arXiv subjects

James P. O'Dwyer

Publications and source records attributed to James P. O'Dwyer.

7 recordsLinked to original sources

arXiv2018

Cross-scale ecological theory sheds light on the maintenance of biodiversity

One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.

q-bio.PE↗

arXiv2017

Widespread bursts of diversification in microbial phylogenies

Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to plant-soil interactions, to marine life. Yet what has remained largely hidden is the interplay of ecological and evolutionary processes that led to the diversity we observe in the present day. We introduce a theoretical framework to quantify the effect of ecological innovations in microbial evolutionary history, using a new, coarse-grained approach that is robust to the incompleteness and ambiguities in microbial community data. Applying this methodology, we identify a balance of gradual, ongoing diversification and rapid bursts across a vast range of microbial habitats. Moreover, we find universal quantitative similarities in the tempo of diversification, independent of habitat type.

q-bio.PE↗

arXiv2017

The impact of species-neutral stage structure on macroecological patterns

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, 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 within-species 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 fecundity and mortality change as an individual transitions from one stage to the other. We explore several qualitatively different scenarios, and compare numerically obtained species abundance distributions to the predictions of unstructured neutral theory. We find that abundance distributions are generally robust to this kind of stage structure, but significant departures from unstructured predictions occur 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 abundance distribution departs from unstructured model predictions. Our findings potentially explain power law-like abundance distributions in organisms with strong demographic structure, such as eusocial insects and humans, and partially rehabilitate species abundance distributions from past criticisms as to their inability to distinguish between biological mechanisms.

q-bio.PE↗

arXiv2017

Reinterpreting Maximum Entropy in Ecology: a null hypothesis constrained by ecological mechanism

Simplified mechanistic models in ecology have been criticized for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions. In particular, we identify the sufficient statistics needed to parametrize a given mechanistic model from data and use them as MaxEnt constraints. Our approach isolates exactly what mechanism is telling us over and above the state variables alone.

q-bio.PE↗

arXiv2017

Inferring processes of cultural transmission: the critical role of rare variants in distinguishing neutrality from novelty biases

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: a classic example is the distribution of baby names. Using an overlapping generations model we show that these distributions consist of two phases: a power law phase with a constant 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 provide a direct way to establish whether observed empirical patterns are consistent with neutral evolution. We apply our approach to a complete data set of baby names from Australia. Crucially we show that analyses based on only the most popular variants, as is often the case in studies of cultural evolution, can provide misleading evidence for underlying transmission hypotheses. While neutrality provides a plausible description of progeny distributions of abundant variants, rare variants deviate from neutrality. Further, we develop a simulation framework that allows for the detection of alternative cultural transmission processes. We show that anti-novelty bias is able to replicate the complete progeny distribution of the Australian data set.

q-bio.PE↗

arXiv2015

Comparing process-based and constraint-based approaches for modeling macroecological patterns

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.

q-bio.PE↗

arXiv2005

Non-Perturbative Tachyon Potential from the Wilsonian Renormalization Group

The derivative expansion of the Wilsonian renormalization group generates additional terms in the effective beta-functions not present in the perturbative approach. Applied to the nonlinear sigma model, to lowest order the vanishing of the beta-function for the tachyon field generates an equation analogous to that found in open string field theory. Although the nonlinear term depends on the cut-off function, this arbitrariness can be removed by a rescaling of the tachyon field.

hep-th↗