Theoretical & evolutionary community ecology

A major challenge in ecology is the need for a better theoretical framework for understanding how species assemblages (ecological communities) arise, why some are species-rich and others species-poor, and why some species are present or dominant whereas others are not.

Current community assembly theory is largely based on static models. However, ecological dynamics (e.g. ecological drift, competition, immigration), or evolutionary dynamics (e.g. genetic drift, natural selection, speciation) generate continual changes in the constituents of communities and the sources from which they are assembled. The dynamical models that do exist do not take the community perspective or do not readily allow inferences from data. Moreover, there is often a mismatch between models and data.

Current research projects

We attempt to solve these problems simultaneously by developing a fully stochastic, dynamical and data-friendly theory of community assembly, and testing and informing this theory with model-oriented experiments and field studies of both macro-organisms and micro-organisms. The theory should contain models of speciation, extinction, immigration and demographic change that vary in spatial, phylogenetic and biotic complexity, and which I design for confrontation with data by providing each model’s likelihood given the data.

We conduct evolutionary experiments on the mite Tetranychus urticae and the bacterium Escherichia coli, which are ideal model organisms due to their short generation times. The experiments will provide insight into how diversity affects diversification, a great unknown in current macro-evolutionary theory.

Apart from these highly controlled experiments, we apply the theory to naturally occurring micro-landsnails in South-East Asia, and micro-organisms in geothermal pools in New Zealand. Their small size, endemism and spatially limited, discrete habitat create a miniature world that facilitates sampling and confrontation with models.

We provide software tools for scientists and conservationists to assess the processes underlying natural communities and predict their future composition and diversity.

Main findings over the last decade

My main line of research has been on the influence of macro-evolution (speciation, extinction) on biodiversity, the influence of ecology (diversity) on macro-evolution, and the development of new methods to enable inferences on these influences to be made from empirical data.

I have done this from two paradigms. The first is the paradigm of the neutral theory of biodiversity. While the theory was in its infancy in the mid-2000s, only applicable to species abundance data for a single local community sample subject to a simplis¬tic mode of speciation, I have significantly advanced the theory by formulating (approximate) sampling formulas for alternative, more realistic, speciation modes, and for multiple samples. I have provided software, programmed in PARI/GP, to facilitate use by other researchers, who have developed faster C⁺⁺ implementations. I have also explored spatially explicit neutral models, neutral models with genetic speciation, and non-neutral extensions. The most important lesson learnt from these exercises is that poor performance of the neutral theory of biodiversity is often not due to its controversial assumption of neutrality, but due to other, auxiliary assumptions on speciation mode and spatial structure. I have established, with J. Rosindell, S. Cornell and S.P. Hubbell, a viable mature neutral model: the protracted speciation model. This model simultaneously solves various problems with the original neutral model regarding speciation rates, species longevity and number of rare species.

The other paradigm is the stochastic species-level birth-death perspective on diversification. Since the seminal paper by Nee et al. in 1994 who derived a formula for the likelihood of a phylogenetic tree under a simple model with constant speciation and extinction rates, no major theoretical progress was made although the data were crying out for more realistic models. For instance, the constant-rate model could not explain observed slowdowns in lineage accumulation. I contributed likelihood formulas for two realistic explanations: the diversity-dependent and the protracted speciation models. I have developed a new framework of adaptive radiations based on diversity-dependence that can simultaneously explain slowdowns in lineage accumulations, stasis in the fossil record, adaptive radiations and incumbent replacement/evolutionary succession. Application of this new model has already confirmed a key innovation in vangas and in pediomelum. As in neutral theory, the protracted speciation idea resolves various anomalies of the standard model regarding tree balance, lineage accumulation and non-monophyly, and allows estimating the duration of speciation from phylogenies of extant data alone.