Author Archives: ryanchisholm

Martin’s paper on a density functional theory for ecology published in Nature Communications

In a new paper led by Martin Trappe we present density functional theory for ecology (DFTe)—a new framework for ecological modelling. Ecology currently has detailed mechanistic theories that can describe the interaction of a few interacting species at small scales, and statistical theories that can describe the dynamics of large numbers of species at large scales. But a persistent challenge is to develop unified modelling approaches that can span a range of temporal and spatial scales.

In the new paper, we draw on density functional theory, which has found wide application to many-body problems in physics. We take density functional theory’s computational framework and apply it to ecology, demonstrating with several examples its potential power for predicting the outcome of ecological interactions. In essence, our DFTe takes data from simple systems (e.g., two-species competition), fits an energy functional to the data, and uses this to predict the outcomes of more complex systems (e.g., multi-species competition). The applications we present range from classic two-species algal competition experiments to microbial predator–prey systems to tropical forest tree communities. We believe that our DFTe can contribute to a more unified understanding of ecological systems.

Martin is a Senior Research Fellow in the Physics department; this project arose from his two-year 50% appointment in the Biological Sciences department a few years ago. The paper has just been published in Nature Communications.

Trappe, M.-I. and R. A. Chisholm. A density functional theory for ecology across scales. Nature Communications 14:1089

One of our case studies focussed on Tilman’s (1981, Ecology) classic algal experiments. Photos at top show some of the algal species concerned (photo credit: Jason Oyadomari for the first two images and Don Charles for the third). Graphs at bottom show predicted outcomes from a hypothetical experiment of four algal species competing for two resources (only results for three species are shown because the fourth always went extinct). Predicted algal abundances from our DFTe (vertical axes) were almost identical to those of Tilman’s R* theory (horizontal axes). Each point shows the results for one randomly chosen pair of values for the resource input rates (greener colours indicate points closer to the one-to-one line).

Ryan visits the Department of Integrative Biology at the University of Texas at Austin

Ryan visited the University of Texas at Austin last week and gave the weekly seminar in the Department of Integrative Biology. He talked about our lab’s work on estimating historical extinctions in Singapore and on untangling the roles of dispersal assembly and niche assembly in ecological communities. He was hosted by Asst. Prof. Caroline Farrior, and enjoyed learning about her lab’s work on understanding the structure of plant communities using a combination of theoretical and empirical approaches.

He also visited the Department of Ecology and Evolutionary Biology at Princeton University, where he met with colleagues and presented our lab’s work at the Theoretical Ecology Lab Tea.

Fanhua’s new paper on tree diversity in a subtropical forest in China published in Forest Ecology and Management

Kong Fanhua has been a visiting PhD student in our lab for the last year and her first paper has just been published in Forest Ecology and Management. The paper focuses on the Baishanzu 25 ha forest plot in China, which comprises subtropical forest with a mix of patches of different ages and management histories, and a mix of early-, mid- and late-successional tree species. Fanhua’s main result was that tree diversity is higher around early-successional trees, emphasising the importance in forest management of having a variety of species of different successional stages and a variety of stand ages.

Kong, F., X. Chen, M. Zhang, Y. Liu, S. Jiang, R. A. Chisholm, and F. He. 2022. Pioneer tree species accumulate higher neighbourhood diversity than late-successional species in a subtropical forest. Forest Ecology and Management (in press)

A view across the Baishanzu forest plot in eastern China.

Tak’s new paper on a neutral model with changing community size published in Theoretical Population Biology

Neutral biodiversity models make the simplifying assumption that all species are the same. These models have been used extensively over the last two decades to understand real biodiversity patterns. One failing of neutral models is that they predict species ages that are far too long. For example, for Amazon trees standard neutral models predict species ages that exceed the age of the angiosperms (~140 million years). In a new paper led by Tak, we explore a mechanism that can fix species ages in these models without breaking neutrality: allowing community size to change over time in a non-equilibrium situation. We develop new mathematical formulas for the species abundance distribution and species ages in a neutral model with changing community size. We show that if this model is parameterised to represent changes in the size of the Amazon since a meteor impact obliterated much of the vegetation 66 million years ago, it can produce species ages and a species abundance distribution that are both consistent with reality. The results suggest that a neutral explanation for Amazon tree diversity cannot be completely ruled out.

Fung, T., and R. A. Chisholm. 2022. Improving the realism of neutral ecological models by incorporating transient dynamics with temporal changes in community size. Theoretical Population Biology (in press)

An artist’s impression of the meteor impact that largely obliterated Amazon vegetation 66 million years ago. Image credit: Creative Commons Zero license, and A Owen from Pixabay.

Ryan presents a seminar at the Smithsonian Tropical Research Institute in Panama

Ryan is currently on sabbatical at the Smithsonian Tropical Research Institute (STRI) in Panama and today he gave the weekly Tupper seminar, presenting our lab’s work on transitions between dispersal assembly and niche assembly in ecological communities. The US-based Smithsonian Institution established STRI 100 years ago to study tropical ecosystems, and it is now a major global hub for tropical forest research in particular.

The Gamboa laboratory of the Smithsonian Tropical Research Institute.

Nadiah’s paper on the evolution of cooperation published in Scientific Reports

How co-operation evolved in human societies is a long-standing scientific puzzle. To solve it, we need to explain both how co-operation arose in the first place and how it has been maintained over time. In a new paper led by Nadiah, we show using a mathematical model that two key ingredients can explain the puzzle: high homophily in early human societies, and non-linear pay-offs. Homophily refers to the tendency to interact with genetically related others. Non-linear pay-offs mean that the benefits of an activity such as a hunt may increase sharply once the number of hunters exceeds a certain threshold. The emerging chronological narrative is that human co-operative behaviour arose because ancient human groups were small and comprised mostly family members, and that it has been maintained over subsequent millennia because of non-linear pay-offs, even as human groups have become very large and homophily has dropped. Our mathematical model takes these ideas, which had previously been expressed only verbally, and formalises them and makes them rigorous.

A major challenge in our modelling approach was computing higher-order genetic association between individuals, and to overcome this we used a mathematical framework developed several years ago by our collaborator Hisashi Ohtsuki from the School of Advanced Sciences in Japan. Our new paper is now published in Scientific Reports:

Kristensen, N.P., Ohtsuki, H. & Chisholm, R.A. Ancestral social environments plus nonlinear benefits can explain cooperation in human societies. Scientific Reports 12, 20252 (2022)

Top: The net benefit from an activity such as hunting can increase non-linearly with the number of hunters (co-operators). Bottom: Because of this, an individual may be incentivised to co-operate if the number of co-operators is close to a threshold (although the individual defector pay-off, in red, is always higher than the individual co-operator pay-off, in blue, if there are only four co-operators a defector is incentivised to switch to co-operation because W>Z). This non-linearity is a key ingredient of our model explaining the origin and maintenance of co-operation in human societies.

Ryan presents a seminar at the Blanes Centre for Advanced Studies in Spain

Ryan is currently on sabbatical at the Blanes Centre for Advanced Studies (CEAB) in Spain, and this week he presented a seminar there about our lab’s work on extinctions in Singapore and the transition from niche-assembled to dispersal-assembled ecological communities. The CEAB was set up in 1985 and focuses on various aspects ecology, in particular marine ecology. Ryan is hosted by David Alonso, who is a theoretical ecologist focussed on community ecology and infectious diseases.

Ryan visits Imperial College London

Ryan recently visited Imperial College London for the 75th anniversary of their Silwood Park campus, which was established after World War II for field-based research on topics related to ecology. The event included seminars by distinguished alumni of Silwood park about the campus’s history and the future of research there. Several young Silwood researchers also gave engaging presentations about their recent research. The day before the event, Ryan gave a seminar on our lab’s work on transitions between dispersal assembly and niche assembly in ecological communities.

Lab awarded new grant on population viability analysis in variable environments

We have been awarded a new Tier 2 grant by Singapore’s Ministry of Education to develop new models for assessing the viability of species’ populations in variable environments. Population viability analysis is widely used to assess species’ extinction risk, but there is a need to develop more sophisticated methods for incorporating variation in environmental conditions over time. This is especially true given increasingly volatile climate conditions around the world. This grant will allow us to develop these methods and apply them to key focal species in Singapore, including pangolins (Manis javanica) and straw-headed bulbuls (Pycnonotus zeylanicus).

The grant involves co-principal investigators Frank Rheindt and Lim Jun Ying from NUS, and collaborators Chong Kwek Yan from Singapore National Parks, Shawn Lum and Ngo Kang Min from Nanyang Technological University, and Roopali Ragahavan from Mandai Wildlife Group.

The straw-headed bulbul (Pycnonotus zeylanicus) is globally a critically endangered species but has a stronghold in Singapore, where its extinction risk will be assessed under the recently awarded grant.
Image credit: Francis Yap, Singapore Birds Project

Sean successfully defends his PhD thesis

Sean Pang has successfully defended his doctoral dissertation titled “Impact of climate and land-use change on tree distributions in southeast Asia”. Sean—pictured below with his examiners—joined our lab last year after his former advisor, Ted Webb, moved overseas. Sean’s research has involved species distribution models of dipterocarp trees in Southeast Asia, and the use of novel methods for assessing their vulnerability to climate and land-use change. Two of his chapters have already been published, in the journals Scientific Reports and Diversity & Distributions. Congratulations, Dr. Pang!