Wednesday, March 29, 2017

Thursday, March 16, 2017

Neutral Biogeography of Lake Systems

I am pleased to announce the publication of Sahar Shirani’s paper “Neutral evolution and dispersal limitation produce biogeographic patterns in Microcystis aeruginosa populations of lake systems” in Microbial Ecology

Compared to higher organisms, microbes have large population sizes and high dispersal rates. Consequently, their populations are often assumed to be well connected in space, and any spatial patterns are attributed to environmental differences. In this paper, we explore the role of dispersal limitation and neutral evolution in the biogeography of cyanobacteria in lake systems using an agent-based model (ABM) that simulates individual cells, including their transport, growth, death and mutation. Biogeographic patterns, quantified as nucleotide divergence and computed from the genomes of the model cells, can be substantial in some cases. These results contradict the common notion of no dispersal limitation for microbes, provide a benchmark for future biogeography studies and have implications for how lakes may respond to change.

In this project, we used a novel modeling methodology. We simulate 20k individual cells, each with a full Microcystis genome, for up to 20k years. Then we analyze the evolved genomes from the model using BLAST and MAFFT/Bio-Phylo. Application of these bioinformatics tools to models is new and opens new concepts, like a dynamic phylogeny tree (see movie below) and this synergy with observations highlights the realism of the model

Some interesting future applications of this model may include applying it to the human microbiome (see this paper or bacterial dispersal by ship balast water (see this paper The code is available at the link below and I am available to help and/or collaborate.

Image source: NASA WorldView




Enough about simple!

One of the goals of my research program is to bring modern biology into the models we use to manage our waterbodies. When learning about the science in a certain area I am always impressed by how much we know about certain topics. On the other hand I feel that there is an obsession with finding simple solutions to complex systems, which limits the utility of biological research. In this blog post at “On Biology” I argue that biologists should be more like modern car mechanics and delegate understanding (not just number crunching) to computers.

Regular visitors to this blog may realize I am a bit on a crusade here. I have been writing papers criticising our community (of ecosystem modelers) with titles “100 Years since Streeter and Phelps: It Is Time To Update the Biology in Our Water Quality Models” and “75 years since Monod: it is time to increase the complexity of our predictive ecosystem models” and now “Biology 2.0: It is time to delegate understanding to computers”. And I am writing another one as we speak. I guess it is a phase I am going through...


SASM HOMEPAGE (hasn’t been updated for a while)