scholarly journals Genomic plasticity and rapid host switching promote the evolution of generalism in the zoonotic pathogen Campylobacter

2016 ◽  
Author(s):  
Dan J. Woodcock ◽  
Peter Krusche ◽  
Norval J. C. Strachan ◽  
Ken J. Forbes ◽  
Frederick M. Cohan ◽  
...  
Keyword(s):  
Evolutionary Model ◽  
Ecological Specialization ◽  
Effective Response ◽  
Zoonotic Pathogen ◽  
Genomic Plasticity ◽  
Standing Variation ◽  
Low Levels ◽  
Zoonotic Bacteria ◽  
Stochastic Evolutionary Model ◽  
Modelling Approach

AbstractHorizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of niche specifying genes and the opportunity for host transition can interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.

scholarly journals Phylogenetic confidence intervals for the optimal trait value

2014 ◽  
Author(s):  
Krzysztof Bartoszek ◽  
Serik Sagitov
Keyword(s):  
Limit Theorems ◽  
Evolutionary Model ◽  
Uhlenbeck Process ◽  
Sample Mean ◽  
Dependent Observations ◽  
Yule Process ◽  
Large N ◽  
Ornstein Uhlenbeck Process ◽  
Fast Adaptation ◽  
Stochastic Evolutionary Model

We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

scholarly journals Phylogenetic confidence intervals for the optimal trait value

2015 ◽  
Vol 52 (04) ◽  
pp. 1115-1132 ◽  
Author(s):  
Krzysztof Bartoszek ◽  
Serik Sagitov
Keyword(s):  
Confidence Interval ◽  
Limit Theorems ◽  
Evolutionary Model ◽  
Uhlenbeck Process ◽  
Sample Mean ◽  
Dependent Observations ◽  
Yule Process ◽  
Ornstein Uhlenbeck Process ◽  
Fast Adaptation ◽  
Stochastic Evolutionary Model

We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

scholarly journals Interplay of Driver, Mini-Driver, and Deleterious Passenger Mutations on Cancer Progression

2016 ◽  
Author(s):  
Xin Li ◽  
D. Thirumalai
Keyword(s):  
Tumor Growth ◽  
Cancer Progression ◽  
Evolutionary Model ◽  
Mutation Rates ◽  
Fitness Advantage ◽  
Dissipative Dynamical Systems ◽  
Passenger Mutations ◽  
The Relationship ◽  
Surprising Finding ◽  
Stochastic Evolutionary Model

Cancer is caused by the accumulation of a critical number of somatic mutations (drivers) that offer fitness advantage to tumor cells. Moderately deleterious passengers, suppressing cancer progression, and mini-drivers, mildly beneficial to tumors, can profoundly alter the cancer evolutionary landscape. This observation prompted us to develop a stochastic evolutionary model intended to probe the interplay of drivers, mini-drivers and deleterious passengers in tumor growth over a broad range of fitness values and mutation rates. Below a (small) threshold number of drivers tumor growth exhibits a plateau (dormancy) with large burst occurring when a driver achieves fixation, reminiscent of intermittency in dissipative dynamical systems. The predictions of the model, in particular the relationship between the average number of passenger mutations versus drivers in a tumor, is in accord with clinical data on several cancers. When deleterious drivers are included, we predict a non-monotonic growth of tumors as the mutation rate is varied with shrinkage and even reversal occurring at very large mutation rates. This surprising finding explains the paradoxical observation that high chromosomal instability (CIN) correlates with improved prognosis in a number of cancers compared with intermediate CIN.

scholarly journals Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Dan J. Woodcock ◽  
Peter Krusche ◽  
Norval J. C. Strachan ◽  
Ken J. Forbes ◽  
Frederick M. Cohan ◽  
...  
Keyword(s):  
Host Switching ◽  
Zoonotic Pathogen ◽  
Genomic Plasticity

A stochastic evolutionary model of molecular sequences

1992 ◽  
Vol 157 (1) ◽  
pp. 83-94 ◽  
Author(s):  
Liaofu Luo ◽  
L.E.H. Trainor
Keyword(s):  
Evolutionary Model ◽  
Molecular Sequences ◽  
Stochastic Evolutionary Model

scholarly journals Intraspecific Competition and the Promotion of Ecological Specialization

2021 ◽  
Author(s):  
Abdel H. Halloway ◽  
Joel S. Brown
Keyword(s):  
Resource Use ◽  
Intraspecific Competition ◽  
Niche Breadth ◽  
Evolutionary Model ◽  
Ecological Specialization ◽  
Secondary Resources ◽  
Cast Doubt ◽  
The Face ◽  
Game Theoretic ◽  
Diversification Hypothesis

AbstractThe evolution of ecological specialization can be summed up in a single question: why would a species evolve a more-restricted niche space? Various hypotheses have been developed to explain the promotion or suppression of ecological specialization. One hypothesis, competitive diversification, states that increased intraspecific competition will cause a population to broaden its niche breadth. With individuals alike in resource use preference, more individuals reduce the availability of preferred resources and should grant higher fitness to those that use secondary resources. However, recent studies cast doubt on this hypothesis with increased intraspecific competition reducing niche breadth in some systems. We present a game-theoretic evolutionary model showing greater ecological specialization with intraspecific competition under specific conditions. This is in contrast to the competitive diversification hypothesis. Our analysis reveals that specialization can offer a competitive advantage. Largely, when facing weak competition, more specialized individuals are able to acquire more of the preferred resources without greatly sacrificing secondary resources and therefore gain higher fitness. Only when competition is too great for an individual to significantly affect resource use will intraspecific competition lead to an increased niche breadth. Other conditions, such as a low diversity of resources and a low penalty to specialization, help promote ecological specialization in the face of intraspecific competition. Through this work, we have been able to discover a previously unseen role that intraspecific competition plays in the evolution of ecological specialization.

scholarly journals Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis

2015 ◽  
Author(s):  
Kiyoshi Ezawa ◽  
Dan Graur ◽  
Giddy Landan
Keyword(s):  
Markov Model ◽  
Ab Initio ◽  
Sequence Alignment ◽  
Continuous Time ◽  
Evolutionary Model ◽  
Rate Variation ◽  
Sequence Evolution ◽  
Insertions And Deletions ◽  
Indel Rate ◽  
Stochastic Evolutionary Model

AbstractBackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, such probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment. However, it is not a priori clear how these models are related with any genuine stochastic evolutionary model, which describes the stochastic evolution of an entire sequence along the time-axis. Moreover, none of these models can fully accommodate biologically realistic features, such as overlapping indels, power-law indel-length distributions, and indel rate variation across regions.ResultsHere, we theoretically tackle the ab initio calculation of the probability of a given sequence alignment under a genuine evolutionary model, more specifically, a general continuous-time Markov model of the evolution of an entire sequence via insertions and deletions. Our model allows general indel rate parameters including length distributions but does not impose any unrealistic restrictions on indels. Using techniques of the perturbation theory in physics, we expand the probability into a series over different numbers of indels. Our derivation of this perturbation expansion elegantly bridges the gap between Gillespie’s (1977) intuitive derivation of his own stochastic simulation method, which is now widely used in evolutionary simulators, and Feller’s (1940) mathematically rigorous theorems that underpin Gillespie′s method. We find a sufficient and nearly necessary set of conditions under which the probability can be expressed as the product of an overall factor and the contributions from regions separated by gapless columns of the alignment. The indel models satisfying these conditions include those with some kind of rate variation across regions, as well as space-homogeneous models. We also prove that, though with a caveat, pairwise probabilities calculated by the method of Miklós et al. (2004) are equivalent to those calculated by our ab initio formulation, at least under a space-homogenous model.ConclusionsOur ab initio perturbative formulation provides a firm theoretical ground that other indel models can rest on.[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend the ab initio perturbative formulation of a general continuous-time Markov model of indels.]

scholarly journals Las incidencias cataclismáticas de las bravezas en la evolución de la costa de Chile Central

1979 ◽  
pp. 19
Author(s):  
José F. Araya Vergara
Keyword(s):  
Evolutionary Model ◽  
Response Models ◽  
Geomorphological Mapping ◽  
Jointed Rocks ◽  
Joint Plane ◽  
Critical Slope ◽  
Frontal Systems ◽  
Low Levels ◽  
Dip Angle ◽  
Geomorphological Changes

The coast of Northern and Middle Chile suffers incidental surges or "bravezas", wich are meteorological surges. They have as cause the swells originated in the Pacific's storms, without important tide influence, as evidenced by the tide wave analysis and sinoptic interpretation. For the last great meteorological surge ocurred in 1968, the forecast gaves nearly stationary fronts over 2.000 n.m. S-SW from the coast. Perhaps the convergence of these frontal systems is the critical situation or threshold of surge incidence.The waves of the surge swells arrive into low holocenic coastal platform. Sometimes, their action can to attack the low levels of the Upper Pleistocene, showing a marine morphogenetic recurrence. The 1968 "bravezas" gaves the opportunity for appling an evolutionary model in a cliff with crystalline, jointed rocks, wich dip into the sea. The boulder removal on the joint plane produces an evolution by parallel retreat, wheter there is an unimpeded basal removal. The dip angle of the joints is greater than the angle of friction and the critical slope is equal than the dip angle.The geomorphological changes produced, are more stable on reefs and cliffs than on beaches. In the back-shore there is a tendency to recover the ancient profile. Every surge is a break of equilibrium and the seasonal conditions tend to restore themselves, but some forms are more permanentas the abrasion cliff of the marginal dune, realted to a new transverse concave profile including the back and foreshore together.This experience shows that in the aperiodic geomorphological mapping it does not must be distinguished as taxons the erosion beach from the accumulation beach, because they are transitional forms.Finally, it is possible to elaborate process response models of "braveza" coastal changes for danger forecasting. By using the frecuency and threshold notions, danger forecasting maps can be made.

scholarly journals Phylogenetic confidence intervals for the optimal trait value

2015 ◽  
Vol 52 (4) ◽  
pp. 1115-1132 ◽  
Author(s):  
Krzysztof Bartoszek ◽  
Serik Sagitov
Keyword(s):  
Confidence Interval ◽  
Limit Theorems ◽  
Evolutionary Model ◽  
Uhlenbeck Process ◽  
Sample Mean ◽  
Dependent Observations ◽  
Yule Process ◽  
Ornstein Uhlenbeck Process ◽  
Fast Adaptation ◽  
Stochastic Evolutionary Model

We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

scholarly journals A stochastic evolutionary model for capturing human dynamics

2015 ◽  
Vol 2015 (8) ◽  
pp. P08015 ◽  
Author(s):  
Trevor Fenner ◽  
Mark Levene ◽  
George Loizou
Keyword(s):  
Evolutionary Model ◽  
Human Dynamics ◽  
Stochastic Evolutionary Model
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