Category Archives: Uncategorized

Nadiah’s new paper on Singapore plant extinctions out in Conservation Biology

Have you ever wondered how many species were lost before we had the chance to discover them? In a paper now out in Conservation Biology, led by Nadiah, we estimated just that, for plant species in Singapore, following on from our lab’s related work on Singapore birds and butterflies.

All over the world, many species remain undiscovered while both known and unknown species continue to go extinct. This is particularly true in the tropics, where biodiversity is high and development continues apace. Singapore provides an invaluable case study of tropical biodiversity loss. Since British colonisation in 1819, most of Singapore’s forest cover has been replaced with urban landscape. However, Singapore also has one of the best-documented floras in the world, in terms of taxonomic and temporal coverage, with historical collections beginning only a few years after colonisation.


The orchid species Grammatophyllum speciosum has not been recorded in Singapore since 1918.
Photo credit: Cerlin Ng

We collated a high-quality database of over 30,000 Singapore plant collections representing over 2,000 species, and we applied our lab’s previously developed “SEUX” model to estimate extinction rates and total numbers over time. The SEUX model is based on a straightforward idea: if we assume that the per-year per-species extinction rates have been the same for discovered and undiscovered extinctions, then we have a basis for working backwards in time to estimate the number of undiscovered species and the proportion that went extinct. In the new paper we also developed a more accurate method for obtaining confidence intervals on the estimates.

We estimated that 30–38% of Singapore plant species have gone extinct since 1819. The central estimate using classical methods was 32% and that using Bayesian methods was 35%. Crucially, these numbers are much higher than the 22% extinction rate that one obtains from the naïve method of simply dividing the number of known extinctions by the total number of discovered species, demonstrating the importance of calculating extinction rates in a way that accounts for unknown species.

Also check out Nadiah’s blog post on the paper, her previous blog post giving a SEUX tutorial, and her SEUX for R package on GitHub. The full reference for the paper is below.

Kristensen, N. P., Seah, W. W., Chong, K. Y., Yeoh, Y. S., Fung, T., Berman, L. M., Tan, H. Z., Chisholm, R. A. (2020) Extinction rate of discovered and undiscovered plants in Singapore, Conservation Biology (in press)


From the Singapore plants database, we inferred the number of discovered species that were extant and extinct over time. We then used the SEUX model on these data to estimate the number of undiscovered species that were extant and extinct over time.


Aloysius’s paper on estimating tropical plant litter decomposition published in Pedobiologia

Aloysius Teo completed his PhD in the lab in 2017, and a chapter from his thesis has just been published in Pedobiologia. The “tea bag method” was developed several years ago by our coauthor Joost Keuskamp for estimating decomposition rates of plant litter. The method relies on commercially available tea bags, thus facilitating standardisation of methods across studies. Aloysius explored the applicability of the method to tropical forests, where a particular problem is that abundant termites readily damage tea bags.

Aloysius found that tea bag attack rates by termites were large enough in tropical forests in Singapore to invalidate experimental results relying on the tea bag method. He trialed methods for excluding termites and, based on his results, recommended an extended tea bag method for future use in the tropics that relies on a combination of unmodified tea bags and termite exclusion treatments.

Teo, A., N. P. Kristensen, J. A. Keuskamp, T. A. Evans, M. Foo, R. A. Chisholm. 2020. Validation and extension of the tea bag index to collect decomposition data from termite-rich ecosystems. Pedobiologia (in press)

tea bags

Top: Physical termite exclusion barriers used for tea bags in the study, along with unmodified tea bags. Bottom: A tea bag undetected by termites (left) alongside two bags that were detected (centre and right).


Tak coauthors new genetic modelling paper with Frank Rheindt’s lab

A new paper led by Tang Qian and  Frank Rheindt from the Avian Evolution Lab at NUS, with Tak Fung as a co-author, has just been published in Molecular Ecology Resources.

The paper describes how they developed a new R package called ResDisMapper, which helps in the management of biological invasions and habitat degradation by allowing users to generate a map showing resistance to dispersal over a landscape, as defined using genetic data. The R package is novel because there are few programs available that map resistance to dispersal over the relatively short spatiotemporal scales required for the management of biological invasions and habitat degradation.

They tested ResDisMapper against two other programs (DResD and EEMS) using a suite of simulated datasets and found that overall, it performed substantially better. They further demonstrated the utility of ResDisMapper by applying it to genetic data collected for rock pigeons (Columbia livia) in Singapore and Golden-crowned sifakas (Propithecus tattersalli) in northern Madagascar, to identify regions with high and low resistance to dispersal.

Tang, Q., T. Fung, and F. E. Rheindt. 2020. ResDisMapper: An R package for fine-scale mapping of resistance to dispersal. Molecular Ecology Resources


Resistance map produced by ResDismapper for rock pigeons in Singapore, with annotations describing the meaning of the different colours and contours. A significant barrier/corridor refers to areas with resistance values that are higher/lower than those from a null distribution with high probability, and lie within the red/green contours. Areas that lie inside the blue contours have resistance values with high probability of being positive or negative (high “certainty”). The yellow circles indicate sampling points.

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, R. 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:]

UPDATE: Ellner et al. wrote a technical comment on our paper, and our response is here.

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:]