Biology subjects

Joshua S Weitz

Publications and source records attributed to Joshua S Weitz.

4 recordsLinked to original sources

bioRxiv2016

A revised dilution methodology and implications for estimates of rates of plankton mortality

Author contribution statementSJB and JSW designed the research questions and approach. SJB wrote the code and performed the experiments. SJB and JSW wrote the paper.\n\nScientific significance statementZooplankton grazing is an important driver of plankton mortality and is a core component of the microbial loop. The dilution method is the prevailing tool used to measure the impact of zooplankton in marine microbial communities. However, the theoretical model underlying the interpretation of experimental measurements using this method does not account for niche competition between plankton. As a consequence, we show that the dilution method may conflate the effects of grazing with those of niche competition, implying that previously reported grazing rates could be overestimated. We propose modifying the classical dilution method by diluting only the zooplankton and then measuring the response of plankton. This \"Z-dilution\" method explicitly accounts for the effects of niche competition in limiting net plankton growth. We find the Z-dilution method provides robust grazing rate estimates in theory and suggest ways in which the relative strength of niche competition to zooplankton grazing could be measured by combining the Z-dilution and classical dilution methods.\n\nData availability statementCode is available from http://github.com/WeitzGroup/DilutionMethod-NicheCompetition and is archived on Zenodo at http://dx.doi.org/10.5281/zenodo.61196 (Beckett and Weitz, 2016).\n\nAbstractThe dilution method is the principal tool used to infer in situ microzooplankton grazing rates. However, grazing is the only mortality process considered by the theoretical model underlying the interpretation of dilution method experiments. We show an alternative interpretation arises when there is concurrent niche competition within the plankton community. We find that grazing rates may be overestimated - the degree of overestimation is related to the importance of niche competition relative to zooplankton grazing. Thus, we propose a modification to the dilution method to disentangle the effects of niche competition and zooplankton grazing. Our theoretical results suggest the revised \"Z-dilution\" method can robustly infer grazing mortality, regardless of the dominant plankton mortality driver. Further, we show it is possible to independently estimate both grazing mortality and niche competition when the classical and Z-dilution methods are used in tandem. We discuss the significance of these results for quantifying plankton mortality rates.

Ecology↗

bioRxiv2016

Inferring phage-bacteria infection networks from time series data

In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infects which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold-standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage-bacteria infection networks. This method uses time series data of fluctuating population densities to estimate the complete interaction network without having to test each phage-bacteria pair individually. We use in silico experiments to analyze the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network and mitigate against the possibility of evolutionary changes to infection during the time-course of measurement.

Ecology↗

bioRxiv2016

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

Multiple virus particles can infect a target host cell. Such multiple infections (MIs) have significant and varied ecological and evolutionary consequences for both virus and host populations. Yet, the in situ rates and drivers of MIs in virusmicrobe systems remain largely unknown. Here, we develop an individual-based model (IBM) of virus-microbe dynamics to probe how spatial interactions drive the frequency and nature of MIs. In our IBMs, we identify increasingly spatially correlated clusters of viruses given sufficient decreases viral movement. We also identify increasingly spatially correlated clusters of viruses and clusters of hosts given sufficient increases in viral infectivity. The emergence of clusters is associated with an increase in multiply infected hosts as compared to expectations from an analogous mean-field model. We also observe longtails in the distribution of the multiplicity of infection (MOI) in contrast to mean-field expectations that such events are exponentially rare. We show that increases in both the frequency and severity of MIs occur when viruses invade a cluster of uninfected microbes. We contend that population-scale enhancement of MI arises from an aggregate of invasion dynamics over a distribution of microbe cluster sizes. Our work highlights the need to consider spatially explicit interactions as a potentially key driver underlying the ecology and evolution of virus-microbe communities.

Ecology↗

bioRxiv2016

Replicator Dynamics with Feedback-Evolving Games: Towards a Co-Evolutionary Game Theory

A tragedy of the commons occurs when individuals take actions to maximize their payoffs even as their combined payoff is less than the global maximum had the players coordinated. The originating example is that of over-grazing of common pasture lands. In game theoretic treatments of this example there is rarely consideration of how individual behavior subsequently modifies the commons and associated payoffs. Here, we generalize evolutionary game theory by proposing a class of replicator dynamics with feedback-evolving games in which environment-dependent payoffs and strategies coevolve. We initially apply our formulation to a system in which the payoffs favor unilateral defection and cooperation, given replete and depleted environments respectively. Using this approach we identify and characterize a new class of dynamics: an oscillatory tragedy of the commons in which the system cycles between deplete and replete environmental states and cooperation and defection behavior states. We generalize the approach to consider outcomes given all possible rational choices of individual behavior in the depleted state when defection is favored in the replete state. In so doing we find that incentivizing cooperation when others defect in the depleted state is necessary to avert the tragedy of the commons. In closing, we propose new directions for the study of control and influence in games in which individual actions exert a substantive effect on the environmental state.

Evolutionary Biology↗