by Staff Writers
Urbana IL (SPX) Jul 16, 2015
While teaching a class on coarse-graining methods in physics, James O'Dwyer realized that the technique could be used to understand how microbes evolve over time. The results, published in PNAS, reveal microbial family trees with distinct evolutionary patterns that may one day help us understand how harmful microbes evolve.
"The species concept is difficult for microbes," said O'Dwyer, an assistant professor of plant biology and member of the Carl R. Woese Institute for Genomic Biology at the University of Illinois.
Microbes typically reproduce asexually, which makes it difficult to use the traditional biological species concept, which defines species as organisms that can reproduce together. Ecologists and microbiologists have often lumped microbes with similar DNA sequences together as effective, `operational' taxonomic (or classification) units.
In this paper, O'Dwyer and co-authors Steven Kembel from the Universite du Quebec a Montreal and Thomas Sharpton from Oregon State University have sorted these sequence data into a new kind of family tree, that displays sudden bursts of diversification. This is likely the first time that coarse-graining, a physics principle, and ?-coalescents, a set of mathematical models, have been used to address questions in ecology.
What are phylogenetic trees?
When diversification happens relatively quickly, and multiple lineages have similar genes, a branch could appear to split into multiple branches, instead of just two. Ordinarily, biologists would try resolve this ambiguity, by figuring out the order in which lineages diversified.
Introducing a new phylogenetic tree
Using phylogenetic trees to understand diversification is like using Google Maps to understand automobile travel, said O'Dwyer. You can zoom in to look at detailed information, studying individual city streets, or you could zoom out to look at the bigger picture of how people are moving across the state using interstates.
So far, ecologists have typically used phylogenetic trees that are "zoomed in" to show all the branches. In this paper, coarse-graining condenses many short binary branches into large nodes that suddenly split into multiple branches, resembling the tines of a fork.
The result is a simpler, "zoomed out" tree that shows bursts of diversification over time. These bursts were found in phylogenetic trees created for 22 microbial communities, chosen to represent a breadth of habitat types: plant, marine, and human gut and skin.
"They provide us with an echo of real ecological processes, like adaptive radiations, when an organism rapidly diversifies due to a change in environment or to fill a new niche," O'Dwyer said. "And these bursts are there throughout these phylogenetic trees, deep within their history."
Finding an ecological theory that fits
Real-world applications and future work
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
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