Category Archives: Uncategorized

New paper on estimating tree diameters from drones and LiDAR published in Remote Sensing

Remote sensing of forest physical structure currently relies mainly on satellite data, aeroplanes, and above-canopy drones, but sensors on these above-canopy platforms have difficulty penetrating into deeper layers of forests, especially in dense evergreen tropical forests. Below-canopy drones can complement above-canopy surveys and provide more-holistic assessments of forest structure.

We teamed up with our colleague Feng Lin, formerly of the Department of Electrical and Computer Engineering at NUS and now of Peng Cheng Laboratory in China, to use data from an autonomous drone flight in parkland for estimating tree diameters. The drone used LiDAR sensors and simultaneous localisation and mapping (SLAM) to navigate the small area of parkland, and in post-processing we used the LiDAR and SLAM data as inputs to automated algorithms for detecting and measuring trees. The automated measurements of tree diameter were closely correlated with subsequent manual measurements (R2 = 0.92). The study has just been published in Remote Sensing.

This study is a step towards fully automated below-canopy forest assessment, although many challenges remain, including the development of software for autonomous navigation of real forests, which are typically more complex than parkland.

The graphical abstract of our study from the journal website.

Chisholm, R. A., M. E. Rodríguez-Ronderos, and F. Lin. 2021. Estimating tree diameters from an autonomous below-canopy UAV with mounted LiDAR. Remote Sensing 13(3):2576

New book chapter published on species–area relationships

Ryan and collaborator James Rosindell, from Imperial College London, have just published a chapter in a new book about the species–area relationship (SAR), edited by Thomas Matthews, Kostas Triantis, and Robert Whittaker, and published by Cambridge University Press. Their chapter concerns the SARs of neutral ecology theory, and covers topics ranging from SARs predicted by simple non-spatial neutral models to those predicted under habitat fragmentation scenarios in spatial models.

J. Rosindell & R. A. Chisholm, in The Species–Area Relationship: Theory and Application, T. J. Matthews, K. A. Triantis, R. J. Whittaker, Eds. (Cambridge University Press, Cambridge, UK, 2020), pp. 259-288.

The Species–Area Relationship

Chapter on automated forest restoration monitoring published in online volume

In 2015, Ryan attended a workshop in Chiang Mai, Thailand on automated forest restoration. The proceeds of that workshop have now finally been published in the online volume “Automated Forest Restoration: Could Robots Revive Rain Forests?” by FORRU (the Forest Restoration Unit at Chiang Mai University), edited by Steve Elliott, George Gale and Mark Robertson. The volume is intended as a resource for field practitioners setting up restoration projects and as a manifesto for guiding future research priorities.

Ryan coauthored chapter 12 of the volume with Tom Swinfield, on the topic of current and future techniques for monitoring forest restoration autonomously using drones, LiDAR and other technologies.

Chisholm, R. A., and T. Swinfield. 2020. Automated Vegetation Monitoring for Forest Restoration. In S. Elliott, G. Gale, and M. Robertson (editors), Automated Forest Restoration: Could Robots Revive Rain Forests? FORRU-CMU

A schematic diagram of a hypothetical integrated system for monitoring forest restoration autonomously.

Lab awarded new grant on dengue epidemic modelling

We have been awarded a new grant to work on mechanistic modelling of dengue epidemics in Singapore. The three-year project is funded by the National University of Singapore’s Reimagine grant scheme, and will be a collaborative effort with Hannah Clapham and Natasha Howard at the School of Public Health, as well as Duane Loh in the Department of Biological Sciences / Department of Physics.

Dengue is the world’s most prevalent mosquito-borne viral disease, and outbreaks are becoming increasingly severe. In 2020, Singapore saw its worst epidemic in years, with over 34,000 reported cases and dozens of deaths. What factors drive the severity of an epidemic? What mitigation measures could be most effective for managing future epidemics? We will be tackling these questions with mechanistic mathematical models informed by epidemiological data. This will complement existing work on statistical modelling of dengue epidemics in Singapore, and inform epidemic management policy in the coming years.

Dengue cases in Singapore from 2017 to the present. (Source: National Environmental Agency)

Lab awarded new grant on evolutionary game theory and conservation problems

Our lab has been awarded a new grant to apply evolutionary game theory to conservation problems. Standard economic theory predicts that individual rational behaviour will lead to overexploitation of common resources, leading to environmental degradation, as embodied in Garrett Hardin’s classic Tragedy of the Commons. And yet, as Nobel laureate Elinor Ostrom showed, many traditional societies have spontaneously developed effective means of sustainable resource management. One possible explanation for this is that humans have an evolved intrinsic tendency to co-operate that is not accounted for by standard economic theory.

We will explore this intriguing idea under the new grant, in collaboration with Hisashi Ohtsuki at the Graduate University for Advanced Studies in Japan. We will use Ohtsuki’s recently developed framework for non-co-operative evolutionary game theory to better understand the structure of conservation problems and their potential solutions. Non-co-operative evolutionary game theory is the appropriate tool for this task because its defining feature is the absence of an external authority that could impose rules (by contrast, co-operative evolutionary game theory, which has previously been broadly applied to conservation problems, does assume an external authority).

The award is for three years and comes through Singapore’s Ministry of Education Tier 1 grant programme. Our post-doctoral fellow Nadiah Kristensen will be leading the work on the grant.

New multi-authored article on the history of the ForestGEO network published in Biological Conservation

In recent years, our lab has played a lead role in several cross-site analyses of data from the global ForestGEO (formerly CTFS) network (see here, here, here, and here). In a new article just published in Biological Conservation, Stuart Davies, the director of the ForestGEO network, relates the history of the network and summarises some of the main scientific results emerging from it. Ryan is among the 100+ coauthors of the article.

Davies, S. J., I. Abiem, K. Abu Salim, S. Aguilar, D. Allen, A. Alonso, K. Anderson-Teixeira, A. Andrade, G. Arellano, P. S. Ashton, P. J. Baker, M. E. Baker, J. L. Baltzer, Y. Basset, P. Bissiengou, S. Bohlman, N. A. Bourg, W. Y. Brockelman, S. Bunyavejchewin, D. F. R. P. Burslem, M. Cao, D. Cárdenas, L.-W. Chang, C.-H. Chang-Yang, K.-J. Chao, W.-C. Chao, H. Chapman, Y.-Y. Chen, R. A. Chisholm, C. Chu, G. Chuyong, K. Clay, L. S. Comita, R. Condit, S. Cordell, H. S. Dattaraja, A. A. de Oliveira, J. den Ouden, M. Detto, C. Dick, X. Du, Á. Duque, S. Ediriweera, E. C. Ellis, N. L. E. Obiang, S. Esufali, C. E. N. Ewango, E. S. Fernando, J. Filip, G. A. Fischer, R. Foster, T. Giambelluca, C. Giardina, G. S. Gilbert, E. Gonzalez-Akre, I. A. U. N. Gunatilleke, C. V. S. Gunatilleke, Z. Hao, B. C. H. Hau, F. He, H. Ni, R. W. Howe, S. P. Hubbell, A. Huth, F. Inman-Narahari, A. Itoh, D. Janík, P. A. Jansen, M. Jiang, D. J. Johnson, F. A. Jones, M. Kanzaki, D. Kenfack, S. Kiratiprayoon, K. Král, L. Krizel, S. Lao, A. J. Larson, Y. Li, X. Li, C. M. Litton, Y. Liu, S. Liu, S. K. Y. Lum, M. S. Luskin, J. A. Lutz, H. T. Luu, K. Ma, J.-R. Makana, Y. Malhi, A. Martin, C. McCarthy, S. M. McMahon, W. J. McShea, H. Memiaghe, X. Mi, D. Mitre, M. Mohamad, L. Monks, H. C. Muller-Landau, P. M. Musili, J. A. Myers, A. Nathalang, K. M. Ngo, N. Norden, V. Novotny, M. J. O’Brien, D. Orwig, R. Ostertag, K. Papathanassiou, G. G. Parker, R. Pérez, I. Perfecto, R. P. Phillips, N. Pongpattananurak, H. Pretzsch, H. Ren, G. Reynolds, L. J. Rodriguez, S. E. Russo, L. Sack, W. Sang, J. Shue, A. Singh, G.-Z. M. Song, R. Sukumar, I. F. Sun, H. S. Suresh, N. G. Swenson, S. Tan, S. C. Thomas, D. Thomas, J. Thompson, B. L. Turner, A. Uowolo, M. Uriarte, R. Valencia, J. Vandermeer, A. Vicentini, M. Visser, T. Vrska, X. Wang, X. Wang, G. D. Weiblen, T. J. S. Whitfeld, A. Wolf, S. J. Wright, H. Xu, T. L. Yao, S. L. Yap, W. Ye, M. Yu, M. Zhang, D. Zhu, L. Zhu, J. K. Zimmerman, and D. Zuleta. 2021. ForestGEO: Understanding forest diversity and dynamics through a global observatory network. Biological Conservation 253:108907.

New review paper on conspecific negative density dependence and tree diversity published in Trends in Ecology and Evolution

We have just published a review paper, led by Lisa Hülsmann of the University of Regensburg, about conspecific negative density dependence and its ability to explain tree diversity. The predominant pattern in global tree diversity is increased species richness towards the tropics. One proposed explanation for this is the greater climatic stability of tropical forests, which allows greater prevalence of pests (e.g., herbivorous insects and fungi), which in turn keep the abundances of their host tree species in check, thus maintaining overall tree diversity. For this mechanism to work, a pest must have greater per-tree impacts when the host tree is at high population density. This is an example of a more general phenomenon called conspecific negative density dependence.

The idea that pests maintain the tree diversity of tropical forests was proposed 50 years ago by Daniel Janzen and Joseph Connell and eventually became known as the Janzen–Connell hypothesis. In the years since, many empirical studies have reported that tree species do suffer more when surrounded by individuals of their own species, consistent with the hypothesis. These observations have provoked optimism among forest ecologists that the Janzen–Connell hypothesis is close to proven.

In our review, we present a more cautious appraisal. Our summary of the current state of knowledge reveals two important unresolved questions. Firstly, it is not clear whether the effect of neighbouring conspecific trees is strong enough to have a substantial influence on the overall tree diversity in a forest. Secondly, it is not yet possible to say whether the regulatory effect is indeed stronger or more frequent in the tropics.

We conclude that the explanation of Janzen and Connell remains a hypothesis yet to be proven. More precisely, although the existence of the mechanism is relatively well established, its importance in comparison to many other alternative explanations for tropical tree diversity remains unclear. To weigh these hypotheses against each other and to test the Janzen–Connell hypothesis in its entirety, new data and collaborations between experimental and theoretical ecologists will be necessary.

We hatched the idea for this review during a visit to Florian Hartig‘s lab in Regensburg in 2018.

Hülsmann, L., R. A. Chisholm, F. Hartig. 2020. Is variation in conspecific negative density dependence driving tree diversity patterns at large scales? Trends in Ecology and Evolution (in press)

Deon’s paper on comparing undescribed extinction models published in Conservation Biology

In recent years, the lab has been working on how to account for undescribed species when estimating extinction rates (see previous posts here, here, and here). The issue at stake is that some species may go extinct before they become known to science, and that failure to account for these statistically can lead to underestimates of extinction rates. In a new paper led by Deon, we compare our lab’s SEUX model with an earlier model by Tedesco et al. (2014). For the new paper we collaborated with Tedesco and tested the two models against his original global data sets as well as simulated data.

Reassuringly, the two models produced fairly similar estimates of the proportion of extinct species, accounting for undescribed species, when applied to the global data sets (see figure below). For example, the SEUX and Tedesco models estimated, respectively, that 12% and 11% of Australian mammals have gone extinct over the last 200 years, compared to the naïve estimate of 7% (which ignores undescribed extinctions). However, a few caveats emerged. Firstly, the SEUX model assumes that there are no extant undescribed species in the present day, and as a result of this assumption may underestimate the absolute number of extinctions (as opposed to the proportion). Secondly, both models assume that the probability of a species going extinct is independent of its probability of being described. Applications to our simulated data showed that violation of this latter assumption can lead to large biases in the extinction estimates. We also found evidence that the assumption may be violated in a few of our real-world data sets. More work is needed to investigate possible correlations between extinction and detection rates. Despite these caveats, our two models reinforce the notion that undescribed extinctions can be large and need to be accounted for in holistic assessments of human impacts on the environment.

Lum, D. W. H., P. A. Tedesco, B. Hugueny, X. Giam, and R. A. Chisholm. 2020. Quantifying the relative performance of two undetected-extinction models. Conservation Biology (in press)

The two undescribed extinction models (Tedesco and SEUX) produce similar estimates of the proportion extinct species for most data sets.

New paper on Janzen–Connell effects published in The American Naturalist

The high diversity of tropical plant communities is an enduring mystery, and a range of hypotheses have been proposed to explain it. In a new paper, Tak and Ryan evaluate the plausibility of the prominent Janzen–Connell hypothesis, which proposes that tropical plant diversity is maintained by selection against common species via impacts of natural enemies. Using a modelling approach informed by data from tropical forests in Panama, they find generally weak support for the hypothesis, with high diversity being maintained only in the idealised case where all species are equivalent. The paper has just come out online at The American Naturalist, and will be published in the forthcoming November issue. The lay summary and Abstract from the journal website are reproduced below.

R. A. Chisholm & T. Fung. 2020. Janzen–Connell effects are a weak impediment to competitive exclusion. The American Naturalist (in press)

UPDATE (December 2020): Our paper has been recommended on Faculty Opinions (formerly F1000).

Rainforest canopy crane at Fort Sherman, Panama.

A tropical forest, such as this one at Fort Sherman, Panama, can contain over 100 tree species within a single hectare. (Marcos A. Guerra/Smithsonian Tropical Research Institute)

Are pests and pathogens responsible for high tree diversity in tropical forests?

Step into a tropical forest and before long something will attack you. A mosquito bites you, a tick latches on, a chigger bores under your skin. You sit on the ground and get a nasty case of worms. Eventually, fungi eat away at your clothes. Such pests and pathogens can make life difficult—not just for humans but for plants and other tropical forest organisms as well. But could these “natural enemies” in fact be essential to the ecosystem, by preventing any one species from getting the upper hand? In a new study, two ecologists from the National University of Singapore tested this idea for tropical forest trees by building mathematical models in which each tree species is attacked by its own specialised enemy. In real tropical forests, there can be dozens or hundreds of tree species in a single hectare. Did their model produce similar diversity? The answer in general was no. Only in a very special case, the ecological equivalent of a pin landing on its head, did they e get such high tree diversity. This special case was when all species were equivalent—they all had the same death rate, same birth rate, and so on. Because pins generally do not land on their heads in nature, this scenario is implausible. The idea that pests and pathogens, through their voracious activities, can maintain forest diversity is vivid and appealing, but it does not stand up to scrutiny. The quest for a rigorous explanation of tropical forest diversity continues.


A goal of ecology is to identify the stabilizing mechanisms that maintain species diversity in the face of competitive exclusion and drift. For tropical forest tree communities, it has been hypothesized that high diversity is maintained via Janzen–Connell effects, whereby host-specific natural enemies prevent any one species from becoming too abundant. Here, we explore the plausibility of this hypothesis with theoretical models. We confirm a previous result that when added to a model with drift but no competitive exclusion, i.e., a neutral model where intrinsic fitnesses are perfectly equalized across species, Janzen–Connell effects maintain very high species richness that scales strongly with community size. However, when competitive exclusion is introduced, i.e., when intrinsic fitnesses vary across species, the number of species maintained by Janzen–Connell effects is substantially reduced, and scales much less strongly with community size. Because fitness variation is pervasive in nature, we conclude that the potential of Janzen–Connell effects to maintain diversity is probably weak, and that the mechanism does not yet provide a sufficient explanation for the observed high diversity of tropical forest tree communities. We also show that, surprisingly, dispersal limitation can further reduce the ability of Janzen–Connell effects to maintain diversity.

Sam’s paper presenting his neutral coalescence simulation packages published in Methods in Ecology and Evolution

Computational methods for efficiently simulating ecological communities are increasingly in demand. In 2008, James Rosindell popularised coalescence methods for simulating neutral ecological communities. These methods can be orders of magnitude faster than the alternatives, and can make spatially explicit neutral simulations on an effectively infinite landscape feasible. However, the technical challenge of implementing coalescence methods has left them out of reach of many ecologists. Now, Sam Thompson, who recently graduated from the lab with a PhD, being co-supervised by Rosindell at Imperial College London, has published user-friendly high-performance software packages for performing coalescence simulations in R and Python. The packages are described in a new paper in Methods in Ecology and Evolution.

The essence of coalescence methods is that they run backwards in time, which increases efficiency because only past lineages that lead directly to individuals within the focal community in the present day need to be tracked. In contrast, with standard forward-time-simulations, a much larger number of lineages needs to be tracked because it is not known in advance which ones will persist and be part of the focal community in the future. The catch is that coalescence can only be applied to particular types of ecological models, in particular to neutral models where an individual’s chances of birth and death are independent of its species identity. Coalescence techniques were originally invented in population genetics, and then imported to ecology by Rosindell.

Sam’s new software packages include the basic features from Rosindell’s 2008 paper, along with many enhancements and novel features, including varying individual density across a landscape, changing landscape configuration over time, and a variety of dispersal and speciation modes. The software was also used in Sam’s recent Ecology Letters paper on extinction debt. The core package code is written in C++, but the R and Python packages give a user-friendly interface, that should enable easy uptake by any ecologists interested in running fast spatially explicit neutral simulations.

Samuel E. D. Thompson, Ryan A. Chisholm & James Rosindell. pycoalescence and rcoalescence: Packages for simulating spatially explicit neutral models of biodiversity. Methods in Ecology and Evolution (in press)

Screen Shot 2020-08-17 at 4.58.44 pm

Output from the new software packages, showing (c) change in species richness over time in a hypothetical scenario after (d) part of a landscape surrounding a national park (green area) has been cleared.