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 http://science.sciencemag.org/content/326/5960/1694) or bacterial dispersal by ship balast water (see this paper http://pubs.acs.org/doi/pdf/10.1021/acs.est.6b03108). The code is available at the link below and I am available to help and/or collaborate.
Image source: NASA WorldView
PAPER:
https://link.springer.com/article/10.1007/s00248-017-0963-5
MOVIE:
https://youtu.be/LV8th6TfALo
CODE:
https://github.com/fhellweger/LargeLakes
www.systemsbioecology.org
No comments:
Post a Comment