September 2017

Welcome to two new members of the lab! Ruth Davidson is a mathematician with extensive interests in mathematical biology, and joins us as a research scientist, while Euphy Wu is a new undergraduate trainee who will be working with Rafael D’Andrea and myself. Welcome!

August 2017

Several members of the lab present at ESA this year. Alice spoke on how microbial evolutionary trees show evidence for bursts of branching (Tuesday 10:10am, B113 COS 41, preprint available here), Nick Sutton on optimal escape behavior with prior+new information, Mario Muscarella on origins and rates of appearance of microbial traits, and Rafael spoke about our recent paper published in Theoretical Ecology on demographic structure and species abundance distributions (pre-print here).

July 2017

Fantastic to have Allison Barner to visit the lab, jam on ecological network theory, and present a nice talk on how difficult (and debated) network inference is.

March 2017

New papers! Members/collaborators of the lab posted three new preprints this week:

Novelty, popularity, and emergent neutrality: bias in the choice of baby names and lessons for analyzing cultural data
James P. O’Dwyer, Anne Kandler

Neutral evolution assumes that there are no selective forces distinguishing different variants in a population. Despite this striking assumption, many recent studies have sought to assess whether neutrality can provide a good description of different episodes of cultural change. One approach has been to test whether neutral predictions are consistent with observed progeny distributions, recording the number of variants that have produced a given number of new instances within a specified time interval: the classic example is the distribution of baby names registered within a given year. Here we develop new methods to analyze the shape of progeny distributions. Previous work had approximated the neutral progeny distribution as a power law with an exponent varying with population size and innovation rate. Using an overlapping generations model we show that the progeny distribution consists of two phases: a power law phase with an universally-applicable exponent of -3/2, followed by an exponential cut-off for variants with very large numbers of progeny. Maximum likelihood estimations of the model parameters then provide a direct way to parameterize the neutral model. We apply our approach to a data set of baby names from Australia. While neutrality provides a plausible description of the progeny distribution of abundant variants, rare variants deviate from neutrality. This indicates that analyses based on only the most popular variants can provide misleading evidence for underlying transmission hypotheses. To determine whether the progeny distribution is a meaningful statistic to distinguish between different processes of cultural transmission we analyze the effects of novelty biases. We show that a kind of anti-novelty bias, where new variants are at a disadvantage by virtue of their novelty, is able to replicate more closely the complete progeny distribution of the Australian data set.

Who Constrains the Constraints? Using Maximum Entropy to test the value of Mechanistic Models
James P. O’Dwyer, Andrew Rominger, Xiao Xiao

Ecologists have developed simplified models of large-scale patterns like the species abundance distribution, or species-area relationship, and implicitly we assume in these models that only some subset of mechanisms scale up to impact these predictions. Applications of the maximum entropy principle in ecology has also developed predictions for these patterns, with the goal of making predictions fixed by just a handful of ecological state variables, like total abundance and species richness. But one outstanding question remains: what principle tells us which state variables to constrain? We take the approach of using mechanistic models to inform this choice, thus translating mechanism into a set of state variables. In addition to providing a mechanistic basis for the state variables, our approach isolates exactly what the mechanistic model is telling us over and above the state variables alone, and whether this additional information is useful in explaining empirical data. This provides a general framework for developing robust null hypotheses against which to compare mechanistic models.

The impact of species-neutral stage structure on macroecological patterns
Rafael D’Andrea, James P. O’Dwyer

Despite its radical assumption of ecological equivalence between species, neutral biodiversity theory can often provide good fits to species abundance distributions observed in nature. Major criticisms of neutral theory have focused on interspecific differences, which are in conflict with ecological equivalence. However, individual-level neutrality in nature is also broken by differences between conspecific individuals at different life stages, which in many communities may vastly exceed interspecific differences between individuals at similar stages. These individual-level asymmetries have not been fully explored in species-neutral models, and it is not known whether demographic stage structure affects macroecological patterns in neutral theory. Here we present a two-stage neutral model, where both fecundity and mortality are allowed to change as an individual moves from a stage to the other. We explore qualitatively different scenarios, and compare numerically obtained species abundance distributions to the predictions of unstructured neutral theory. We find that abundance distributions are robust to this kind of stage structure, but only so long as subpopulations at different stages fluctuate in synchrony. On the other hand, species abundance distributions can differ significantly from the unstructured case if adults have sufficiently low fecundity and mortality. In addition, we show that the cumulative number of births per species, which is distributed as a power law with a 3/2 exponent, is invariant even when the SAD departs from unstructured model predictions. Our findings potentially explain power law-like abundance distributions in systems with strong demographic structure, such as eusocial insects and human given names, and may partially rehabilitate species abundance distributions from past criticisms as to their inability to distinguish between biological mechanisms.

February 2017

Congratulations to Nick Sutton, a MS student in the lab, who won the overall faculty prize at the annual GEEB symposium. Well done, Nick!

February 2017

Mercedes Pascual visited the lab from the University of Chicago, and gave a fantastic PEEC seminar on viruses, ecology, and identifying niches.

October 2016

Rafael D’Andrea joined the lab, moving from the University of Michigan where he completed his PhD. Rafael will be working on projects supported by the Simons Foundation. Welcome, Rafael!

August 2016

This month we welcomed new postdoc, Mario Muscarella to the lab! Mario will be working on projects supported by the NSF and McDonnell Foundation.

May 2016

James was quoted by Newsweek in reference to an exciting new paper by Ken Locey and Jay Lennon. Can we predict the number of microbial species on Earth? They think yes!

May 2016

New paper! Comparing process-based and constraint-based approaches for modeling macroecological patterns. In collaboration with Xiao Xiao and Ethan White a development of our earlier pre-print has now been peer-reviewed and published in Ecology.

Abstract Ecological patterns arise from the interplay of many different processes, and yet the emergence of consistent phenomena across a diverse range of ecological systems suggests that many patterns may in part be determined by statistical or numerical constraints. Differentiating the extent to which patterns in a given system are determined statistically, and where it requires explicit ecological processes, has been difficult. We tackled this challenge by directly comparing models from a constraint-based theory, the Maximum Entropy Theory of Ecology (METE) and models from a process-based theory, the size-structured neutral theory (SSNT). Models from both theories were capable of characterizing the distribution of individuals among species and the distribution of body size among individuals across 76 forest communities. However, the SSNT models consistently yielded higher overall likelihood, as well as more realistic characterizations of the relationship between species abundance and average body size of conspecific individuals. This suggests that the details of the biological processes contain additional information for understanding community structure that are not fully captured by the METE constraints in these systems. Our approach provides a first step towards differentiating between process- and constraint-based models of ecological systems and a general methodology for comparing ecological models that make predictions for multiple patterns.

May 2016

New paper! Species-abundance distributions under colored environmental noise. In collaboration with Tak Fung and Ryan Chisholm, we have shown that temporal autocorrelation in environmental fluctuations can significantly impact classic biodiversity patterns like the species abundance distribution.

Abstract Natural communities at all spatiotemporal scales are subjected to a wide variety of environmental pressures, resulting in random changes in the demographic rates of species populations. Previous analyses have examined the effects of such environmental variance on the long-term growth rate and time to extinction of single populations, but studies of its effects on the diversity of communities remain scarce. In this study, we construct a new master-equation model incorporating demographic and environmental variance and use it to examine how statistical patterns of diversity, as encapsulated by species-abundance distributions (SADs), are altered by environmental variance. Unlike previous diffusion models with environmental variance uncorrelated in time (white noise), our model allows environmental variance to be correlated at different timescales (colored noise), thus facilitating representation of phenomena such as yearly and decadal changes in climate. We derive an exact analytical expression for SADs predicted by our model together with a close approximation, and use them to show that the main effect of adding environmental variance is to increase the proportion of abundant species, thus flattening the SAD relative to the log-series form found in the neutral case. This flattening effect becomes more prominent when environmental variance is more correlated in time and has greater effects on species’ demographic rates, holding all other factors constant. Furthermore, we show how our model SADs are consistent with those from diffusion models near the white noise limit. The mathematical techniques we develop are catalysts for further theoretical work exploring the consequences of environmental variance for biodiversity.

April 2016

Super visit from Ian Hatton, from McGill, who also gave the lab group seminar on The predator-prey power law: Biomass scaling across terrestrial and aquatic biomes.

April 2016

New paper! Maintenance of biodiversity on islands. With collaborators at the National University of Singapore we have published a new development inspired by the classic theory of island biogeography, developed by MacArthur and Wilson. Our new paper seeks to show how a combination of ecological niches and neutral drift can explain the so-called `small island effect’, whereby small islands show deviations from the classic theory.

Abstract MacArthur and Wilson’s theory of island biogeography predicts that island species richness should increase with island area. This prediction generally holds among large islands, but among small islands species richness often varies independently of island area, producing the so-called ‘small-island effect’ and an overall biphasic species–area relationship (SAR). Here, we develop a unified theory that explains the biphasic island SAR. Our theory’s key postulate is that as island area increases, the total number of immigrants increases faster than niche diversity. A parsimonious mechanistic model approximating these processes reproduces a biphasic SAR and provides excellent fits to 100 archipelago datasets. In the light of our theory, the biphasic island SAR can be interpreted as arising from a transition from a niche-structured regime on small islands to a colonization–extinction balance regime on large islands. The first regime is characteristic of classic deterministic niche theories; the second regime is characteristic of stochastic theories including the theory of island biogeography and neutral theory. The data furthermore confirm our theory’s key prediction that the transition between the two SAR regimes should occur at smaller areas, where immigration is stronger (i.e. for taxa that are better dispersers and for archipelagos that are less isolated).

March 2016

New paper with collaborators at the National University of Singapore was covered in an awesome article by Veronique Greenwood, in both Quanta and the Atlantic.
(image credit: Olena Shmahalo / Quanta Magazine)

March 2016

New paper! Environmental forcings, from storms to fires and insect outbreaks to elephants, drive tree population dynamics in forests across the world. What effect does environmental variance have on patterns of forest diversity? In our new paper, in press at Ecology, we show that a model with realistically strong environmental forcings can accurately reproduce both static and dynamic patterns of diversity in two tropical forest plots, one in Malaysia and one in Panama.

Poulsenia armata, a tree that was formerly dominant in the canopy at the Panama plot but suffered 50% mortality during a 1980s drought (image credit: STRI).

Abstract Ecological communities are subjected to stochasticity in the form of demographic and environmental variance. Stochastic models that contain only demographic variance (neutral models) provide close quantitative fits to observed species-abundance distributions (SADs) but substantially underestimate observed temporal species-abundance fluctuations. To provide a holistic assessment of whether models with demographic and environmental variance perform better than neutral models, the fit of both to SADs and temporal species-abundance fluctuations at the same time has to be tested quantitatively. In this study, we quantitatively test how closely a model with demographic and environmental variance reproduces total numbers of species, total abundances, SADs and temporal species-abundance fluctuations for two tropical forest tree communities, using decadal data from long-term monitoring plots and considering individuals above two size thresholds for each community. We find that the model can indeed closely reproduce these static and dynamic patterns of biodiversity in the two communities at the two size thresholds, with better overall fits than corresponding neutral models. Therefore, our results provide evidence that stochastic models incorporating demographic and environmental variance can simultaneously capture important static and dynamic biodiversity patterns arising in tropical forest communities.

March 2016

Great visit from Andy Rominger, UC Berkeley, who also gave the lab group seminar on Evolution and the statistical mechanics of biodiversity.

February 2016

Rogier Braakman visited the lab for a few days from MIT, and gave the NASA Astrobiology Institute Seminar on Evolution of Electron and Nutrient Flows and the Organization of Ecosystems.

November 2015

Check out the latest from James in Nautilus magazine on power laws, scaling, and some of the ongoing work in our lab.
(Image courtesy of Edhv,

October 2015

Fantastic to have Mario Muscarella visit from Indiana University at Bloomington, and give the lab group seminar on Microbes and Resources: Individuals, Communities, and Ecosystem Function.

October 2015

Congratulations to Zachary Cohen, an undergraduate researcher in the lab. Zack received an honorable mention in the Volterra competition at the recent Ecological Society of America meeting, for his poster on inferring microbial community dynamics from time series data. Nice work, Zack!

September 2015

The O’Dwyer lab is now supported by the James S McDonnell Foundation’s Complexity Scholar award, joining a fantastic group of researchers working to understand complex systems.

August 2015

Exciting news—Nicholas Sutton joins the lab as a Masters student, through the PEEC program at Illinois. Nick is broadly interested in decision-making processes and the proximate causes of behavior, and he is specifically interested in ungulate species.

August 2015

The O’Dwyer Lab at ESA! Check out our talks:

James: Wednesday 3:20pm in Room 343 in the Theoretical Ecology COS
Philippe: Thursday 3:40pm Room 301 in the Biodiversity II COS

Meanwhile undergraduate researchers Nicholas Sutton and Zachary Cohen will be presenting posters on Tuesday and Friday. Check out their work on flight initiation for white-tailed deer, and time series analysis for microbiome communities.

July 2015

Our recent paper on microbial communities and phylogenies is one of PNAS’ Top 50 most read papers for July.

July 2015

Exciting news for the O’Dwyer lab—we’ll be funded by a Simons Foundation Investigator award in the Mathematical Modeling of Living Systems.

Simons Foundation

June 2015

New paper: Backbones of evolutionary history test biodiversity theory for microbes published in PNAS Early Edition.

Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

May 2015

Collaborator Ryan Chisholm visits the O’Dwyer lab from Singapore.

May 2015

Philippe attends Symposium and Summer School in Phylogenomics and Metagenomics in Ann Arbor, MI.

Feb 2015

James visits the Santa Fe Institute to entertain the current crop of postdoc fellows.

October 2014

James visits University of Chicago to give the Ecology and Evolution seminar.

September 2014

New paper: On Theory in Ecology published in BioSciences, and mentioned on the Dynamic Ecology blog. Please contact us if you have any difficulty accessing the paper.

We argue for expanding the role of theory in ecology to accelerate scientific progress, enhance the ability to address environmental challenges, foster the development of synthesis and unification, and improve the design of experiments and large-scale environmental-monitoring programs. To achieve these goals, it is essential to foster the development of what we call efficient theories, which have several key attributes. Efficient theories are grounded in first principles, are usually expressed in the language of mathematics, make few assumptions and generate a large number of predictions per free parameter, are approximate, and entail predictions that provide well-understood standards for comparison with empirical data. We contend that the development and successive refinement of efficient theories provide a solid foundation for advancing environmental science in the era of big data.

September 2014

Stefano Allesina visits the lab and gives the department seminar in Natural Resources and Environmental Sciences

September 2014

Invited talk at the annual International Meeting on Microbial Genomics.

August 2014

Graduate students Philippe Doucet Beaupre and Stacey Butler join the lab. Welcome!

July 2014

Collaborator Ryan Chisholm visits the O’Dwyer lab from Singapore, and entertains PEEC with a Summer seminar.

July 2014

Our recent Ecology Letters paper on Red Queen Hypothesis discussed in article by Brandon Keim for Nautilus Magazine.

June 2014

New paper with Ryan Chisholm on Red Queen models and macroecology, published online early at Ecology Letters

Individual species are distributed inhomogeneously over space and time, yet, within large communities of species, aggregated patterns of biodiversity seem to display nearly universal behaviour. Neutral models assume that an individual’s demographic prospects are independent of its species identity. They have successfully predicted certain static, time-independent patterns. But they have generally failed to predict temporal patterns, such as species ages or population dynamics. We construct a new, multispecies framework incorporating competitive differences between species, and assess the impact of this competition on static and dynamic patterns of biodiversity.

June 2014

Seminar and visit to Ecole Normal Superieure/College de France, hosted by Helene Morlon and Jessica Green

April 2014

Seminar and visit to University of Indiana Bloomington, hosted by Jay Lennon and Ken Locey

March 2014

New paper with Ryan Chisholm on species ages in neutral models published in Theoretical Population Biology

Neutral biodiversity models predict species ages that are unrealistically long—sometimes exceeding even the age of the Earth. But the exact extent of the problem with these models has been unknown until now, because we have lacked analytical species age formulas appropriate to ecological contexts. In our new paper, we have derived such formulas and used them to provide new neutral estimates of species ages of tropical trees. We show that neutral species ages are still too long, but by about a factor of ten less than previously thought.

March 2014

Seminar and Visit to University of Illinois at Chicago, hosted by Emily Minor