africa. The focal plots are in Lopé National Park in Gabon, and are especially interesting because forest elephants are common there, and play an important role in dispersal and growth dynamics of trees. However, elephants are not the only animal in these forests - check out what Sam's game camera picked up last week!
By Finella Blair - Data manager for the Human Modified Tropical Forest Progamme
In November 2016, as part of my role as data manager for the NERC Human Modified Tropical Forest Programme (HMTF), I had the chance to attend the Heart of Borneo conference in Kota Kinabalu, Sabah and visit the SAFE project where the BALI and LOMBOK consortia researchers conduct most of their fieldwork.
One of my tasks as data manager is to ensure that the datasets (nearly 200 to date but still increasing) produced by over 50 researchers, are identified and documented so that at the end of the programme they are available for reference in future research. With so many people and datasets, the only way to track it all is with a database so the majority of my job is desk based. To manage data effectively it is important to understand the information you manage so I like to learn as much as possible about the research projects. The opportunity to get into the field and see them first hand is one not to be missed.
My first few days were spent at the conference, the first day hearing all about Heart of Borneo and the work of the Sabah Forestry Department. On the second day Greg Asner gave the Keynote speech, announcing that LIDAR imagery produced by the Carnegie Airborne Observatory had confirmed measurements to show that not only was the tallest tree in the tropics in Sabah, but also the top 50 tallest trees.
I then had a perfect introduction to the work of the LOMBOK researchers, as each gave a short presentation about their work, including my personal favourite, Rosie Drinkwater’s work on analysing leech blood meals as a potential method for identifying the presence of host species that are hard to survey by standard methods.
At the end of the conference I travelled to the SAFE project site. Over the week I stayed in camp, each day I followed a different team. While I don’t consider myself particularly unfit and I have done fieldwork in the tropics before, I was very impressed by the fitness levels and dedication of all the field researchers I followed!
The first day was spent with BALI’s Sam Robinson (photo right), Daffyd Elias (CEH) and their research assistant, taking soil cores, collecting hyphal growth bags and surveying canopy gaps.
On the second day I joined LOMBOK researchers (photo below) Ute Skibe and Julia Drewer as they worked with their PhD student from ITBC, University of Malaysia, Melissa Leduning. For Melissa, this was the final field work trip of her studies on the impact of land use change on soil greenhouse gas fluxes.
I later joined Proffessor Owen Lewis from the University of Oxford Zoology Department and his research assistant, Ross Gray, as they tested the design of a capture-mark-recapture experiment, using bait traps to investigate how moths and butterflies use riparian zones within oil palm landscapes.
The highlight of the trip for me was the day I spent with University of Kent MRes. student, Dave Seaman walking a 2.5km primate survey transect. We were at the start of the transect at dawn and when we emerged from the forest many hours later, I had not only seen and heard gibbons and langurs but had had the privilege to stand quietly and watch a young female wild orang utan barely 10 metres away staring calmly back at us. The temptation to click away with my camera was strong, but instead I just enjoyed the moment and it is one I shall never forget.
The rest of the week was filled with more field excursions and evening data sessions in the camp lab.
It was a very useful and interesting trip that has helped me understand so much better the information I am being sent and I appreciate just how much hard work is behind the spreadsheets I see back in the comfort of the Ecosystems lab!
Thank you to all of the BALI and LOMBOK teams who let me tag along and ask basic (but hopefully not stupid) questions! I will be chasing you for your metadata shortly!
A few of the many photos I took on the trip are below...
Viva phenology! A celebration in Oxford as Cecilia Chavana-Bryant's DPhil research reaches fruition.
For her doctoral research, Cecilia Chavana Bryant investigated the impacts of leaf age on the spectral and physiochemical traits of canopy trees in Amazonian rainforests, and analysed the implications for Earth Observation-derived indices. Using hard won tropical forest field data, combined with modelling and remote sensing, Cecilia conducted in-depth studies in tropical phenology - focusing on the timing of leaf flushing and abscission. We celebrate Cecilia's viva this week with a champagne reception in the department.
I've just got back from five weeks fieldwork in Malaysian Borneo. It was a successful trip and I got to see some of the worlds tallest trees - which are pretty amazing! This is particularly exciting for me because my work is all about the how trees grow so tall (from a mechanical point of view).
Danum Valley is a well established field centre near (via 72km dirt track) the town of Lahad Datu. There's herbarium, a restaurant and even a floodlit badminton court - which seems to be an essential part of life for the locals. I arrived late in the evening after a pretty exciting drive down the long dirt track in a shiny new 4x4. Unfortunately, my work requires me to carry a lot of equipment around with me and I had a few days just unpacking and sorting out big piles of tangled wires. Once it was all sorted, me and Azlin - my local research assistant - carried the wires and data loggers out into the forest to set up. This involves attaching small sensors to trees and climbing the biggest trees in the plot to attach wind sensors. We got all of this done in just over two weeks and left the equipment running.
Now that I am back in Oxford, Azlin is looking after the equipment for me. Every two weeks the data needs to be downloaded and the batteries changed - this means a 4km walk into the forest carrying five heavy batteries. The plan is to leave the equipment running until March 2017, when I will head back over to Danum and pack up. This will hopefully result in six months data on the local wind speeds and the movement of the trees. Using this data I will be able to test whether my model of wind damage works in the rain forest as well as it does in UK forests. I will also be able to better understand how the trees in Borneo come to be so tall!