Introducinguntb, anRPackage For Simulating Ecological Drift Under the Unified Neutral Theory of Biodiversity

Abstract

The distribution of abundance amongst species with similar ways of life is a classical problem in ecology.The unified neutral theory of biodiversity, due to Hubbell, states that observed population dynamics may be explained on the assumption of per capita equivalence amongst individuals. One can thus dispense with differences between species, and differences between abundant and rare species: all individuals behave alike in respect of their probabilities of reproducing and death.It is a striking fact that such a parsimonious theory results in a non-trivial dominancediversity curve (that is, the simultaneous existence of both abundant and rare species) and even more striking that the theory predicts abundance curves that match observations across a wide range of ecologies. This paper introduces the untb package of R routines, for numerical simulation of ecological drift under the unified neutral theory. A range of visualization, analytical, and simulation tools are provided in the package and these are presented with examples in the paper.

Genomic characteristics of Staphylococcus aureus strains associated with high within-herd prevalence of intramammary infections in dairy cows

“…This index indicates the probability that 2 strains sampled randomly from a population will belong to 2 different types (Hunter, 1990) and ideally, it should be equal to 1.0. The Simpson function from the R package untb (Hankin, 2007) was used to estimate Simpson's index.…”

A conceptual framework for invasion in microbial communities

“…In b, the curve associated with drift highlights the fact that, in a drift-only situation, invasion success increases rapidly with the size of the invading population. For example, simulating drift with the untb package (Hankin, 2007) shows that if an alien enters at 1% relative abundance or more in a community with a death and birth rate of 5% per generation, invasion success (persistence of at least one alien cell) after 5 biomass turnover times is almost certain.…”

Linking management to biodiversity in built ponds using metacommunity simulations

“…We used the untb package (Hankin, 2007) to fit a Fisher of Fisher's log series (Fisher et al, 1943) to the regional rank-abundance curve for observed zooplankton diversity, and the estimate of a Fisher was used to generate regional rank abundance curves to seed the metacommunity simulations. The value estimated for the rank abundance curve for cladoceran and rotifer families was 1.46, and this was used to seed simulations.…”