BEACON Researchers at Work: The Origin of a Species?

This week’s BEACON Researchers at Work blog post is by MSU postdoc Zachary Blount.

Zack in a treeI love big questions. I tend to walk around, my head in the clouds, questions flitting through my head. I admit that I have walked into trees whilst in oblivious abstraction. One of the best parts of being a scientist is that I get to work on answering big questions. Biology features a lot of big questions, and how new species evolve is one of the biggest and most important. Speciation increases diversity and complexity, and, importantly, it allows organisms to explore new evolutionary paths. There is little in biology that isn’t touched by speciation, and it is little wonder that Darwin himself referred to it as “that mystery of mysteries.”

Despite all the fantastic work done since Darwin’s day, speciation is still mysterious. Speciation is complex, multifaceted, tricky to study, and, most importantly, hard to “catch in the act.” It would help if we had a model system in which we could study speciation in fine detail as it occurs, examine and manipulate the processes involved, and to do so over a humanly reasonable time scale.

My work as a BEACON postdoc deals with a possible laboratory speciation event that might be a good model. It arose in the course of the E. coli Long-term Evolution Experiment (LTEE), which recently celebrated its 25th anniversary. The experiment was begun in 1988, when Richard Lenski founded 12 identical E. coli populations. Every day 1% of each population is transferred to a fresh growth medium containing a small amount of glucose for food. Each population grows by about 6.64 generations per day, and so far each has evolved for more than 55,000 generations! Samples are frozen every 500 generations, and because bacteria survive freezing, we have a complete, viable fossil record of the evolution of each.

cloudy vs clear beakerIn early 2003, 15 years and 33,000 generations into the experiment, something nifty happened. One of the 12 populations, called Ara-3, became much cloudier, meaning that it had suddenly gotten much larger. What happened? The growth medium contains a potential second food source called citrate, which is added to help the bacteria take up iron. I say potential because E. coli cannot grow on citrate when oxygen is present, as it is during the experiment. This Cit phenotype is one of the major traits used to define E. coli as a species, in large part because mutant E. coli that can grow aerobically on citrate (Cit+) are incredibly rare. (Only one was reported in the entire 20th century!) And yet, one of the populations was now full of Cit+ E. coli. (My doctoral research examined how Cit+ evolved. That story is told in full in my dissertation defense video.) Amazingly, Cit bacteria continued to coexist in the Cit+-dominated population.

Ara-3 Phylogenetic Tree

Is Cit+ a new species? That is a trickier question than you might think. Speciation is a process and not a sudden, instantaneous event, and there is no single, universally accepted species definition. (This reflects how nature really doesn’t conform to the human need for sharply-drawn categories.) The most widely accepted, however, is Ernst Mayr’s Biological Species Concept (BSC), which equates speciation with the evolution of reproductive isolation. This means that a group of organisms is a new species when its members can mate, mingle genes, and produce fertile offspring with each other, but not with members of its parent species.

Ecotype Species ConceptUnfortunately, the BSC is hard to apply to asexual bacteria. The most compelling bacterial species concept, Frederick Cohan’s Ecotype Species Concept (ESC), emphasizes the evolution of ecological differences. It argues that a bacterial species is born when a mutation grants access to a new niche, resulting in a new lineage called an ecotype. Because the new ecotype and its parent occupy difference niches, they are able to coexist and evolve independently. Under the ESC, a new species must have a mutation that gives access to a new niche, have originated once, and it must be pursuing its own evolutionary path.

Does Cit+ fit the characteristics of an ecotype species? The Cit+ trait opened a niche that is new to E. coli. If we look at a phylogenetic tree of Ara-3, we see that the Cit+ lineage evolved once, and forms a new branch on the tree. We can also see that the Cit clones that persist after Cit+ became dominant are on another branch, meaning that Cit+ and Cit are evolving separately. Cit+ might be a new ecotype species…

Despite these findings, I am not quite comfortable calling Cit+ a new species just yet. If Cit+ really is evolving to become well-adapted to the citrate niche, it might become better at growing on citrate, and worse at growing on glucose. This pattern could mean that some of the same mutations that are making Cit+ better at eating citrate are also making it worse at eating glucose. I can even test this. I can use genetic engineering techniques to move candidate beneficial mutations I find in later Cit+ genomes into earlier Cit+ genomes, and then measure their fitness effects with competition experiments. I can then move the Cit+-beneficial mutations I find into Cit genomes to see if they reduce fitness in the glucose niche. If they do, these citrate Niche-Specific Adaptive Mutations (NSAMs) would have a really nifty consequence. Even though bacteria don’t reproduce sexually, NSAMs are the sort of genetic changes that can produce reproductive barriers between new sexual species. Finding citrate NSAMs would therefore mean that Cit+ is evolving exactly the sort of genetic changes expected in species that also fit the Biological Species Concept. Then I would feel comfortable saying that Cit+ is a new species!

I have a lot work to do to test these ideas. However, if Cit+ really can be considered a new species, it would mean that Cit+ will be both a great example of evolution in action, and a model with which to investigate the tricky mysteries and big questions of speciation. Ahh! It’s great to be a scientist!

For more information about Zack’s work, you can contact him at blountza at msu dot edu.

About Danielle Whittaker

Danielle J. Whittaker, Ph.D. Managing Director of BEACON
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