An improved neutral community model for temporal observations in microbial communities

Niche theory and neutral theory propose two alternative mechanisms for explaining the long-term coexistence of species in ecological communities. However, the true dynamic mechanisms of ecological communities likely fall in between these two theories of niches and neutrality. Thus, models reconciling the niche and neutral theories to interpret these mechanisms are of high significance. Using temporal observations of microbial communities, Ofiţeru et al. (2010) demonstrated a version of the neutral community model that quantifies the contributions of neutral forces and environmental factors on the population dynamics of species in the community. They use a novel weighted least squares method to estimate the parameters. However, this method estimates compound parameters and the population size cannot be disentangled from the immigration rate, becoming computationally intractable when there are zero values existing in the temporal observations. In the current study, we suggest a new version of the neutral community model, modified from the work of Ofiţeru et al. that does not suffer from these limitations. We also provide a new method for estimating the parameters for our model, which can resolve the estimates of individual parameters. We apply the new model to a real data set and compare our results with those of Ofiţeru et al.