N. Lehman et al., The genotypic landscape during in vitro evolution of a catalytic RNA: Implications for phenotypic buffering, J MOL EVOL, 50(5), 2000, pp. 481-490
The Tetrahymena group I ribozyme catalyzes the cleavage of a phosphodiester
linkage in specific sequences of RNA. This phenotype can be used in an in
vitro selection-amplification process to evolve variants that are capable o
f RNA catalysis in the presence of Ca2+ as the sole available cation. With
sufficient genotypic characterization of the population as it evolves, we h
ave a rare opportunity of observing how the information stored in an evolvi
ng population responds to selective pressures, such as the requisite of cat
alyzing RNA cleavage in the absence of Mg2+ or Mn2+. In the present work, w
e examine the population dynamics of this system using sequence information
from previous experimental work. We focus on two issues: How does the info
rmation content of the population evolve? and Is the system evolving as an
adaptive walk on a rugged landscape? To investigate these questions, inform
ation theoretical parameters are examined. The evolution of the population
is visualized by mapping the genotypic frequency distribution onto a two-di
mensional projection of sequence space. The projection was generated using
Hamming distances from the wild-type, starting sequence and a catalytically
successful, evolved sequence. The evolution of the information content of
the system was measured by calculating the grammar complexity of the observ
ed sequences, which showed a very slight increase over 12 generations. This
result is consistent with the system performing a search for a local optim
um. The dynamics of the population in this sequence space is consistent wit
h an adaptive walk on an uncorrelated, or "rugged," genotypic landscape, de
spite the observation that the phenotypic progress of the population appear
s smooth. The relative insensitivity of the phenotypic landscape to the var
iegation of the genotypic landscape suggests that the former is buffered ag
ainst variation in the latter through various epigenetic-like mechanisms.