Category Archives: Uncategorized

Ryan presents our dengue modelling work at the NUS One Health Symposium

Earlier this year our lab received an NUS Reimagine grant to conduct modelling of dengue dynamics in Singapore in collaboration with colleagues at the School of Public Health. On 29 November, Ryan presented early results from this work at the One Health & Outbreak Surveillance Symposium 2021, organised by the Centre for Infectious Disease Epidemiology & Research at NUS. The symposium was held online due to the ongoing COVID-19 pandemic, but participants nevertheless enjoyed a series of fascinating talks on topics ranging from outbreak surveillance with big data to the detection of novel pathogens.

New paper on transitions from niche-structured to immigration-structured communities published in Theoretical Ecology

What forces structure the diversity of ecological communities on local scales? One perspective is that local niche factors determine how many species can coexist locally. A very different perspective is that local diversity is mainly a function of immigration and regional diversity. Pioneering ecologist Robert MacArthur (1930–1972) made seminal contributions to theory embodying both perspectives. The dichotomy between the two perspectives has thus been termed “MacArthur’s paradox”.

In previous work, we built a unified mathematical model of island biodiversity and showed that increasing immigration with island area drives a transition from niche-structured to immigration-structured communities. The model predicts a biphasic island species–area curve that is commonly seen in nature. In a new paper just out in Theoretical Ecology, we explore this transition in more detail. We modify MacArthur & Wilson’s (1967) classical graphical paradigm of island biogeography to include niches and show that it leads to a biphasic species–area relationship (SAR), consistent with our previous mathematical model (see graph below). We show that three classic mathematical niche models predict a similar SAR when immigration is added. We also reconcile this biphasic island SAR with the classic triphasic SAR seen on mainlands, and predict a tetraphasic SAR in low-diversity mainland systems, with a sampling phase at very small spatial scales and an elusive niche-structured phase at intermediate spatial scales.

By continuing the unification of the niche and immigration perspectives, our work helps resolve MacArthur’s paradox. We propose experiments that manipulate immigration directly to explore the transition between the niche- and immigration-structured regimes. And we propose large-scale data analyses to find the elusive niche-structured phase of the SAR on mainlands.

The standard theory of island biography predicts that (A) island diversity arises from a balance between immigration and extinction, with extinction being lower and immigration being higher on large islands, leading to (B) an increasing island species–area relationship. Our unified theory additionally predicts that (C) niches buffer species from extinction when island species richness is low, leading to (D) a biphasic species–area relationship.

Chisholm, R. A. and T. Fung. 2021. Examining the generality of the biphasic transition from niche-structured to immigration-structured communities. Theoretical Ecology (in press)

Martin Trappe presents his work at the Institute of Physics Meeting Singapore 2021

Martin Trappe, a former Senior Research Fellow in our lab, today presented his work on density functional theory for ecology at the Institute of Physics Meeting Singapore 2021. Martin is based at the Centre for Quantum Technologies at NUS, and had a joint appointment in our lab for two years, during which time he was taking the powerful tools of density functional theory from physics and using them to model complex multi-scale ecological systems. His work is available on bioRxiv and is currently undergoing peer review.

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

UPDATE December 2021: The book is now available in printed form.

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.

(Elinor Ostrom image credit: © Holger Motzkau 2010, Wikipedia/Wikimedia Commons (cc-by-sa-3.0))