Author Archives: ryanchisholm

New students join the lab

Three new students have joined the lab this month. Angelica See is a new PhD student, who recently completed her undergraduate degree in ecology at Nanyang Technological University. Her thesis research will focus on the effects of habitat fragmentation on tropical ecosystems. Kong Fanhua is a visiting PhD student from East China Normal University, where she is supervised by He Fangliang. She is studying species coexistence using empirical and theoretical approaches, and will be with us for two years. Nicholas Foong is an undergraduate student who will be doing his Honours project on global patterns of mangrove diversity. Welcome all!

New paper on unifying models of temporal environmental stochasticity published in Oikos

Ecological communities are universally subject to temporal environmental stochasticity—random variation in environmental conditions over time that cause species’ vital rates to change. This can have both positive and negative effects on species richness. For example, negative effects can arise because stochasticity makes a species more vulnerable to extinction, whereas positive effects can arise because stochasticity reduces the strength of competition between species. Is the net effect on species richness typically negative or positive, and what mechanisms typically dominate? Answering this question is of paramount importance for our understanding of the effects of temporally varying environments on biodiversity. In a study just published in Oikos, Tak and Ryan together with James O’Dwyer from the University of Illinois tackled this topic using a novel mathematical approach that unified past models of temporal environmental stochasticity and generated new insights.

Our novel approach was to focus on one species and approximate the rest of the multispecies community as a single entity, thus converting a many-body problem into a one-body problem and greatly simplifying the mathematics. We developed methods for separating the effects of temporal environmental stochasticity into population-level effects and community-level effects, and found that the strength and direction of these effects varied in complex and surprising ways as a function of temporal correlation in the environmental stochasticity.

Our most tantalising result was that there is a threshold value of temporal correlation above which the net effect of temporal environmental stochasticity on species richness switches from positive to negative. The threshold is approximately twice the reciprocal of the rate at which new species enter the community. This points the way to a practical method for assessing whether temporal environmental stochasticity has a net positive or negative effect on biodiversity in reality, although further theoretical work is needed to test the generality of our result.

Species richness S for competitive model communities exposed to temporal environmental stochasticity, as a function of temporal autocorrelation T (measured in generations; horizontal axis) and the coefficient of variation cb (colours). Below a critical threshold of temporal autocorrelation indicated by the dashed grey line, species richness is typically greater than in the baseline scenario with no temporal environmental stochasticity (i.e., a neutral scenario), while to the right of the line species richness is typically lower than in the baseline scenario. (Other model parameters for this figure are community size J=10,000 individuals and new species input rate ν=0.01; the critical threshold is T=2/(Jν)).

Fung, T., J. P. O’Dwyer, and R. A. Chisholm. 2021. Effects of temporal environmental stochasticity on species richness: A mechanistic unification spanning weak to strong temporal correlations. Oikos (in press)

New paper led by Frank Rheindt’s lab on bird diversity on Sundaic islands published in the Journal of Biogeography

MacArthur & Wilson’s (1967) classic theory of island biogeography predicts that island species richness arises from an equilibrium between immigration and extinction, with islands further from a mainland receiving fewer immigrants and thus having lower species richness. A twist on the basic paradigm occurs for land-bridge islands, i.e., islands that were previously connected to a mainland. Such islands may exhibit more species than expected if insufficient time has passed for the immigration–extinction equilibrium to be reached. For example, in Baja California more lizard species are found on islands that have become isolated more recently in geological time (Wilcox 1978).

In a paper just published in the Journal of Biogeography, we explored whether this effect exists for birds on the islands of Sundaland. The project was led by Keita Sin, a former Honours student in Frank Rheindt’s lab, who created a database of bird diversity on 94 of these islands, from both published inventories and his own field work. We tested whether shelf islands, which have been connected to major landmasses at various points over the last 20,000 years, have higher bird diversity than do oceanic islands. Surprisingly, we found that they do not. Our explanation is that both immigration and extinction rates for birds on islands are higher than for most other taxa, such as lizards and plants, and thus the immigration–extinction equilibrium is reached faster. Immigration rates are higher because birds are effective dispersers; extinction rates may be higher because bird species’ population sizes on islands are typically small. Our results help shed light on the processes that structure species diversity on islands.

Bird species richness on deep sea (oceanic) islands in Sundaland is not substantially lower than that on shelf islands.

Sin, Y. C. K., N. P. Kristensen, C. Y. Gwee, R. A. Chisholm, and F. E. Rheindt. 2021. Bird diversity on shelf islands does not benefit from recent land-bridge connections. Journal of Biogeography (in press)

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