Author Archives: ryanchisholm

Meryl’s new paper on Singapore butterfly extinctions published in Biological Conservation

In a paper just out in Biological Conservation, we estimate that 46% of Singapore’s butterfly species have been extirpated since 1854. Our study, one of the most comprehensive of its kind for tropical insects, gives a window on to how insect biodiversity may suffer as habitat destruction and degradation continues across the tropics. The paper was led by Meryl Theng, who was a research assistant in our lab and has recently started a PhD at the University of Adelaide.

To make our estimate of Singapore butterfly extirpations, we first put together an extensive database of butterfly records in Singapore going back to the first major collections in 1854. This included records from the Natural History Museum London, to which we sent two staff members to search for Singapore butterfly records. We then applied statistical models, recently developed in our lab, that estimate the total extirpation rate accounting for both observed and unobserved species.

We also looked at traits associated with early detection and early extirpation among Singapore’s butterflies. We found that species with rare larval host plants tended to be discovered later and extirpated earlier. Additionally, species with small wingspans tended to be discovered later, and species that were forest-dependent tended to be extirpated earlier.

Our paper provides an informative and timely case study of tropical insect extirpations. The estimated 46% extirpation rate of butterflies in Singapore (95% confidence interval [41%, 51%]) is greater than that previously estimated for birds in Singapore (33% [31%, 36%]), and suggests that tropical insects may be suffering more than other groups from human impacts.

Theng M., W. F. A. Jusoh, A. Jain, B. Huertas, D. J. X. Tan, H. Z. Tan, N. P. Kristensen, R. Meier, Ryan A. Chisholm. A comprehensive assessment of diversity loss in a well-documented tropical insect fauna: Almost half of Singapore’s butterfly species extirpated in 160 years. Biological Conservation 242:108401

Update: Our work has been reported on in the Straits Times (paywall) and in the Star online.

Ancistroides gemmifer.png

Ancistroides gemmifer, a species of skipper butterfly last recorded in Singapore 1926 and presumed extirpated there. The species persists in other parts of the region, including Penang, Malaysia, where this photo was taken. Image Credit: Gan Cheong Weei

New paper critically examining Modern Coexistence Theory published in Ecology Letters

In collaboration with colleagues from Bar-Ilan University in Israel we have just published a new paper in Ecology Letters critically examining key aspects of Modern Coexistence Theory—a theory that seeks to understand which mechanisms allow large numbers of species to coexist in nature. Specifically, we examine the theory’s reliance on using a species’ mean invasion growth rate as a measure of its ability to persist in a community.

Modern Coexistence Theory assumes that higher invasion growth rates imply greater persistence. We found that although the sign of the mean invasion growth rate correctly characterises two qualitatively different domains of species persistence, the magnitude of the mean invasion growth rate is not a reliable indicator of species persistence. The underlying reason is that the mean invasion growth rate ignores the effects of temporal variations in species abundances on species persistence. We suggest further investigation of metrics of species persistence that incorporate temporal variations in species abundances.

The project was led by Jayant Pande, a post-doctoral researcher in Nadav Shnerb’s lab at Bar-Ilan University. It is part of our collaborative grant with Shnerb’s lab under the Singapore–Israel research grants programme.

Pande, J., T. Fung, R. A. Chisholm, N. M. Shnerb (2019). Mean growth rate when rate is not a reliable metric for persistence of species. Ecology Letters. [link:]

New paper on resource facilitation models published in Oikos

A new paper in Oikos by Lam Weng Ngai (who recently defended his PhD thesis in Hugh Tan‘s lab at NUS) and Ryan looks at theoretical conditions under which one species—a facilitator—can promote the persistence of another—a recipient—by providing it with resources. A classic example of a facilitator species is a “nurse” plant, which creates an environment suitable for the germination of other plant species under its canopy. In the paper, we were particularly interested in examining the stress gradient hypothesis, which predicts that such positive species interactions should be stronger in environments suffering greater resource stress.

We analysed two simple dynamical mathematical models of resource facilitation and found that positive interactions between a facilitator and a resource recipient species occur only when the facilitator-mediated resource conversion rate is higher than the background rate. We found limited support for the stress gradient hypothesis in our two models—the hypothesis holds only when certain mathematical conditions on the model parameters are satisfied. Our work on these simple models establishes a mathematical framework on which future studies can build and explore the robustness of our conclusions about when and how resource facilitation operates.

W. N. Lam and R. A. Chisholm. Resource conversion: a generalizable mechanism for resource-mediated positive species interactions. Oikos (in press)

Facts about Gorse in New Zealand

The introduced plant Gorse (Ulex europaeus) in New Zealand can act as a nurse plant for regenerating native forest by stabilising the soil and providing an understorey environment that shelters seedlings from excessive wind and sun.



Tak’s new paper assessing the effects of a varying environment on tree species richness published in Ecology Letters

Do fluctuating environmental conditions have a positive or negative effect on biodiversity? This question is of profound ecological interest, and of growing practical relevance as climate variability around the world continues to increase. The answer to the question depends on the balance of two opposing forces. On the one hand, a fluctuating environment has negative effects on biodiversity by increasing stochasticity, which can lead to more extinctions by chance. On the other hand, a fluctuating environment can have positive effects on biodiversity by creating “temporal niches”. The net effect of these two opposing forces in natural communities was an outstanding knowledge gap.

A new Ecology Letters paper by Tak, Ryan and 46 collaborators from the CTFS-ForestGEO network addressed this key knowledge gap by quantifying the net effect of fluctuation-dependent mechanisms on tree species richness in 21 large forest plots, across a large latitudinal gradient. For each plot, we used tree census data over at least two censuses to quantify temporal population variability of tree species populations at the plot, which is an indicator of the strength of fluctuation-dependent mechanisms. We then fitted a mechanistic model to the observed temporal population variability at each plot, to determine whether the variability is having a net negative or positive effect on tree species richness.

We found that in our 21 forest plots, temporal population variability increased strongly with latitude, by a factor of about 3 to 4 over the latitudinal range of our data set. However, our model estimated that in these plots temporal population variability had mixed net effects on species richness: positive in some cases and negative in others. Thus, our results imply that temporal population variability makes no clear contribution to the strong latitudinal gradient in local tree species richness. This provides a nuanced perspective on the effects of temporal population variability on tree species richness.

Fung, T., R. A. Chisholm, K. Anderson-Teixeira, N. Bourg, W. Y. Brockelman, S. Bunyavejchewin, C.-H. Chang-Yang, R. Chitra-Tarak, G. Chuyong, R. Condit, H. S. Dattaraja, S. J. Davies, C. E. N. Ewango, G. Fewless, C. Fletcher, C. V. S. Gunatilleke, I. A. U. N. Gunatilleke, Z. Hao, J. A. Hogan, R. Howe, C.-F. Hsieh, D. Kenfack, Y. Lin, K. Ma, J.-R. Makana, S. McMahon, W. J. McShea, X. Mi, A, Nathalang, P. S. Ong, G. Parker, E.-P. Rau, J. Shue, S.-H. Su, R. Sukumar, I.-F. Sun, H. S. Suresh, S. Tan, D. Thomas, J. Thompson, R. Valencia, M. I. Vallejo, X. Wang, Y. Wang, P. Wijekoon, A. Wolf, S. Yap, J. Zimmermann (2019). Temporal population variability in local forest communities has mixed effects on tree species richness across a latitudinal gradient. Ecology Letters. [link:]


Temporal population variability of tree species populations against absolute latitude for the 21 CTFS-ForestGEO plots that we examined.


Tak’s new paper on probability distributions of extinction times, species richness, and immigration and extinction rates from neutral models published in Journal of Theoretical Biology

Neutral models in ecology make the parsimonious assumption that all species are demographically equivalent, and so their abundances only differ due to demographic stochasticity. Despite neutral models being stochastic models, previous studies have focused mainly on their mean behaviour owing to the lack of formulae for specifying the full probability distributions for biodiversity indicators of interest. In a new paper by Tak, Sonali (former Chisholm lab intern) and Ryan, we use classic results from birth–death processes to derive formulae specifying the probability distributions of extinction times (e.g., see figure below), species richness, and immigration and extinction rates in the classic spatially implicit neutral ecological model.

We demonstrate the utility of our formulae in providing greater ecological insight in a few ways:

1. Firstly, we parameterised a neutral metacommunity model for trees in the Amazon, and used it to show that the age of a common tree species in the Amazon, which by time-symmetry of a neutral model is equivalent to the extinction time of the species, is greater than the oldest estimated age of angiosperms with very high probability. Thus, neutral models produce slow species-abundance dynamics that severely overestimate species age.

2. Secondly, we show how our formula for the probability distribution of species richness can be used to fit a neutral local community model to observed species richness at Barro Colorado Island in Panama, given an independent estimate of the immigration rate. This is more parsimonious than the standard approach of fitting to the full species abundance distribution.

3. Thirdly, we show that the curves of immigration and extinction rates versus species richness in the local community component of the neutral model are for the most part approximately linear, reflecting low variation of species richness around the mean value.



Probability distributions of extinction time for a species population with initial abundance 1 or 2 and per-capita birth and death rates equal to 1/yr, in a neutral metacommunity model with 500 individuals and a per-capita speciation probability of 0.05. The distributions were calculated using the new formula that we derived.

Fung, T., S. Verma, and R. A. Chisholm (2020). Probability distributions of extinction times, species richness, and immigration and extinction rates in neutral ecological models. Journal of Theoretical Biology, 485: 110051. [link:]

Sam’s paper on modelling extinction debt published in Ecology Letters

When natural habitat is cleared, some species go extinct immediately, but others only after a period of time—the latter constitute an “extinction debt”. More habitat loss generally leads to greater species loss and greater extinction debt. But does the spatial pattern of habitat fragmentation matter? This issue is currently the topic of fervent debate in the ecological literature (see, e.g., here and here and here).

In a new Ecology Letters paper led by Sam Thompson, our recently graduated Imperial-NUS PhD student, we developed analytical methods for calculating extinction debt after habitat fragmentation in a spatial neutral model, i.e., a model that treats all species equally. Sam’s paper built on previous work by our lab looking at the immediate response of fragmentation to species richness, i.e., before extinction debt has been paid. Our new methods for estimating extinction debt in a neutral model are accurate and efficient to compute. They involve first calculating two key metrics, termed effective area and effective connectivity, and then plugging these into formulas.

Modelling approaches such as these are invaluable for understanding species loss with habitat fragmentation, because of the difficulty of carrying out large-scale habitat fragmentation experiments. One general insight from our analysis is that for a fragmentation metric to be biologically meaningful, it should be based on the way that the affected species interact with the landscape, rather than on what looks “fragmented” to the human eye.

Overall, we found that even in a neutral model the effect of habitat fragmentation on species loss is non-trivial and varies with spatial scale, temporal scale, and the degree of fragmentation. If this is true even in a neutral model, surely it must be true in reality. We suggest that this degree of subtlety is sometimes missing from the ongoing fragmentation debate, and that any discussion of fragmentation and species richness should be informed by rigorous modelling.

The paper was also coauthored by James Rosindell, Sam’s advisor at Imperial College London.

Thompson, S. E. D., R. A. Chisholm, and J. Rosindell (2019). Characterising extinction debt following habitat fragmentation using neutral theory. Ecology Letters (in press)


Trajectories of species loss following habitat clearing under different model scenarios for tropical forest trees corresponding to an area of ~5 km2. The shaded grey area to the right of each graph indicates extinction debt in every simulation, with light red and light blue areas additionally indicating the range of extinction debt across all simulations.

Population dynamics and species diversity workshop at Macquarie University

Ryan has just returned from a workshop on population dynamics and species diversity at Macquarie University, Sydney, Australia. The ten participants spent three days brainstorming new approaches to understanding how the dynamics of individual populations aggregate to determine properties of whole communities, including species diversity. As part of this, the participants spent time analysing a global dataset of community and population dynamics compiled from various sources by the workshop leaders, John Alroy and Drew Allen.

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