Is the distribution of plasmid lengths bimodal?

The length of a plasmid is a key property which is linked to many aspects of plasmid biology. When distributions of plasmid lengths are shown in the literature, they are usually plotted with length on a logarithmic scale. However, a quantity and its logarithm have distinct distributions which may differ considerably in shape. Mistaking the distribution of log-lengths for the distribution of lengths can therefore lead to distorted conclusions about the distribution; in particular, the distribution of log-lengths may be bimodal when the distribution of lengths is only unimodal. This particular confusion has arisen in the literature where the length distribution is often claimed to be bimodal based on examination of what is in fact the log-length distribution. While the length distribution is indeed bimodal within many bacterial families, it is not across the ensemble of all plasmids. We suggest that authors should be careful to show the plasmid length distribution, or to distinguish the two distributions, to avoid misleading inferences.

A mathematician's guide to plasmids: an introduction to plasmid biology for modellers.

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.

I Smell a Mouse: Indirect Genetic Effects on Voluntary Wheel-Running Distance, Duration and Speed.

Indirect genetic effects (IGEs; the heritable influence of one organism on a conspecific) can affect the evolutionary dynamics of complex traits, including behavior. Voluntary wheel running is an important model system in quantitative genetic studies of behavior, but the possibility of IGEs on wheel running and its components (time spent running and average running speed) has not been examined. Here, we analyze a dataset from a replicated selection experiment on wheel running (11,420 control and 26,575 selected mice measured over 78 generations) in which the standard measurement protocol allowed for the possibility of IGEs occurring through odors because mice were provided with clean cages attached to a clean wheel or a wheel previously occupied by another mouse for 6 days. Overall, mice ran less on previously occupied wheels than on clean wheels, and they ran significantly less when following a male than a female. Significant interactions indicated that the reduction in running was more pronounced for females than males and for mice from selected lines than control mice. Pedigree-based "animal model" analyses revealed significant IGEs for running distance (the trait under selection), with effect sizes considerably higher for the initial/exploratory phase (i.e., first two of six test days). Our results demonstrate that IGEs can occur in mice interacting through scent only, possibly because they attempt to avoid conspecifics.