The common gut bacteria, Escherichia coli, typically known as E. coli.
Image: Dennis Kunkel.
Evolution is a random process — or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent evolution, one is tempted to hypothesize that, even if the mutations that underly evolution itself are random, the “end result” of evolution is not. In fact, this is the central premise of an interesting book by Simon Conway Morris, Life’s Solution (Cambridge University Press, 2004), where he postulates that ”the evolutionary routes are many, but the destinations are limited”. This is in direct conflict with the late Stephen Jay Gould’s hypothesis that a far different evolutionary outcome would occur if we could only replay the “tape of life”. So which is it?
Of course, replaying this tape of life is impossible, except when the organisms being studied have a fast enough generation time that we can watch their evolution during our own lifetimes. One scientist, Richard E. Lenski, a professor in the department of Microbiology and Molecular Genetics at Michigan State University, has been conducting this very experiment for the past 20 years. His organism of choice is our own humble gut bacteria, Escherichia coli, which has a generation time of approximately 20 minutes under optimum conditions.
To investigate the repeatability of evolutionary trajectories and outcomes within a population, Lenski set up a long term evolution experiment in 1988 where he obtained twelve founding bacterial lineages from the same clone of E. coli. According to his experimental design, all twlve populations were grown separately from each other under identical conditions for more than 44,000 generations, so far (the experiment is ongoing). At time intervals of 500 generations, samples were collected from each of the twelve lineages and frozen. These samples can later be thawed, revived and grown in culture, providing a glimpse into the evolutionary past for each lineage, revealing a detailed living fossil record of evolutionary changes that occurred in each population, providing researchers with the opportunity to study the contributions from genetic mutation and drift, and of natural selection to evolutionary change.
Part of Lenski’s experimental design was to grow the twelve E coli lineages under poor conditions, where their preferred energy source, glucose, was severely limited. Thus, one of the first characteristics that these bacterial populations evolved was the ability to rapidly metabolize all the available glucose in the culture and then wait patiently for their next daily meal. The culture broth also included a second energy source; citrate. But unlike glucose, which was limited, citrate was present in abundance. At first, the abundance of citrate was unimportant because E coli cannot metabolize this molecule when oxygen is present, and in fact, citrate metabolism (Cit+) is a characteristic that has long been used to differentiate this species from other similar, bacterial species.
Surprisingly, after 31,500 generations had passed, one of the twelve E coli lineages did the impossible: it evolved the capacity to metabolize citrate in the presence of oxygen.
But when exactly, did the citrate metabolic ability first appear? Referring to frozen bacterial stocks for this particular lineage, Lenski’s team discovered that Cit+ variants first appeared after 31,000 generations had passed, but were unable to expand to dominance until a further 2000 generations had passed. This suggests that the Cit+ variants needed to accumulate several more mutations that enhanced their metabolic efficiency so they could out-compete their Cit- relatives.
The long period of time that elapsed before Cit+ appeared within one — and only one — population suggested one of two evolutionary possibilities; either the Cit+ mutational event was especially unusual or the evolution of this particular character is contingent upon a complex series of earlier mutations, at least some of which were not uniquely advantageous to the organisms possessing them. This second, more complex form of evolution is known as contingent adaptation.
To clarify the evolutionary events that underlie the appearance of citrate metabolism, the researchers asked if Cit+ would always arise among descendants from the evolutionary ancestors wihtin this one lineage. In short, would the Cit+ variant always appear in this lineage if the “tape of life” could be replayed? When the researchers replayed the “tape of life” for this lineage by reviving older bacterial stocks and growing them again, they found that Cit+ never appeared in populations grown from samples that were frozen before 20,000 generations had passed, that citrate metabolizers were “extremely rare” in populations grown from samples frozen afterwards up until 27,000 generations had passed, and after that point, citrate metabolizers then were only “rare”. Based on all these data, Lenski’s team concluded that evolution is a process of historical contingencies so that, if one can replay the “tape of life,” the evolutionary trajectory would yield different outcomes.
But what traits had to change before Cit+ arose? To identify the specific mutations that gave rise to Cit+ variants, the team is currently sequencing the entire genome of this bacterial lineage, using samples that were frozen before and after Cit+ appeared. Conveniently, an ecological balance formed in this lineage; even though a large majority of the community consisted of Cit+ specialists, a minority of the bacteria in the population remained Cit- generalists. This fortuitous development allows Lenski’s team to identify specific mutations that contribute to Cit+ by comparing genomic sequence data from Cit- clones to Cit+ after citrate metabolism appeared in the population.
Further, because there are now two subpopulations in this lineage, this experiment presents the unique opportunity for scientists to study population dynamics that govern the emergence of a new character and to understand how one phenotype affects the other under a variety of environmental conditions.
As a result of this experiment, Lenski’s team hypothesizes that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.
Blount, Z.D., Borland, C.Z., Lenski, R.E. (2008). Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, 105(23), 7899-7906. DOI: 10.1073/pnas.0803151105