Muller plot
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Muller plots are plots which combine information about succession of different OTUs (genotypes, phenotypes, species, ...) and information about dynamics of their abundances (populations or frequencies) over time. They are powerful and fascinating tools to visualize evolutionary dynamics[1][2]. They may be employed also in study of diversity and its dynamics, i.e. how diversity emerges and how changes over time.
They are called Muller plots in honor of Hermann Joseph Muller who used them to explain his idea of Muller's ratchet [3].
In a Muller plot, usually horizontal axis shows time or generations and vertical axis represents relative abundances of OTUs at the corresponding times or generations. Different OTUs are usually shown with polygons or areas with different colors and each OTU originates somewhere in the middle of its parent area in order to illustrate their succession in evolutionary process.
A big difference between Muller plots and normal bar plots of abundances is that a Muller plot depicts not only the relative abundances but also succession of OTUs based on their genealogy/phylogeny/parental relation.
To generate a Muller plot one needs the genealogy/phylogeny/parental relation of OTUs and their abundances over time.
References
- ^ Herron, Matthew D.; Doebeli, Michael (2013). "Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli". PLoS Biology. 11 (2): 1–11. doi:10.1371/journal.pbio.1001490.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Maddamsetti, Rohan; Lenski, Richard E.; Barrick, Jeffrey E. (2015). "Adaptation, Clonal Interference, and Frequency Dependent Interactions in a Long Term Evolution Experiment with Escherichia coli". Genetics. 200 (2): 619–631. doi:10.1534/genetics.115.176677.
- ^ Muller, Hermann Joseph (1932). "Some Genetic Aspects of Sex". The American Naturalist. 66 (703): 118–138. doi:10.1086/280418.
External links
- MullerPlot: A package for generating Muller plots in R
- ggmuller: Create Muller Plots of Evolutionary Dynamics (package on GitHub)
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