Category Archives: Uncategorized

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!

Lynette’s review on measuring habitat complexity published in Ecology Letters

Our review on measuring habitat complexity in ecology has just been published in Ecology Letters. The review is led by Lynette Loke, a post-doctoral fellow at Macquarie University and previous collaborator of our lab. Ecologists have theorised that habitats with higher complexity have higher diversity, and there is some empirical evidence to support this. But generalisations are difficult, partly because complexity is not measured in a standardised way. We review frequently used metrics of habitat complexity and identify qualities that an ideal metric of complexity should possess.

We find that fractal dimension, one of the most commonly used metrics of complexity, is fraught with problems: fractal dimension is hard to measure accurately (see second figure below); most real ecological habitats may not have fractal properties; and fractal dimension is often poorly correlated with diversity. Rugosity, or surface roughness, is another commonly used metric that is easier to measure and better correlated with diversity, but it may not capture important aspects of habitat complexity. We see promise in information-based metrics of complexity, such as entropy, which are more holistic.

Loke, L.H.L. & Chisholm, R.A. (2022) Measuring habitat complexity and spatial heterogeneity in ecology. Ecology Letters (in press)

Examples of complex surfaces. (a) Three simulated surfaces with different fractal dimensions (D). (b) Three real surfaces at different spatial scales: a rock surface; a rocky shore; and a forest landscape.
Estimates of fractal dimension (vertical axis) can be inaccurate, even under the idealised conditions here where the simulated object being measured is generated from a truly fractal process with known fractal dimension (horizontal axis). The best-performing method is the box-counting method at intermediate scales, but this is rarely if ever applied in ecology (the standard box-counting and variation methods are more prevalent but exhibit strong biases).

Congratulations to Annabel for being awarded valedictorian!

Our recently graduated Honours student Annabel Lim has been awarded valedictorian of the 2021–2022 undergraduate class in Biological Sciences. Annabel specialised in Environmental Biology and completed a minor in Communications and New Media. She was also awarded the Navjot Sodhi prize and the Malayan Nature Society Silver Medal for Academic Excellence. Her Honours thesis explored conservation planning for dipterocarp forests in the Philippines under future climate-change scenarios. She plans to go on to post-graduate study at the NUS Centre for Nature-based Climate Solutions. Her valedictory speech can be viewed here at 1:48:00. Congratulations, Annabel!

Deon’s paper on the history of discovery of avian phylogenetic diversity published in Proceedings of the Royal Society B

Discoveries of new species continue to be reported regularly in scientific journals and the popular media, but how distinct are these new species from known species? In a new paper led by Deon Lum, a former research assistant in our lab, we explored this question for birds. We drew on multiple existing sources to build a robust avian phylogenetic tree, and explored how much each discovery of a new bird species over the last 250 years has added to our knowledge of phylogenetic diversity.

Our main finding is that newly discovered species are increasingly similar to known species. Around the turn of the 19th century, novel species discoveries included the Tawny Frogmouth and the Australian Owlet-nightjar, each of which represented a new taxonomic order and contributed roughly 60 Myr to known phylogenetic diversity at the time. In contrast, the most novel discoveries in recent decades have contributed only about 10% as much to our knowledge. One exception proves the rule: the discovery of the Udzungwa Forest Partridge in the 1990s was by far the most novel species in recent decades, but its novel contribution to known phylogenetic diversity was only about 20 Myr—one third that of the earliest decades’ most novel species. We conclude that our knowledge of the avian tree of life is mostly complete.

Deon recently moved to the UK, where he is starting his PhD in the Department of Earth and Environmental Sciences at the University of Manchester. The paper was also authored by Frank Rheindt of our department’s Avian Evolution Lab.

Lum, D., F. E. Rheindt, and R. A. Chisholm. 2022. Tracking scientific discovery of avian phylogenetic diversity over 250 years. Proceeding of the Royal Society B 289:20220088

The phylogenetic novelty of the most novel bird species discovered in each decade has declined consistently over the last 200 years (PD = phylogenetic diversity). [Image credits: Common Ostrich – Yathin S Krishnappa, CC BY-SA 4.0, via Wikimedia Commons; Southern Brown Kiwi – depositphotos; Giant Ibis – Henrik Grönvold / Ibis 1911, British Ornithologists’ Union; Udzungwa Forest Partridge – Martin Woodcock / Ibis 1994, British Ornithologists’ Union.]

New paper on consumer–resource models published in Journal of Theoretical Biology

According to the stress-gradient hypothesis, mutualistic interactions between species can become stronger in harsher environments. For example, mosquito larvae in water-filled tree hollows can benefit from the presence of beetle larvae—the beetle larvae shred leaves into smaller pieces that the mosquito larvae can consume—and the benefit is greater when the environment is harsher, i.e., when there is less overall leaf litter available. In a previous study, we failed to find theoretical support for the stress-gradient hypothesis in a mathematical consumer–resource model. But in a new study, we show that the stress-gradient hypothesis can hold if there is a sufficient leakage rate of the downstream resource (the small pieces of leaves in the mosquito larvae example). We additionally show that our previous results are robust to the precise mathematical assumptions about how a species’ consumption rate increases with resource availability.

In our consumer–resource model, a “facilitator” species (pictured is a scritid beetle larva; image © Stephen Luk) converts an upstream resource into a form usable by a “beneficiary” species (pictured is a mosquito larva; image credit Harry Weinburgh, USCDCP). According to the stress-gradient hypothesis, the beneficiary species benefits more from the facilitator species under stressful conditions.

The new study was led by undergraduate student Sim Hong Jhun, and came out of his Honours project, which was supervised by Lam Weng Ngai (now at Nanyang Technological University) and Chong Kwek Yan (now at the National Parks Board, Singapore). The paper has just been published in the Journal of Theoretical Biology:

Sim, H. J., W. N. Lam, R. A. Chisholm, and K. W. Chong. 2022. Downstream resource leakage a necessary condition for the stress-gradient hypothesis in processing chain commensalisms. Journal of Theoretical Biology 538:111043

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.