94,366 research outputs found
Adaptive evolution on neutral networks
We study the evolution of large but finite asexual populations evolving in
fitness landscapes in which all mutations are either neutral or strongly
deleterious. We demonstrate that despite the absence of higher fitness
genotypes, adaptation takes place as regions with more advantageous
distributions of neutral genotypes are discovered. Since these discoveries are
typically rare events, the population dynamics can be subdivided into separate
epochs, with rapid transitions between them. Within one epoch, the average
fitness in the population is approximately constant. The transitions between
epochs, however, are generally accompanied by a significant increase in the
average fitness. We verify our theoretical considerations with two analytically
tractable bitstring models.Comment: 16 pages, 4 eps figures, Latex (academic press style file), submitted
to the Bulletin of Mathematical Biolog
Effects of neutral selection on the evolution of molecular species
We introduce a new model of evolution on a fitness landscape possessing a
tunable degree of neutrality. The model allows us to study the general
properties of molecular species undergoing neutral evolution. We find that a
number of phenomena seen in RNA sequence-structure maps are present also in our
general model. Examples are the occurrence of "common" structures which occupy
a fraction of the genotype space which tends to unity as the length of the
genotype increases, and the formation of percolating neutral networks which
cover the genotype space in such a way that a member of such a network can be
found within a small radius of any point in the space. We also describe a
number of new phenomena which appear to be general properties of neutrally
evolving systems. In particular, we show that the maximum fitness attained
during the adaptive walk of a population evolving on such a fitness landscape
increases with increasing degree of neutrality, and is directly related to the
fitness of the most fit percolating network.Comment: 16 pages including 4 postscript figures, typeset in LaTeX2e using the
Elsevier macro package elsart.cl
Adaptive evolution of transcription factor binding sites
The regulation of a gene depends on the binding of transcription factors to
specific sites located in the regulatory region of the gene. The generation of
these binding sites and of cooperativity between them are essential building
blocks in the evolution of complex regulatory networks. We study a theoretical
model for the sequence evolution of binding sites by point mutations. The
approach is based on biophysical models for the binding of transcription
factors to DNA. Hence we derive empirically grounded fitness landscapes, which
enter a population genetics model including mutations, genetic drift, and
selection. We show that the selection for factor binding generically leads to
specific correlations between nucleotide frequencies at different positions of
a binding site. We demonstrate the possibility of rapid adaptive evolution
generating a new binding site for a given transcription factor by point
mutations. The evolutionary time required is estimated in terms of the neutral
(background) mutation rate, the selection coefficient, and the effective
population size. The efficiency of binding site formation is seen to depend on
two joint conditions: the binding site motif must be short enough and the
promoter region must be long enough. These constraints on promoter architecture
are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive
evolution of genetic switches and of signal integration through binding
cooperativity between different sites. Experimental tests of this picture
involving the statistics of polymorphisms and phylogenies of sites are
discussed.Comment: published versio
Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology
Cis-regulatory networks (CRNs) play a central role in cellular decision
making. Like every other biological system, CRNs undergo evolution,
which shapes their properties by a combination of adaptive
and nonadaptive evolutionary forces. Teasing apart these forces is
an important step toward functional analyses of the different components
of CRNs, designing regulatory perturbation experiments,
and constructing synthetic networks. Although tests of neutrality
and selection based on molecular sequence data exist, no such tests
are currently available based on CRNs. In this work, we present
a unique genotype model of CRNs that is grounded in a genomic
context and demonstrate its use in identifying portions of the
CRN with properties explainable by neutral evolutionary forces
at the system, subsystem, and operon levels.We leverage our model
against experimentally derived data from Escherichia coli. The
results of this analysis show statistically significant and substantial
neutral trends in properties previously identified as adaptive
in originïŸdegree distribution, clustering coefficient, and motifsïŸ
within the E. coli CRN. Our model captures the tightly coupled genomeïŸ
interactome of an organism and enables analyses of how
evolutionary events acting at the genome level, such as mutation,
and at the population level, such as genetic drift, give rise to neutral
patterns that we can quantify in CRNs
Evolutionary Dynamics on Protein Bi-stability Landscapes Can Potentially Resolve Adaptive Conflicts
Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bistable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149â21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed
Evolution of Canalizing Boolean Networks
Boolean networks with canalizing functions are used to model gene regulatory
networks. In order to learn how such networks may behave under evolutionary
forces, we simulate the evolution of a single Boolean network by means of an
adaptive walk, which allows us to explore the fitness landscape. Mutations
change the connections and the functions of the nodes. Our fitness criterion is
the robustness of the dynamical attractors against small perturbations. We find
that with this fitness criterion the global maximum is always reached and that
there is a huge neutral space of 100% fitness. Furthermore, in spite of having
such a high degree of robustness, the evolved networks still share many
features with "chaotic" networks.Comment: 8 pages, 10 figures; revised and extended versio
Chance and Necessity in Evolution: Lessons from RNA
The relationship between sequences and secondary structures or shapes in RNA
exhibits robust statistical properties summarized by three notions: (1) the
notion of a typical shape (that among all sequences of fixed length certain
shapes are realized much more frequently than others), (2) the notion of shape
space covering (that all typical shapes are realized in a small neighborhood of
any random sequence), and (3) the notion of a neutral network (that sequences
folding into the same typical shape form networks that percolate through
sequence space). Neutral networks loosen the requirements on the mutation rate
for selection to remain effective. The original (genotypic) error threshold has
to be reformulated in terms of a phenotypic error threshold. With regard to
adaptation, neutrality has two seemingly contradictory effects: It acts as a
buffer against mutations ensuring that a phenotype is preserved. Yet it is
deeply enabling, because it permits evolutionary change to occur by allowing
the sequence context to vary silently until a single point mutation can become
phenotypically consequential. Neutrality also influences predictability of
adaptive trajectories in seemingly contradictory ways. On the one hand it
increases the uncertainty of their genotypic trace. At the same time neutrality
structures the access from one shape to another, thereby inducing a topology
among RNA shapes which permits a distinction between continuous and
discontinuous shape transformations. To the extent that adaptive trajectories
must undergo such transformations, their phenotypic trace becomes more
predictable.Comment: 37 pages, 14 figures; 1998 CNLS conference; high quality figures at
http://www.santafe.edu/~walte
Self-adaptive exploration in evolutionary search
We address a primary question of computational as well as biological research
on evolution: How can an exploration strategy adapt in such a way as to exploit
the information gained about the problem at hand? We first introduce an
integrated formalism of evolutionary search which provides a unified view on
different specific approaches. On this basis we discuss the implications of
indirect modeling (via a ``genotype-phenotype mapping'') on the exploration
strategy. Notions such as modularity, pleiotropy and functional phenotypic
complex are discussed as implications. Then, rigorously reflecting the notion
of self-adaptability, we introduce a new definition that captures
self-adaptability of exploration: different genotypes that map to the same
phenotype may represent (also topologically) different exploration strategies;
self-adaptability requires a variation of exploration strategies along such a
``neutral space''. By this definition, the concept of neutrality becomes a
central concern of this paper. Finally, we present examples of these concepts:
For a specific grammar-type encoding, we observe a large variability of
exploration strategies for a fixed phenotype, and a self-adaptive drift towards
short representations with highly structured exploration strategy that matches
the ``problem's structure''.Comment: 24 pages, 5 figure
- âŠ