63 research outputs found
Finite-size scaling of the quasiespecies model
We use finite-size scaling to investigate the critical behavior of the
quasiespecies model of molecular evolution in the single-sharp-peak replication
landscape. This model exhibits a sharp threshold phenomenon at Q=Q_c=1/a, where
Q is the probability of exact replication of a molecule of length L and a is
the selective advantage of the master string.
We investigate the sharpness of the threshold and find that its
characteristic persist across a range of Q of order L^(-1) about Q_c.
Furthermore, using the data collapsing method we show that the normalized mean
Hamming distance between the master string and the entire population, as well
as the properly scaled fluctuations around this mean value, follow universal
forms in the critical region.Comment: 8 pages,tex. Submitted to Physical Review
Dynamic fitness landscapes: Expansions for small mutation rates
We study the evolution of asexual microorganisms with small mutation rate in
fluctuating environments, and develop techniques that allow us to expand the
formal solution of the evolution equations to first order in the mutation rate.
Our method can be applied to both discrete time and continuous time systems.
While the behavior of continuous time systems is dominated by the average
fitness landscape for small mutation rates, in discrete time systems it is
instead the geometric mean fitness that determines the system's properties. In
both cases, we find that in situations in which the arithmetic (resp.
geometric) mean of the fitness landscape is degenerate, regions in which the
fitness fluctuates around the mean value present a selective advantage over
regions in which the fitness stays at the mean. This effect is caused by the
vanishing genetic diffusion at low mutation rates. In the absence of strong
diffusion, a population can stay close to a fluctuating peak when the peak's
height is below average, and take advantage of the peak when its height is
above average.Comment: 19 pages Latex, elsart style, 4 eps figure
A Population Genetic Approach to the Quasispecies Model
A population genetics formulation of Eigen's molecular quasispecies model is
proposed and several simple replication landscapes are investigated
analytically. Our results show a remarcable similarity to those obtained with
the original kinetics formulation of the quasispecies model. However, due to
the simplicity of our approach, the space of the parameters that define the
model can be explored. In particular, for the simgle-sharp-peak landscape our
analysis yelds some interesting predictions such as the existence of a maximum
peak height and a mini- mum molecule length for the onset of the error
threshold transition.Comment: 16 pages, 4 Postscript figures. Submited to Phy. Rev.
Error threshold in the evolution of diploid organisms
The effects of error propagation in the reproduction of diploid organisms are
studied within the populational genetics framework of the quasispecies model.
The dependence of the error threshold on the dominance parameter is fully
investigated. In particular, it is shown that dominance can protect the
wild-type alleles from the error catastrophe. The analysis is restricted to a
diploid analogue of the single-peaked landscape.Comment: 9 pages, 4 Postscript figures. Submitted to J. Phy. A: Mat. and Ge
Error threshold in simple landscapes
We consider the quasispecies description of a population evolving in both the
"master sequence" landscape (where a single sequence is evolutionarily
preferred over all others) and the REM landscape (where the fitness of
different sequences is an independent, identically distributed, random
variable). We show that, in both cases, the error threshold is analogous to a
first order thermodynamical transition, where the overlap between the average
genotype and the optimal one drops discontinuously to zero.Comment: 10 pages and 2 figures, Plain LaTe
Error threshold in finite populations
A simple analytical framework to study the molecular quasispecies evolution
of finite populations is proposed, in which the population is assumed to be a
random combination of the constiyuent molecules in each generation,i.e.,
linkage disequilibrium at the population level is neglected. In particular, for
the single-sharp-peak replication landscape we investigate the dependence of
the error threshold on the population size and find that the replication
accuracy at threshold increases linearly with the reciprocal of the population
size for sufficiently large populations. Furthermore, in the deterministic
limit our formulation yields the exact steady-state of the quasispecies model,
indicating then the population composition is a random combination of the
molecules.Comment: 14 pages and 4 figure
Mutation-Selection Balance: Ancestry, Load, and Maximum Principle
We show how concepts from statistical physics, such as order parameter,
thermodynamic limit, and quantum phase transition, translate into biological
concepts in mutation-selection models for sequence evolution and can be used
there. The article takes a biological point of view within a population
genetics framework, but contains an appendix for physicists, which makes this
correspondence clear. We analyze the equilibrium behavior of deterministic
haploid mutation-selection models. Both the forward and the time-reversed
evolution processes are considered. The stationary state of the latter is
called the ancestral distribution, which turns out as a key for the study of
mutation-selection balance. We find that it determines the sensitivity of the
equilibrium mean fitness to changes in the fitness values and discuss
implications for the evolution of mutational robustness. We further show that
the difference between the ancestral and the population mean fitness, termed
mutational loss, provides a measure for the sensitivity of the equilibrium mean
fitness to changes in the mutation rate. For a class of models in which the
number of mutations in an individual is taken as the trait value, and fitness
is a function of the trait, we use the ancestor formulation to derive a simple
maximum principle, from which the mean and variance of fitness and the trait
may be derived; the results are exact for a number of limiting cases, and
otherwise yield approximations which are accurate for a wide range of
parameters. These results are applied to (error) threshold phenomena caused by
the interplay of selection and mutation. They lead to a clarification of
concepts, as well as criteria for the existence of thresholds.Comment: 54 pages, 15 figures; to appear in Theor. Pop. Biol. 61 or 62 (2002
Field theory for a reaction-diffusion model of quasispecies dynamics
RNA viruses are known to replicate with extremely high mutation rates. These
rates are actually close to the so-called error threshold. This threshold is in
fact a critical point beyond which genetic information is lost through a
second-order phase transition, which has been dubbed the ``error catastrophe.''
Here we explore this phenomenon using a field theory approximation to the
spatially extended Swetina-Schuster quasispecies model [J. Swetina and P.
Schuster, Biophys. Chem. {\bf 16}, 329 (1982)], a single-sharp-peak landscape.
In analogy with standard absorbing-state phase transitions, we develop a
reaction-diffusion model whose discrete rules mimic the Swetina-Schuster model.
The field theory representation of the reaction-diffusion system is
constructed. The proposed field theory belongs to the same universality class
than a conserved reaction-diffusion model previously proposed [F. van Wijland
{\em et al.}, Physica A {\bf 251}, 179 (1998)]. From the field theory, we
obtain the full set of exponents that characterize the critical behavior at the
error threshold. Our results present the error catastrophe from a new point of
view and suggest that spatial degrees of freedom can modify several mean field
predictions previously considered, leading to the definition of characteristic
exponents that could be experimentally measurable.Comment: 13 page
Finite-size scaling of the error threshold transition in finite population
The error threshold transition in a stochastic (i.e. finite population)
version of the quasispecies model of molecular evolution is studied using
finite-size scaling. For the single-sharp-peak replication landscape, the
deterministic model exhibits a first-order transition at , where is the probability of exact replication of a molecule of length , and is the selective advantage of the master string. For
sufficiently large population size, , we show that in the critical region
the characteristic time for the vanishing of the master strings from the
population is described very well by the scaling assumption \tau = N^{1/2} f_a
\left [ \left (Q - Q_c) N^{1/2} \right ] , where is an -dependent
scaling function.Comment: 8 pages, 3 ps figures. submitted to J. Phys.
Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory
We express the Crow-Kimura and Eigen models of quasispecies theory in a
functional integral representation. We formulate the spin coherent state
functional integrals using the Schwinger Boson method. In this formulation, we
are able to deduce the long-time behavior of these models for arbitrary
replication and degradation functions.
We discuss the phase transitions that occur in these models as a function of
mutation rate. We derive for these models the leading order corrections to the
infinite genome length limit.Comment: 37 pages; 4 figures; to appear in J. Stat. Phy
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