Category Archives: Uncategorized

Lynette’s paper on the maintenance of diversity in seawall communities published in Nature

What determines the number of species that occur together in a given ecological community? One view is that species richness is driven mainly by characteristics of the local site, such as resource availability and habitat diversity. This is the niche perspective. Another view is that species richness is driven mainly by immigration from a larger region. This is the dispersal perspective. A long-standing goal of ecology is to reconcile these two perspectives. A classic unified theory predicts that dispersal assembly is observed only when immigration to a system is very low, and that niche assembly is observed in most other situations. A novel unified theory, developed by our lab (see here and here), predicts just the opposite: that niche assembly is observed only when immigration is very low, with dispersal assembly prevailing otherwise.

In a paper led by Lynette Loke and just published in Nature, we present the results of an experiment designed to test these two unified theories by systematically varying the rate of immigration and observing the response of species richness. Our focal system was intertidal animal communities on artificial seawalls in Singapore. The communities comprise crustaceans, gastropods, bivalves, tunicates and other creatures. Each experimental unit was a concrete tile overlain by a stainless steel cage with polycarbonate sheet panels, into which we punched variable numbers of holes to allow different immigration rates across treatments.

The results were consistent with the novel unified theory. The number of species was roughly constant, at around five, for low-immigration treatments with one to five holes, but then began to increase substantially with the addition of further holes (see graph below). This implies that roughly five animal species can coexist via niche assembly in these seawall communities in the absence of substantial immigration, but in practical settings the communities will usually be in a dispersal-assembly regime with many more than five species, because natural immigration is higher than even in our highest-immigration experimental treatment. If these results can be generalised to other systems, it would follow that the species diversity we see small-scale ecological communities in the natural world is largely due to dispersal assembly rather than niche assembly.

This project is the most recent in a series of collaborations between Lynette and our lab (see here and here). Lynette is currently a post-doctoral researcher Macquarie University in Sydney. The experimental work for this project involved her going out alone into the field for a few days every fortnight for 12 months and navigating various challenges including pandemic social-distancing restrictions. The journal has also published a Research Briefing about the work.

Loke, L. and R. A. Chisholm. 2023. Unveiling the transition from niche to dispersal assembly in ecology. Nature

The relationship of species richness to immigration rate in our seawall communities is close to flat for low immigration rates, suggesting that niche assembly dominates here, but strongly increasing above a threshold immigration rate, indicating that dispersal assembly dominates at high immigration rates. The blue curve shows the fit of the classic unified theory (which predicts saturation of species richness under high immigration at the blue dashed line; hypothesis 1), and the red curve shows the fit of the new unified theory (which predicts a lower bound on species richness under low immigration at the red dashed line; hypothesis 2).

Nadiah visits Hisashi Ohtsuki’s lab at SOKENDAI, Japan

Nadiah is currently on a ten-week visit to Hisashi Ohtsuki’s lab at SOKENDAI (The Graduate University for Advanced Studies) in Japan. We have been collaborating with Hisashi over the past couple of years exploring questions related to the evolution of co-operation using a novel mathematical framework that accounts for higher-order genetic associations. This work resulted in a publication a few months ago. During Nadiah’s visit to Japan, she and Hisashi have been finalising work extending this mathematical framework to evolutionary games with many different strategies (rather than just two), and exploring new ideas related to homophilic group formation. This week she gave a presentation at SOKENDAI about our lab’s work on this and other topics.

Review of biodiversity–productivity relationships in forests published in Oecologia

Forests are a massive store of carbon and also contain a large fraction of the earth’s species. Conserving forests is thus essential for mitigating both climate change and biodiversity loss. But how synergistic are these goals? Do forests that sequester more carbon also have high biodiversity? If so, that suggests we can get more bang for our conservation buck by protecting such forests. If not, we may need largely complementary approaches to carbon conservation and biodiversity conservation. The answer depends on the form of the biodiversity–productivity relationship.

In a just-published review paper by Ryan and Tanvi Dutta Gupta, an undergraduate student at Stanford University who has been an occasional visitor to our lab, we assess current knowledge about the forest biodiversity–productivity relationship and discuss its implications for conservation. We find that the relationship is generally positive: forests with more tree species tend to be more productive, and thus sequester carbon more rapidly. However, there are several important caveats to this that may limit the relevance to conservation. Firstly, even though on average more species means more productivity, in many cases the most-productive forest stands are monocultures of particular fast-growing species, such as eucalpyts. Secondly, the productivity gains of having more than ten species are hard to perceive. Thirdly, the relationship between biodiversity and productivity may not be causal, but driven by some third variable, such as tree density. Fourthly, the relationship varies markedly across spatial scales and may not be strongly positive at scales relevant to conservation. Lastly, current methods for estimating productivity in forests have large errors associated with them. Clearly, more work is needed before we can confidently quantify the carbon benefits of protecting or planting diverse forests.

Chisholm, R. A., T. Dutta Gupta (2023) A critical assessment of the biodiversity–productivity relationship in forests and implications for conservation. Oecologia (in press)

Pasoh Forest Reserve, Malaysia, has very high tree diversity. Such forests also tend to have higher productivity, but the strength of this relationship depends strongly on factors such as the scale of observation and whether confounding variables are controlled for.

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.