Author Archives: ryanchisholm

New students join the lab

Several new students have recently joined the lab. Nicolás Firbas is starting his PhD, and is broadly interested in topics relating to mathematical modelling of ecological systems. Guan Tong has rejoined the lab following her successful third-year undergraduate (UROPS) project on modelling the COVID-19 pandemic in Singapore; she is now in her Honours year, and will continue this line of research.

In addition, we welcome three students coming to us from the lab of Ted Webb, who is moving to the University of Helsinki. Sean Pang is in the final year of his PhD, and is modelling species distributions of an ensemble of tree species in the tropics. Annabel Lim is starting her Honours project in which she is doing systematic conservation planning for Philippine dipterocarp tree species under future climate change scenarios. Ng Chek Guan is also starting his Honours project, on using species distribution models to map the potential for dragon fruit farming in Nepal.

For more information, see our people page.

Welcome, all students!

New paper on stage-structured neutral biodiversity models published in Oikos

Many populations in the natural world exhibit pronounced stage structure, with individuals at different life stages having different survival and reproduction rates. Although there is a large literature on stage-structured models for single populations, stage structure has been less well studied in models of entire ecological communities. In our new paper, just published in Oikos, we explored the effect of allowing separate juvenile and adult stages on the dynamics of neutral biodiversity models.

We tested whether the addition of stage structure could fix known problems with spatial neutral models’ ability to fit cross-scale patterns of biodiversity in tropical forest tree communities. It could not, but our investigations led to useful mathematical results and new intuitions that have broad relevance for community ecology.

One particularly surprising result was that the presence of a juvenile stage, in which individuals cannot produce offspring, can substantially increase the biodiversity of the system. This occurs because it effectively increases the length of the historical time interval from which the parents of the current crop of individuals are sampled. The result likely applies beyond neutral models and to ecological communities in the real world.

The model predicts an almost linear increase in species richness as the ratio of juvenile to adult stage length increases (this is for a contiguous sample of 1 million individuals from an infinite landscape, with a per-capita speciation rate of 10-6 and a dispersal standard deviation equal to ten times the spacing between adults).

Chisholm, R. A. & T. Fung. Adding stage-structure to a spatial neutral model: implications for explaining local and regional patterns of biodiversity. (In press.) Oikos

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.