2,344 research outputs found
Quasispecies Made Simple
Quasispecies are clouds of genotypes that appear in a population at mutationâselection balance. This concept has recently attracted the attention of virologists, because many RNA viruses appear to generate high levels of genetic variation that may enhance the evolution of drug resistance and immune escape. The literature on these important evolutionary processes is, however, quite challenging. Here we use simple models to link mutationâselection balance theory to the most novel property of quasispecies: the error thresholdâa mutation rate below which populations equilibrate in a traditional mutationâselection balance and above which the population experiences an error catastrophe, that is, the loss of the favored genotype through frequent deleterious mutations. These models show that a single fitness landscape may contain multiple, hierarchically organized error thresholds and that an error threshold is affected by the extent of back mutation and redundancy in the genotype-to-phenotype map. Importantly, an error threshold is distinct from an extinction threshold, which is the complete loss of the population through lethal mutations. Based on this framework, we argue that the lethal mutagenesis of a viral infection by mutation-inducing drugs is not a true error catastophe, but is an extinction catastrophe
Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes
We study the adaptation dynamics of an initially maladapted asexual
population with genotypes represented by binary sequences of length . The
population evolves in a maximally rugged fitness landscape with a large number
of local optima. We find that whether the evolutionary trajectory is
deterministic or stochastic depends on the effective mutational distance
upto which the population can spread in genotype space. For
, the deterministic quasispecies theory operates while for
, the evolution is completely stochastic. Between these
two limiting cases, the dynamics are described by a local quasispecies theory
below a crossover time while above , the population
gets trapped at a local fitness peak and manages to find a better peak either
via stochastic tunneling or double mutations. In the stochastic regime
, we identify two subregimes associated with clonal
interference and uphill adaptive walks, respectively. We argue that our
findings are relevant to the interepretation of evolution experiments with
microbial populations.Comment: Revised version, to appear in Genetics. Note on the role of selection
in defining d_eff added; new figure 4 include
The Importance of DNA Repair in Tumor Suppression
The transition from a normal to cancerous cell requires a number of highly
specific mutations that affect cell cycle regulation, apoptosis,
differentiation, and many other cell functions. One hallmark of cancerous
genomes is genomic instability, with mutation rates far greater than those of
normal cells. In microsatellite instability (MIN tumors), these are often
caused by damage to mismatch repair genes, allowing further mutation of the
genome and tumor progression. These mutation rates may lie near the error
catastrophe found in the quasispecies model of adaptive RNA genomes, suggesting
that further increasing mutation rates will destroy cancerous genomes. However,
recent results have demonstrated that DNA genomes exhibit an error threshold at
mutation rates far lower than their conservative counterparts. Furthermore,
while the maximum viable mutation rate in conservative systems increases
indefinitely with increasing master sequence fitness, the semiconservative
threshold plateaus at a relatively low value. This implies a paradox, wherein
inaccessible mutation rates are found in viable tumor cells. In this paper, we
address this paradox, demonstrating an isomorphism between the conservatively
replicating (RNA) quasispecies model and the semiconservative (DNA) model with
post-methylation DNA repair mechanisms impaired. Thus, as DNA repair becomes
inactivated, the maximum viable mutation rate increases smoothly to that of a
conservatively replicating system on a transformed landscape, with an upper
bound that is dependent on replication rates. We postulate that inactivation of
post-methylation repair mechanisms are fundamental to the progression of a
tumor cell and hence these mechanisms act as a method for prevention and
destruction of cancerous genomes.Comment: 7 pages, 5 figures; Approximation replaced with exact calculation;
Minor error corrected; Minor changes to model syste
Quasispecies evolution in general mean-field landscapes
I consider a class of fitness landscapes, in which the fitness is a function
of a finite number of phenotypic "traits", which are themselves linear
functions of the genotype. I show that the stationary trait distribution in
such a landscape can be explicitly evaluated in a suitably defined
"thermodynamic limit", which is a combination of infinite-genome and strong
selection limits. These considerations can be applied in particular to identify
relevant features of the evolution of promoter binding sites, in spite of the
shortness of the corresponding sequences.Comment: 6 pages, 2 figures, Europhysics Letters style (included) Finite-size
scaling analysis sketched. To appear in Europhysics Letter
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