Genomic Analysis of a Bacterial Evolutionary Pathway Underlying a Phenotypic Innovation

Peter and Rosemary Grant have been responsible for what must be among the longest-running continuous field studies in evolutionary biology (2011).  It will reach forty years in 2013.  In this work, the Grants closely follow multiple species of finches on the Galápagos Island of Daphne Major.  Their results have provided numerous valuable insights into the nature of evolutionary change. 

The closest comparable study in the laboratory setting, with respect to both duration and the number of insights pertaining to the nature of selection and evolution, is perhaps the Long-Term Evolutionary Experiment (LTEE) of Richard Lenski and his associates at Michigan State University.  For almost twenty-five years they have been growing twelve populations of Escherichia coli in a glucose-limited minimal medium and transferring a sample of each population to a fresh flask every day and freezing samples periodically for later analysis.  They have now propagated these bacteria for more than 40,000 generations. 

Under the well-aerated conditions of these cultures, E. coli cannot normally utilize the substantial amount of citrate in the medium as a carbon source.  However, mutation to a Cit⁺ phenotype did occur in one of the long-term populations after about 31,000 generations.  In a Nature paper published last month, Blount et al. (2012) thoroughly characterize the mutational steps required to achieve the Cit⁺ phenotype. 

Because of the availability of the amazing library of E. coli isolates from steps all along the evolutionary trajectory, the authors were able to demonstrate that what they call potentiating mutations were necessary to allow a mutation supporting the Cit⁺ phenotype to be expressed.  These latter mutations, referred to as actualizing mutations, involved gene fusion and duplication as well as the ‘capture’ of a promoter from another locus.  Replay experiments demonstrated that there were different precise genetic configurations that sufficed to generate the minimal Cit⁺ phenotype. 

Lenski and his colleagues also carried out several experiments the results of which strongly suggested that the potentiating mutations worked primarily through epistatic interactions with the actualizing mutations.  The evidence they accrued failed to offer support for the alternative hypothesis that the potentiating mutations potentiated the occurrence of the actualizing mutation by physically increased the likelihood of its occurrence. 

A third and critical step necessary for the persistence of the new phenotype involved refining mutations. The genetic alterations most clearly demonstrated to support substantial increases in the frequency of Cit⁺ bacteria were further amplifications of the key genetic module.  

Several conclusions seem justified.  First, this study impressively reveals the power of the long-term longitudinal study of a population of rapidly reproducing organisms.  Second, it expands our conception of the process by which evolutionarily novel phenotypes can arise.  Third, the results reported by Lenski and colleagues illustrate yet again the functional fluidity of genetic information, in that the actualizing mutation for the Cit⁺ phenotype typically involved a fusion of part of the citrate fermentation operon with another gene bearing no obvious functional relationship thereby coming under the control of a new promoter that serendipitously altered the expression pattern of the key gene product.  Fourth, as noted by Hendrickson and Rainey (2012) in their commentary on the paper, the new findings effectively illustrate both the extreme opportunism of evolution and the profound unpredictability of the potentiating mutations.  

Hendrickson and Rainey end their remarks by suggesting that these results add support to the notion that the genetic changes underlying the evolution of organisms are gradual while phenotypic changes may be more discontinuous.  I would note that no one seems to prospectively define the boundaries that divide gradual from dramatic genotypic or phenotypic change, and in this case, it could be argued that the Cit⁺ phenotype comes about gradually.  

Darwin’s assertion that evolution is gradual is sometimes misinterpreted as meaning that evolution occurs at an absolutely steady pace.  It is not plausible that the tempo of evolution of any species is constant within some arbitrary range of variation on all time scales, and I would speculate that Darwin was too careful a thinker to have committed himself to such a dubious proposition.  Furthermore, there is an important distinction between evolutionary change and net evolutionary change.  As the Grants have noted in their study of finch evolution on Daphne Major (2011), the direction of selection can oscillate such that a given morphological feauture, such as beak size, may increase and then decrease, or vice versa, demonstrating significant morphological evolution despite the absence of net morphological change greater than some threshold.  

The key points may be that: 1) in many cases (perhaps most), significant phenotypic changes will involve multiple genetic alterations that occur with no particular regularity and some of which may be very modest in scope, and 2) there does not have to be any specific relationship between the scale of the genetic change and the scale of any corresponding phenotypic change. 

References  

Grant PR, Grant BR. Causes of lifetime fitness of Darwin’s finches in a fluctuating environment. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):674-9. Epub 2011 Jan 3. PubMed PMID: 21199941; PubMed Central PMCID: PMC3021069. 

Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature. 2012 Sep 27;489(7417):513-8. doi: 10.1038/nature11514. Epub 2012 Sep 19. PubMed PMID:22992527; PubMed Central PMCID: PMC3461117. 

Hendrickson H, Rainey PB. Evolution: How the unicorn got its horn. Nature. 2012 Sep 27;489(7417):504-5. doi: 10.1038/nature11487. Epub 2012 Sep 19. PubMed PMID: 22992522.