Unnamed: 0 int64 0 41k | title stringlengths 4 274 | category stringlengths 5 18 | summary stringlengths 22 3.66k | theme stringclasses 8
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5,400 | Plant defense multigene families: I. Divergence of Fusarium solani-induced expression in Pisum and Lathyrus | q-bio.PE | The defense response in plants challenged with pathogens is characterized by
the activation of a diverse set of genes. Many of the same genes are induced in
the defense responses of a wide range of plant species. How plant defense gene
families evolve may therefore provide an important clue to our understanding of
how ... | biology |
5,401 | Complexity and hierarchical game of life | q-bio.PE | Hierarchical structure is an essential part of complexity, important notion
relevant for a wide range of applications ranging from biological population
dynamics through robotics to social sciences. In this paper we propose a simple
cellular-automata tool for study of hierarchical population dynamics. | biology |
5,402 | Dynamics of Fixation of Advantageous Mutations | q-bio.PE | We investigate the process of fixation of advantageous mutations in an
asexual population. We assume that the effect of each beneficial mutation is
exponentially distributed with mean value $\omega_{med}=1/\beta$. The model
also considers that the effect of each new deleterious mutation reduces the
fitness of the organ... | biology |
5,403 | Phase transition and selection in a four-species cyclic Lotka-Volterra model | q-bio.PE | We study a four species ecological system with cyclic dominance whose
individuals are distributed on a square lattice. Randomly chosen individuals
migrate to one of the neighboring sites if it is empty or invade this site if
occupied by their prey. The cyclic dominance maintains the coexistence of all
the four species ... | biology |
5,404 | The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes | q-bio.PE | Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one,
with anticodon UAG, translates the four-codon family CUN, whilst the other,
with anticodon UAA, translates the two-codon family UUR. These two genes must
differ at the third anticodon position, but in some species the genes differ at
many add... | biology |
5,405 | Computer simulations of history of life: speciation, emergence of complex species from simpler organisms, and extinctions | q-bio.PE | We propose a generic model of eco-systems, with a {\it hierarchical} food web
structure. In our computer simulations we let the eco-system evolve
continuously for so long that that we can monitor extinctions as well as
speciations over geological time scales. {\it Speciation} leads not only to
horizontal diversificatio... | biology |
5,406 | An asymptotic maximum principle for essentially linear evolution models | q-bio.PE | Recent work on mutation-selection models has revealed that, under specific
assumptions on the fitness function and the mutation rates, asymptotic
estimates for the leading eigenvalue of the mutation-reproduction matrix may be
obtained through a low-dimensional maximum principle in the limit N to infinity
(where N is th... | biology |
5,407 | Cellular automaton for bacterial towers | q-bio.PE | A simulation approach to the stochastic growth of bacterial towers is
presented, in which a non-uniform and finite nutrient supply essentially
determines the emerging structure through elementary chemotaxis. The method is
based on cellular automata and we use simple, microscopic, local rules for
bacterial division in n... | biology |
5,408 | Adaptation and enslavement in endosymbiont-host associations | q-bio.PE | The evolutionary persistence of symbiotic associations is a puzzle.
Adaptation should eliminate cooperative traits if it is possible to enjoy the
advantages of cooperation without reciprocating - a facet of cooperation known
in game theory as the Prisoner's Dilemma. Despite this barrier, symbioses are
widespread, and m... | biology |
5,409 | Modelling of SARS for Hong Kong | q-bio.PE | A simplified susceptible-infected-recovered (SIR) epidemic model and a
small-world model are applied to analyse the spread and control of Severe Acute
Respiratory Syndrome (SARS) for Hong Kong in early 2003. From data available in
mid April 2003, we predict that SARS would be controlled by June and nearly
1700 persons ... | biology |
5,410 | Plausible models for propagation of the SARS virus | q-bio.PE | Using daily infection data for Hong Kong we explore the validity of a variety
of models of disease propagation when applied to the SARS epidemic. Surrogate
data methods show that simple random models are insufficient and that the
standard epidemic susceptible-infected-removed model does not fully account for
the underl... | biology |
5,411 | Quantitative patterns in the structure of model and empirical food webs | q-bio.PE | We analyze the properties of model food webs and of fifteen community food
webs from a variety of environments. We first perform a theoretical analysis of
the niche model of Williams and Martinez. We derive analytical expressions for
the distributions of species' number of prey, number of predators, and total
number of... | biology |
5,412 | The Waterwheel in the Waterfall | q-bio.PE | A fundamental problem in evolutionary ecology research is to explain how
different species coexist in natural ecosystems. This question is directly
related with species trophic competition. However, competition theory, based on
the classical logistic Lotka-Volterra equations, leads to erroneous conclusions
about specie... | biology |
5,413 | Entanglement Invariants and Phylogenetic Branching | q-bio.PE | It is possible to consider stochastic models of sequence evolution in
phylogenetics in the context of a dynamical tensor description inspired from
physics. Approaching the problem in this framework allows for the well
developed methods of mathematical physics to be exploited in the biological
arena. We present the tens... | biology |
5,414 | The Speed of Adaptation in Large Asexual Populations | q-bio.PE | In large asexual populations, beneficial mutations have to compete with each
other for fixation. Here, I derive explicit analytic expressions for the rate
of substitution and the mean beneficial effect of fixed mutations, under the
assumptions that the population size N is large, that the mean effect of new
beneficial ... | biology |
5,415 | Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations | q-bio.PE | RNA viruses are a widely used tool to study evolution experimentally. Many
standard protocols of virus propagation and competition are done at nominally
low multiplicity of infection (m.o.i.), but lead during one passage to two or
more rounds of infection, of which the later ones are at high m.o.i. Here, we
develop a m... | biology |
5,416 | Analysis of trends in human longevity by new model | q-bio.PE | Trends in human longevity are puzzling, especially when considering the
limits of human longevity. Partially, the conflicting assertions are based upon
demographic evidence and the interpretation of survival and mortality curves
using the Gompertz model and the Weibull model; these models are sometimes
considered to be... | biology |
5,417 | General functions for human survival and mortality | q-bio.PE | General functions for human survival and mortality may support a possibility
of general mechanisms in human ageing. We discovered that the survival and
mortality curves could be described very simply and accurately by the Weibull
survival function with age-dependent shape parameter. The age-dependence of
shape paramete... | biology |
5,418 | Size of the stable population in the Penna bit-string model of biological aging | q-bio.PE | In this paper the Penna model is reconsidered. With computer simulations we
check how the control parameters of the model influence the size of the stable
population. | biology |
5,419 | The Spread of Infectious Disease with Household-Structure on the Complex Networks | q-bio.PE | In this paper we study the household-structure SIS epidemic spreading on
general complex networks. The household structure gives us the way to
distinguish inner and the outer infection rate. Unlike household-structure
models on homogenous networks, such as regular and random networks, here we
consider heterogeneous net... | biology |
5,420 | The role of mutation rate in a simple colonization model | q-bio.PE | We study the effect of mutations in a simple model of colonization, based on
Montecarlo simulations. When the population colonizes the whole available
habitat, a maximum population density is reached, which depends on the mutation
rate. Depending on the values of other parameters, such as selection pressure,
fecundity ... | biology |
5,421 | Mortality decrease and mathematical limit of longevity | q-bio.PE | We wish to verify that the mortality deceleration (or decrease) is a
consequence of the bending of the shape parameter at old ages. This
investigation is based upon the Weon model (the Weibull model with an
age-dependent shape parameter) for human survival and mortality curves.
According to the Weon model, we are well ... | biology |
5,422 | A model of sympatric speciation through assortative mating | q-bio.PE | A microscopic model is developed, within the frame of the theory of
quantitative traits, to study both numerically and analytically the combined
effect of competition and assortativity on the sympatric speciation process,
i.e. speciation in the absence of geographical barriers. Two components of
fitness are considered:... | biology |
5,423 | The spread of disease with birth and death on networks | q-bio.PE | In this paper, we introduce a modified epidemic model on regular and
scale-free networks respectively. We consider the birth rate $\delta$, cure
rate $\gamma$, infection rate $\lambda$, $\alpha$ from the infectious disease,
and death rate $\beta$ from other factors. Through mean-field analysis, we find
that on regular ... | biology |
5,424 | Noise in ecosystems: a short review | q-bio.PE | Noise, through its interaction with the nonlinearity of the living systems,
can give rise to counter-intuitive phenomena such as stochastic resonance,
noise-delayed extinction, temporal oscillations, and spatial patterns. In this
paper we briefly review the noise-induced effects in three different
ecosystems: (i) two c... | biology |
5,425 | Complementarity principle on human longevity | q-bio.PE | In recent we introduced, developed and established a new concept, model,
methodology and principle for studying human longevity in terms of demographic
basis. We call the new model the "Weon model", which is a general model
modified from the Weibull model with an age-dependent shape parameter to
describe human survival... | biology |
5,426 | A Theoretical Framework for the Analysis of the West Nile Virus Epidemic | q-bio.PE | We present a model for the growth of West Nile virus in mosquito and bird
populations based on observations of the initial epidemic in the U.S. Increase
of bird mortality as a result of infection, which is a feature of the epidemic,
is found to yield an effect which is observable in principle, viz., periodic
variations... | biology |
5,427 | Complementarity between survival and mortality | q-bio.PE | Accurate demographic functions help scientists define and understand
longevity. We summarize a new demographic model, the Weon model, and show the
application to the demographic data for Switzerland (1876-2002). Particularly,
the Weon model simply defines the maximum longevity, which is induced in nature
by the mortali... | biology |
5,428 | Simon-Ando Decomposability and Fitness Landscapes | q-bio.PE | In this paper, we investigate fitness landscapes (under point mutation and
recombination) from the standpoint of whether the induced evolutionary dynamics
have a "fast-slow" time scale associated with the differences in relaxation
time between local quasi-equilibria and the global equilibrium. This dynamical
behavior h... | biology |
5,429 | Demographic trajectories for supercentenarians | q-bio.PE | A fundamental question in aging research concerns the demographic
trajectories at the highest ages, especially for supercentenarians (persons
aged 110 or more). We wish to demonstrate that the Weon model enables
scientists to describe the demographic trajectories for supercentenarians. We
evaluate the average survival ... | biology |
5,430 | The dauer mutation of the caenorhabditis elegans, simulated with the Penna and the Stauffer model | q-bio.PE | Two ageing models were analysed whether they can confirm that the dauer
mutation of the nematode helps to preserve the species. As a result the Penna
model shows that populations with dauer larvae survive bad environmental
conditions, whereas populations without it die out. In the Stauffer model the
advantage of the da... | biology |
5,431 | Stochastic evolution and multifractal classification of prokaryotes | q-bio.PE | We introduce a model for simulating mutation of prokaryote DNA sequences.
Using that model we can then evaluated traditional techniques like parsimony
and maximum likelihood methods for computing phylogenetic relationships. We
also use the model to mimic large scale genomic changes, and use this to
evaluate multifracta... | biology |
5,432 | Mutual information for examining correlations in DNA | q-bio.PE | This paper examines two methods for finding whether long-range correlations
exist in DNA: a fractal measure and a mutual information technique. We evaluate
the performance and implications of these methods in detail. In particular we
explore their use comparing DNA sequences from a variety of sources. Using
software fo... | biology |
5,433 | On the effect of fluctuating recombination rates on the decorrelation of gene histories in the human genome | q-bio.PE | We show how to incorporate fluctuations of the recombination rate along the
chromosome into standard gene-genealogical models for the decorrelation of gene
histories. This enables us to determine how small-scale fluctuations
(Poissonian hot-spot model) and large-scale variations [Kong et al. (2002)] of
the recombinatio... | biology |
5,434 | Introduction to new demographic model for humans | q-bio.PE | The Gompertz model since 1825 has significantly contributed to interpretation
of ageing in biological and social sciences. However, in modern research
findings, it is clear that the Gompertz model is not successful to describe the
whole demographic trajectories. In this letter, a new demographic model is
introduced esp... | biology |
5,435 | Ultimate limit to human longevity | q-bio.PE | Are there limits to human longevity? We suggest a new demographic model to
describe human demographic trajectories. Specifically, the model mathematically
defines the limits of longevity. Through the demographic analysis of trends for
Sweden (between 1751 and 2002), Switzerland (between 1876 and 2002) and Japan
(betwee... | biology |
5,436 | Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications for the Frequency of Horizontal Gene Transfer | q-bio.PE | The current picture of bacterial evolution is based largely on studies of 16S
rRNA. However, this is just one gene. It is known that horizontal gene transfer
can occur between bacterial species, although the frequency and implications of
this are not fully understood. If horizontal transfer were frequent, there
would b... | biology |
5,437 | RNA-based Phylogenetic Methods: Application to Mammalian Mitochondrial RNA Sequences | q-bio.PE | The PHASE software package allows phylogenetic tree construction with a
number of evolutionary models designed specifically for use with RNA sequences
that have conserved secondary structure. Evolution in the paired regions of
RNAs occurs via compensatory substitutions, hence changes on either side of a
pair are correl... | biology |
5,438 | Self Trapping of a Single Bacterium in its Own Chemoattractant | q-bio.PE | Bacteria (e.g. E. Coli) are very sensitive to certain chemoattractants (e.g.
asparate) which they themselves produce. This leads to chemical instabilities
in a uniform population. We discuss here the different case of a single
bacterium, following the general scheme of Brenner, Levitov and Budrene. We
show that in one ... | biology |
5,439 | Effects of neighbourhood size and connectivity on spatial Continuous Prisoner's Dilemma | q-bio.PE | The Prisoner's Dilemma, a 2-person game in which the players can either
cooperate or defect, is a common paradigm for studying the evolution of
cooperation, when individuals exhibit variable degrees of cooperation. It is
known that in the presence of spatial structure, when individuals ``play
against'' their neighbours... | biology |
5,440 | Evolving eco-system: a network of networks | q-bio.PE | Ecology and evolution are inseparable. Motivated by some recent experiments,
we have developed models of evolutionary ecology from the perspective of
dynamic networks. In these models, in addition to the intra-node dynamics,
which corresponds to an individual-based population dynamics of species, the
entire network its... | biology |
5,441 | War of attrition with implicit time cost | q-bio.PE | In the game-theoretic model war of attrition, players are subject to an
explicit cost proportional to the duration of contests. We construct a model
where the time cost is not explicitly given, but instead depends implicitly on
the strategies of the whole population. We identify and analyse the underlying
mechanisms re... | biology |
5,442 | Polynomial epidemics and clustering in contact networks | q-bio.PE | It is widely known that the spread of the HIV virus was slower than
exponential in several populations, even at the very beginning of the epidemic.
We show that this implies a significant reduction in the effective reproductive
rate of the epidemic, and describe a general mechanism, related to the
clustering properties... | biology |
5,443 | The emergence of prime numbers as the result of evolutionary strategy | q-bio.PE | We investigate by means of a simple theoretical model the emergence of prime
numbers as life cycles, as those seen for some species of cicadas. The cicadas,
more precisely, the Magicicadas spend most of their lives below the ground and
then emerge and die in a short period of time. The Magicicadas display an
uncommon b... | biology |
5,444 | Community Structure and Metacommunity Dynamics of Aquatic Invertebrates: a Test of the Neutral Theory | q-bio.PE | We used a metacommunity of 49 discrete communities of aquatic invertebrates
to analyze the dynamical relationship between community and metacommunity
species distributions as a test of the neutral theory of biodiversity and
biogeography. At the community scale, observed variation in species richness
and relative abunda... | biology |
5,445 | Altruism and Antagonistic Pleiotropy in Penna Ageing Model | q-bio.PE | The Penna ageing model is based on mutation accumulation theory. We show that
it also allows for self-organization of antagonistic pleiotropy which helps at
young age at the expense of old age. This can be interpreted as emergence of
altruism. | biology |
5,446 | Maximum principle and mutation thresholds for four-letter sequence evolution | q-bio.PE | A four-state mutation-selection model for the evolution of populations of
DNA-sequences is investigated with particular interest in the phenomenon of
error thresholds. The mutation model considered is the Kimura 3ST mutation
scheme, fitness functions, which determine the selection process, come from the
permutation-inv... | biology |
5,447 | The criticality of the Hantavirus infected phase at Zuni | q-bio.PE | A preliminary analysis of the temporal evolution of a population of
\emph{Peromyscus maniculatus} infected with Hantavirus Sin Nombre is made.
Ecological and epidemiological parameters are derived from the data, and they
are used as inputs for the analytical model presented in [Abramson and Kenkre,
Phys. Rev. E \textbf... | biology |
5,448 | Flexible Foraging of Ants under Unsteadily Varying Environment | q-bio.PE | Using a simple model for the trail formation of ants, the relation between
i)the schedule of feeding which represents the unsteady natural environment,
ii)emerging patterns of trails connecting a nest with food resources, and
iii)the foraging efficiency is studied. Simulations and a simple analysis show
that the emerge... | biology |
5,449 | Evolvability is a Selectable Trait | q-bio.PE | Concomitant with the evolution of biological diversity must have been the
evolution of mechanisms that facilitate evolution, due to the essentially
infinite complexity of protein sequence space. We describe how evolvability can
be an object of Darwinian selection, emphasizing the collective nature of the
process. We qu... | biology |
5,450 | Effects of internal fluctuations on the spreading of Hantavirus | q-bio.PE | We study the spread of Hantavirus over a host population of deer mice using a
population dynamics model. We show that taking into account the internal
fluctuations in the mouse population due to its discrete character strongly
alters the behaviour of the system. In addition to the familiar transition
present in the det... | biology |
5,451 | Simulation and Experiment of Extinction or Adaptation | q-bio.PE | Can unicellular organisms survive a drastic temperature change, and adapt to
it after many generations? In simulations of the Penna model of biological
ageing, both extinction and adaptation were found for asexual and sexual
reproduction as well as for parasex. These model investigations are the basis
for the design of... | biology |
5,452 | Evolution of Spatially Inhomogeneous Eco-Systems: An Unified Model Based Approach | q-bio.PE | Recently we have extended our the "unified" model of evolutionary ecology to
incorporate the {\it spatial inhomogeneities} of the eco-system and the {\it
migration} of individual organisms from one patch to another within the same
eco-system. In this paper an extension of our recent model is investigated so
as to descr... | biology |
5,453 | Recurrent epidemics in small world networks | q-bio.PE | The effect of spatial correlations on the spread of infectious diseases was
investigated using a stochastic SIR (Susceptible-Infective-Recovered) model on
complex networks. It was found that in addition to the reduction of the
effective transmission rate, through the screening of infectives, spatial
correlations may ha... | biology |
5,454 | Competing associations in six-species predator-prey models | q-bio.PE | We study a set of six-species ecological models where each species has two
predators and two preys. On a square lattice the time evolution is governed by
iterated invasions between the neighboring predator-prey pairs chosen at random
and by a site exchange with a probability Xs between the neutral pairs. These
models i... | biology |
5,455 | Collective Dynamics of Active Elements: Task Allocation and Pheromone Trailing | q-bio.PE | Collective behavior of active elements inspired by mass of biological
organisms is addressed. Especially, two topics are focused on among amazing
behaviors performed by colony of ants. First, task allocation phenomena are
treated from the viewpoint of proportion regulation of population between
different states. Using ... | biology |
5,456 | A microscopic model of evolution of recombination | q-bio.PE | We study the evolution of recombination using a microscopic model developed
within the frame of the theory of quantitative traits. Two components of
fitness are considered: a static one that describes adaptation to environmental
factors not related to the population itself, and a dynamic one that accounts
for interacti... | biology |
5,457 | Cooperation driven by mutations in multi-person Prisoner's Dilemma | q-bio.PE | The n-person Prisoner's Dilemma is a widely used model for populations where
individuals interact in groups. The evolutionary stability of populations has
been analysed in the literature for the case where mutations in the population
may be considered as isolated events. For this case, and assuming simple
trigger strat... | biology |
5,458 | Does telomere elongation in cloned organisms lead to a longer lifespan if cancer is considered ? | q-bio.PE | ... By additionally considering a two-mutation model for carcinogenesis and
indefinite proliferation by the activation of telomerase, we demonstrate that
the risk of dying doe to cancer can outweigh the positive effect of longer
telomeres on the longevity. | biology |
5,459 | Stability of evolutionarily stable strategies in discrete replicator dynamics with time delay | q-bio.PE | We construct two models of discrete-time replicator dynamics with time delay.
In the social-type model, players imitate opponents taking into account average
payoffs of games played some units of time ago. In the biological-type model,
new players are born from parents who played in the past. We consider
two-player gam... | biology |
5,460 | Equilibrium selection in evolutionary games with random matching of players | q-bio.PE | We discuss stochastic dynamics of populations of individuals playing games.
Our models possess two evolutionarily stable strategies: an efficient one,
where a population is in a state with the maximal payoff (fitness) and a
risk-dominant one, where players are averse to risks. We assume that
individuals play with rando... | biology |
5,461 | Evolutionary and asymptotic stability in symmetric multi-player games | q-bio.PE | We provide a classification of symmetric three-player games with two
strategies and investigate evolutionary and asymptotic stability (in the
replicator dynamics) of their Nash equilibria. We discuss similarities and
differences between two-player and multi-player games. In particular, we
construct examples which exhib... | biology |
5,462 | A more comprehensive formulation of evolutionary equations | q-bio.PE | As mathematical model for the evolutionary equations of species the
masterequation is choiced. Two formulations will be demonstrated to include the
changes of parameters into the masterequation - that is, on the one hand, the
formation of a second masterequation for the development of parameters, and, on
the other hand... | biology |
5,463 | Self-Organized Criticality, Optimization and Biodiversity | q-bio.PE | By driven to extinction species less or poorly adapted, the Darwinian
evolutionary theory is intrinsically an optimization theory. We investigate two
optimization algorithms with such evolutionary characteristics: the Bak-Sneppen
and the Extremal Optimization. By comparing their mean fitness in the steady
state regime,... | biology |
5,464 | A Unified Model of Codon Reassignment in Alternative Genetic Codes | q-bio.PE | Many modified genetic codes are found in specific genomes in which one or
more codons have been reassigned to a different amino acid from that in the
canonical code. We present a model that unifies four possible mechanisms for
reassignment, based on the observation that reassignment involves a gain and a
loss. The loss... | biology |
5,465 | Inter-species regression analysis | q-bio.PE | When conducting inter-species regression analyses, the phylogenetic
relationships between the individual species need to be taken into account. In
this paper, a procedure for conducting such analyses is proposed, which only
requires the use of a measure of relationship between pairs of species, rather
than a complete p... | biology |
5,466 | An explanatory model for food-web structure and evolution | q-bio.PE | Food webs are networks describing who is eating whom in an ecological
community. By now it is clear that many aspects of food-web structure are
reproducible across diverse habitats, yet little is known about the driving
force behind this structure. Evolutionary and population dynamical mechanisms
have been considered. ... | biology |
5,467 | Solvable senescence model with positive mutations | q-bio.PE | We build upon our previous analytical results for the Penna model of
senescence to include positive mutations. We investigate whether a small but
non-zero positive mutation rate gives qualitatively different results to the
traditional Penna model in which no positive mutations are considered. We find
that the high-life... | biology |
5,468 | Analytical solution of a generalized Penna model | q-bio.PE | In 1995 T.J.Penna introduced a simple model of biological aging. A modified
Penna model has been demonstrated to exhibit behaviour of real-life systems
including catastrophic senescence in salmon and a mortality plateau at advanced
ages. We present a general steady-state, analytic solution to the Penna model,
able to d... | biology |
5,469 | Population Dynamics in the Penna Model | q-bio.PE | We build upon the recent steady-state Penna model solution, Phys.Rev.Lett.
89, 288103 (2002), to study the population dynamics within the Penna model. We
show, that any perturbation to the population can be broken into a collection
of modes each of which decay exponentially with its respective time constant.
The long t... | biology |
5,470 | Scaling effects in the Penna ageing model | q-bio.PE | We have analysed the possibility of scaling the sexual Penna ageing model.
Assuming that the number of genes expressed before the reproduction age grows
linearly with the genome size and that the mutation rate per genome and
generation is constant, we have found that the fraction of defective genes
expressed before the... | biology |
5,471 | The species-area relationship and evolution | q-bio.PE | Models relating to the Species-Area curve are usually defined at the species
level, and concerned only with ecological timescales. We examine an
individual-based model of co-evolution on a spatial lattice based on the
Tangled Nature model, and show that reproduction, mutation and dispersion by
diffusion in an interacti... | biology |
5,472 | Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons | q-bio.PE | Because of the base pairing rules in DNA, some mutations experienced by a
portion of DNA during its evolution result in the same substitution, as we can
only observe differences in coupled nucleotides. Then, in the absence of a bias
between the two DNA strands, a model with at most 6 different parameters
instead of 12 ... | biology |
5,473 | Tradeoff between short-term and long-term adaptation in a changing environment | q-bio.PE | We investigate the competition dynamics of two microbial or viral strains
that live in an environment that switches periodically between two states. One
of the strains is adapted to the long-term environment, but pays a short-term
cost, while the other is adapted to the short-term environment and pays a cost
in the lon... | biology |
5,474 | Love before Sex | q-bio.PE | Much has been debated about the benefit of sexual over asexual reproduction
in terms of evolutionary fitness. Here we focus on the advantage that may be
brought about by the process of mating, where the choosing of mates contributes
to the increase in fitness in a constructive way. We carry out computer
simulations of ... | biology |
5,475 | Equilibrium transitions in finite populations of players | q-bio.PE | We discuss stochastic dynamics of finite populations of individuals playing
games. We review recent results concerning the dependence of the long-run
behavior of such systems on the number of players and the noise level. In the
case of two-player games with two symmetric Nash equilibria, when the number of
players incr... | biology |
5,476 | Stochastic stability in three-player games | q-bio.PE | Animal behavior and evolution can often be described by game-theoretic
models. Although in many situations, the number of players is very large, their
strategic interactions are usually decomposed into a sum of two-player games.
Only recently evolutionarily stable strategies were defined for multi-player
games and thei... | biology |
5,477 | Thermosynthesis as energy source for the RNA World: a new model for the origin of life | q-bio.PE | The thermosynthesis concept, biological free energy gain from thermal
cycling, is combined with the concept of the RNA World. The resulting overall
origin of life model gives new explanations for the emergence of the genetic
code and the ribosome. The first protein named pF1 obtains the energy to
support the RNA world ... | biology |
5,478 | Stochastic models in population biology and their deterministic analogs | q-bio.PE | In this paper we introduce a class of stochastic population models based on
"patch dynamics". The size of the patch may be varied, and this allows one to
quantify the departures of these stochastic models from various mean field
theories, which are generally valid as the patch size becomes very large. These
models may ... | biology |
5,479 | Predator-prey cycles from resonant amplification of demographic stochasticity | q-bio.PE | In this paper we present the simplest individual level model of predator-prey
dynamics and show, via direct calculation, that it exhibits cycling behavior.
The deterministic analogue of our model, recovered when the number of
individuals is infinitely large, is the Volterra system (with density-dependent
prey reproduct... | biology |
5,480 | Dynamics of competing species in a model of adaptive radiations and macroevolution | q-bio.PE | We present a simple model of adaptive radiations in evolution based on
species competition. Competition is found to promote species divergence and
branching, and to dampen the net species production. In the model simulations,
high taxonomic diversification and branching take place during the beginning of
the radiation.... | biology |
5,481 | Evolution of Variance in Offspring Number: the Effects of Population Size and Migration | q-bio.PE | It was shown by Gillespie (1974) that if two genotypes produce the same
average number of offspring on but have a different variance associated within
each generation, the genotype with a lower variance will have a higher
effective fitness. Specifically, the effective fitness is W(effective)=w-var/N,
where w is the mea... | biology |
5,482 | Sympatric Speciation in a Simple Food Web | q-bio.PE | Observations of the evolution of species groups in nature, such as well
recognized Galapagos finches, have motivated much theoretical research aimed at
understanding the processes associated with such radiations. The Penna model is
one such model and has been widely used to study aging. In this paper we use
the basic P... | biology |
5,483 | Biodiversity in model ecosystems, I: Coexistence conditions for competing species | q-bio.PE | This is the first of two papers where we discuss the limits imposed by
competition to the biodiversity of species communities. In this first paper we
study the coexistence of competing species at the fixed point of population
dynamic equations. For many simple models, this imposes a limit on the width of
the productivi... | biology |
5,484 | Biodiversity in model ecosystems, II: Species assembly and food web structure | q-bio.PE | This is the second of two papers dedicated to the relationship between
population models of competition and biodiversity. Here we consider species
assembly models where the population dynamics is kept far from fixed points
through the continuous introduction of new species, and generalize to such
models thecoexistence ... | biology |
5,485 | Simulations of a mortality plateau in the sexual Penna model for biological ageing | q-bio.PE | The Penna model is a strategy to simulate the genetic dynamics of
age-structured populations, in which the individuals genomes are represented by
bit-strings. It provides a simple metaphor for the evolutionary process in
terms of the mutation accumulation theory. In its original version, an
individual dies due to inher... | biology |
5,486 | Harvesting in a resource dependent age structured Leslie type population model | q-bio.PE | We analyse the effect of harvesting in a resource dependent age structured
population model, deriving the conditions for the existence of a stable steady
state as a function of fertility coefficients, harvesting mortality and
carrying capacity of the resources. Under the effect of proportional harvest,
we give a suffic... | biology |
5,487 | On the Statistical Law of Life | q-bio.PE | In this paper we derive a statistical law of Life. It governs the probability
of death, or complementary of survival, of the living organisms. We have
deduced such a law coupling the widely used Weibull statistics, developed for
describing the distribution of the strength of solids, with the universal model
for ontogen... | biology |
5,488 | Sociophysics Simulations III: Retirement Demography | q-bio.PE | This third part of the lecture series deals with the question: Who will pay
for your retirement? For Western Europe the answer may be ``nobody'', but for
Algeria the demography looks more promising. | biology |
5,489 | Mimivirus Relatives in the Sargasso Sea | q-bio.PE | The discovery and genome analysis of Acanthamoeba polyphaga Mimivirus, the
largest known DNA virus, challenged much of the accepted dogma regarding
viruses. Its particle size (>400 nm), genome length (1.2 million bp) and huge
gene repertoire (911 protein coding genes) all contribute to blur the
established boundaries b... | biology |
5,490 | Scaling properties of the Penna model | q-bio.PE | We investigate the scaling properties of the Penna model, which has become a
popular tool for the study of population dynamics and evolutionary problems in
recent years. We find that the model generates a normalised age distribution
for which a simple scaling rule is proposed, that is able to reproduce
qualitative feat... | biology |
5,491 | Sharp gene pool transition in a population affected by phenotype-based selective hunting | q-bio.PE | We use a microscopic model of population dynamics, a modified version of the
well known Penna model, to study some aspects of microevolution. This research
is motivated by recent reports on the effect of selective hunting on the gene
pool of bighorn sheep living in the Ram Mountain region, in Canada. Our model
finds a ... | biology |
5,492 | Density-Dependence as a Size-Independent Regulatory Mechanism | q-bio.PE | The growth function of populations is central in biomathematics. The main
dogma is the existence of density dependence mechanisms, which can be modelled
with distinct functional forms that depend on the size of the population. One
important class of regulatory functions is the $\theta$-logistic, which
generalises the l... | biology |
5,493 | Parametric Resonance May Explain Virologic Failure to HIV Treatment Interruptions | q-bio.PE | Pilot studies of structured treatment interruptions (STI) in HIV therapy have
shown that patients can maintain low viral loads whilst benefiting from reduced
treatment toxicity. However, a recent STI clinical trial reported a high degree
of virologic failure. Here we present a novel hypothesis that could explain
virolo... | biology |
5,494 | Study of Arbitrary Nonlinearities in Convective Population Dynamics with Small Diffusion | q-bio.PE | Convective counterparts of variants of the nonlinear Fisher equation which
describes reaction diffusion systems in population dynamics are studied with
the help of an analytic prescription and shown to lead to interesting
consequences for the evolution of population densities. The initial value
problem is solved explic... | biology |
5,495 | Environmental effects on the spread of the Neolithic | q-bio.PE | The causes and implications of the regional variations in the spread of the
incipient agriculture in Europe remain poorly understood. We apply population
dynamics models to study the dispersal of the Neolithic in Europe from a
localized area in the Near East, solving the two-dimensional reaction-diffusion
equation on a... | biology |
5,496 | Simulation of geographical trends in Chowdhury ecosystem model | q-bio.PE | A computer simulation based on individual births and deaths gives a
biodiversity increasing from cold to warm climates, in agreement with reality.
Complexity of foodwebs increases with time and at a higher rate at low
latitudes, and there is a higher rate of species creation at low latitudes.
Keeping many niches empty ... | biology |
5,497 | Evolution of polymorphism and sympatric speciation through competition in a unimodal distribution of resources | q-bio.PE | A microscopic agent dynamical model for diploid age-structured populations is
used to study evolution of polymorphism and sympatric speciation. The
underlying ecology is represented by a unimodal distribution of resources of
some width. Competition among individuals is also described by a similar
distribution, and its ... | biology |
5,498 | Diversity as a product of interspecial interactions | q-bio.PE | We demonstrate diversification rather than optimisation for highly
interacting organisms in a well mixed biological system by means of a simple
model and reference to experiment, and find the cause to be the complex network
of interactions formed, allowing species less well adapted to an environment to
flourish by co-i... | biology |
5,499 | A Predation Behavior Model Based on Game Theory | q-bio.PE | This article adopts game theory to build a model for explaining the predation
behavior of animals.We assume that both the prey and the preydator have two
stratigies in this game,the active one and the passive one.By calculating the
outcome and the income of energy in different stratigies, we find the solution
to analyz... | biology |
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