In a recent study (that yielded some exceptionally interesting results), catalytic RNA molecules were used in order to advance the understanding of Darwinian evolution. Researchers Dr. Sarah Voytek and Professor Gerald Joyce of the Scripps Research Kellogg School of Science and Technology, choose RNA molecules because they evolve rapidly and self-replicating RNA molecules are hypothesized to be the first organic “life forms” on earth. With a trillion molecules in a test tube replicating every few minutes, such an approach permits evolution to occur over the course of just a few days.



Observing an evolutionary process in action isn’t always possible considering that in order for novel adaptations to emerge and become fixed within a population typically requires long periods of time. This is especially true in more complex organisms, however in a laboratory environment, populations of bacteria, viruses and complex molecules have been used to demonstrate evolutionary principles since their generation times are much shorter and therefore observing an immediate physical change directly is possible.



For several years, Dr. Joyce has been experimenting with a particular type of enzymatic RNA molecule (single-stranded nucleic acid which catalyzes its own replication) that is able to continuously evolve in a test tube setting. Evolution happens when the RNA molecule replicates—there is a chance the molecule will mutate (approximately once per round of replication) and acquire new traits over time. The RNA enzymes require a specific substrate (food source) in order for replication to occur. These characteristics make RNA enzymes the molecular equivalent of a single specie organismal population, while their substrate represents an environmental resource necessary for the specie to survive and reproduce.



The logistic model of population growth predicts that when two species that require the same limited resources coexist in the same community (interspecific competition), one population will ultimately die out or will evolve dependency on another resource. Collectively, this occurrence is referred to as the competitive exclusion principle.



The competitive exclusion principle scenario isn’t readily observed in nature considering, as stated, the competing specie has already gone extinct or has adapted to a new ecological niche. What we observe in present ecological relationships is the result of past competitions. Evidence for competitive exclusion includes observable resource partitioning trends—coexisting similar species are typically adapted to different niches within a community.



Ecological relationships are wildly complex with countless variables, so any trend observed in a natural setting is most certainly a strong case for a good biological “rule of thumb.” Furthermore, to replicate the same evolutionary process in a laboratory setting solidifies the hypothesis—the Scripps researchers did just that, and their work will undoubtedly become a classic experiment that future textbooks will cite.



Two RNA enzyme “species,” CL1 and DSL, were used in the study and both are capable of continual evolution upon substrate provission. The aim of the researchers was to study coadaptation to an environment consisting of only enzyme substrates.



In the first experiment, CL1 and DSL were placed in the same environment and forced to compete for the same limited food source. The outcome was that the “les fit” enzyme would ultimately disappear. Researchers repeated this experiment for several different substrates and although the outcome of one RNA specie outcompeting the other was consistent, the RNA specie that “won” or “lost” depended on the actual substrate itself.



For the second part of the experiment, CL1 and DSL were challenged to undergo continuous evolution in an environment consisting of five different substrates. The different substrates provided the opportunity for each RNA specie to undergo the process of niche partitioning (adpatation to one substrate only). At the beginning of the experiment, each RNA could utilize all five substrates, however, not very efficiently. After hundreds of generations of evolution, the two molecules each became independently adapted to a particular substrate. Furthermore, their ability to utilize the resource became more efficient and they shunned the other RNA molecule’s food source, therefore avoiding competition.



Upon analysis of the two evolved enzymes, there were observable differences in their kinetics as a result of their differing adaptive strategies.



In ecological theory, an organism that experiences selective pressures will evolve to be either an “r” or “K” species in regards to reproductive strategy. In general, r-selected species are better suited for fluctuating environments and are characterized by short generation time and high reproductive output. On the other hand, K-selected species are more successful in stable environments, take full advantage of their resources, and are characterized by low mortality and less progeny.



Biological characterization of the DSL and CL1 enzymes revealed that r/K adpatation occurred in this experiment:









I n broad terms, the evolved CL1 enzyme is a K-strategist that generates fewer copies per round of replication compared with DSL but more effectively utilizes the available substrate because of its very rapid rate of catalysis.



The evolved DSL enzyme, in contrast, is an r-strategist that generates 2.5-fold more copies per round of replication compared with CL1...





The CL1 enzyme evolved to have an extraordinary rate of reaction made possible by fully utilizing its substrate and in turn, almost every CL1 molecule was able to give rise to progeny. Whereas DSL evolved to be an r-strategist that has a lower rate of reaction but compensates by yielding a higher number of progeny per parent molecule.

