scholarly journals Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations

2006 ◽  
Vol 2 (2) ◽  
pp. 236-238 ◽  
Author(s):  
Rowan D.H Barrett ◽  
R Craig MacLean ◽  
Graham Bell
Keyword(s):  
Pseudomonas Fluorescens ◽  
Sole Carbon Source ◽  
Fundamental Property ◽  
Selective Advantage ◽  
Ancestral Population ◽  
Selection Coefficient ◽  
Beneficial Mutation ◽  
Average Effect ◽  
Stressful Environments ◽  
Intermediate Effect

The fixation of a beneficial mutation represents the first step in adaptation, and the average effect of such mutations is therefore a fundamental property of evolving populations. It is nevertheless poorly characterized because the rarity of beneficial mutations makes it difficult to obtain reliable estimates of fitness. We obtained 68 genotypes each containing a single fixed beneficial mutation from experimental populations of Pseudomonas fluorescens , evolving in medium with serine as the sole carbon source and estimated the selective advantage of each by competition with the ancestor. The distribution of selection coefficients is modal and closely resembles the Weibull distribution. The average selection coefficient (2.1) and beneficial mutation rate (3.8×10 −8 ) are high relative to previous studies, possibly because the ancestral population grows poorly in serine-limited medium. Our experiment suggests that the initial stages of adaptation to stressful environments will involve the substitution of mutations with large effect on fitness.

scholarly journals Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape

2021 ◽  
Vol 118 (4) ◽  
pp. e2015665118
Author(s):  
Yuri Bakhtin ◽  
Mikhail I. Katsnelson ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Fitness Landscape ◽  
Large Population ◽  
Saddle Points ◽  
Selection Coefficient ◽  
Beneficial Mutation ◽  
Effective Population ◽  
Phenotypic Changes ◽  
Self Organized ◽  
Evolving System ◽  
Self Organized Criticality

A mathematical analysis of the evolution of a large population under the weak-mutation limit shows that such a population would spend most of the time in stasis in the vicinity of saddle points on the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNe/s time (Ne, effective population size; s, selection coefficient of a mutation), when a new beneficial mutation is fixed in the evolving population, which accordingly moves to a different saddle, or on much rarer occasions from a saddle to a local peak. Phenomenologically, this mode of evolution of a large population resembles punctuated equilibrium (PE) whereby phenotypic changes occur in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but the phenotype does not change substantially. Theoretically, PE has been linked to self-organized criticality (SOC), a model in which the size of “avalanches” in an evolving system is power-law-distributed, resulting in increasing rarity of major events. Here we show, however, that a PE-like evolutionary regime is the default for a very simple model of an evolving population that does not rely on SOC or any other special conditions.

scholarly journals Degradation of Substituted Phenylurea Herbicides byArthrobacter globiformis Strain D47 and Characterization of a Plasmid-Associated Hydrolase Gene,puhA

2001 ◽  
Vol 67 (5) ◽  
pp. 2270-2275 ◽  
Author(s):  
Gillian A. Turnbull ◽  
Margaret Ousley ◽  
Allan Walker ◽  
Eve Shaw ◽  
J. Alun W. Morgan
Keyword(s):  
Protein Sequence ◽  
Sole Carbon Source ◽  
Selective Advantage ◽  
Arthrobacter Globiformis ◽  
Plasmid Curing ◽  
Phenylurea Herbicides ◽  
Reading Frame ◽  
E Coli ◽  
Degrading Bacteria

ABSTRACT Arthrobacter globiformis D47 was shown to degrade a range of substituted phenylurea herbicides in soil. This strain contained two plasmids of approximately 47 kb (pHRIM620) and 34 kb (pHRIM621). Plasmid-curing experiments produced plasmid-free strains as well as strains containing either the 47- or the 34-kb plasmid. The strains were tested for their ability to degrade diuron, which demonstrated that the degradative genes were located on the 47-kb plasmid. Studies on the growth of these strains indicated that the ability to degrade diuron did not offer a selective advantage to A. globiformis D47 on minimal medium designed to contain the herbicide as a sole carbon source. The location of the genes on a plasmid and a lack of selection would explain why the degradative phenotype, as with many other pesticide-degrading bacteria, can be lost on subculture. A 22-kbEcoRI fragment of plasmid pHRIM620 was expressed inEscherichia coli and enabled cells to degrade diuron. Transposon mutagenesis of this fragment identified one open reading frame that was essential for enzyme activity. A smaller subclone of this gene (2.5 kb) expressed in E. colicoded for the protein that degraded diuron. This gene and its predicted protein sequence showed only a low level of protein identity (25% over ca. 440 amino acids) to other database sequences and was named after the enzyme it encoded, phenylurea hydrolase (puhAgene).

scholarly journals Evolutionary rescue by beneficial mutations in environments that change in space and time

2013 ◽  
Vol 368 (1610) ◽  
pp. 20120082 ◽  
Author(s):  
Mark Kirkpatrick ◽  
Stephan Peischl
Keyword(s):  
Branching Processes ◽  
Selective Advantage ◽  
Maximum Speed ◽  
Selection Coefficient ◽  
Beneficial Mutations ◽  
Changing Environments ◽  
Classic Theory ◽  
Evolutionary Rescue ◽  
Effective Selection ◽  
Establishment Probability

A factor that may limit the ability of many populations to adapt to changing conditions is the rate at which beneficial mutations can become established. We study the probability that mutations become established in changing environments by extending the classic theory for branching processes. When environments change in time, under quite general conditions, the establishment probability is approximately twice the ‘effective selection coefficient’, whose value is an average that gives most weight to a mutant's fitness in the generations immediately after it appears. When fitness varies along a gradient in a continuous habitat, increased dispersal generally decreases the chance a mutation establishes because mutations move out of areas where they are most adapted. When there is a patch of favourable habitat that moves in time, there is a maximum speed of movement above which mutations cannot become established, regardless of when and where they first appear. This critical speed limit, which is proportional to the mutation's maximum selective advantage, represents an absolute constraint on the potential of locally adapted mutations to contribute to evolutionary rescue.

scholarly journals Contribution of Gene Loss to the Pathogenic Evolution of Burkholderia pseudomallei and Burkholderia mallei

2004 ◽  
Vol 72 (7) ◽  
pp. 4172-4187 ◽  
Author(s):  
Richard A. Moore ◽  
Shauna Reckseidler-Zenteno ◽  
Heenam Kim ◽  
William Nierman ◽  
Yan Yu ◽  
...  
Keyword(s):  
Carbon Source ◽  
Burkholderia Pseudomallei ◽  
Sole Carbon Source ◽  
Lethal Dose ◽  
Selective Advantage ◽  
Burkholderia Mallei ◽  
Closely Related Species ◽  
Transposon Insertion ◽  
Genes Encoding ◽  
Pathogenic Evolution

ABSTRACT Burkholderia pseudomallei is the causative agent of melioidosis. Burkholderia thailandensis is a closely related species that can readily utilize l-arabinose as a sole carbon source, whereas B. pseudomallei cannot. We used Tn5-OT182 mutagenesis to isolate an arabinose-negative mutant of B. thailandensis. Sequence analysis of regions flanking the transposon insertion revealed the presence of an arabinose assimilation operon consisting of nine genes. Analysis of the B. pseudomallei chromosome showed a deletion of the operon from this organism. This deletion was detected in all B. pseudomallei and Burkholderia mallei strains investigated. We cloned the B. thailandensis E264 arabinose assimilation operon and introduced the entire operon into the chromosome of B. pseudomallei 406e via homologous recombination. The resultant strain, B. pseudomallei SZ5028, was able to utilize l-arabinose as a sole carbon source. Strain SZ5028 had a significantly higher 50% lethal dose for Syrian hamsters compared to the parent strain 406e. Microarray analysis revealed that a number of genes in a type III secretion system were down-regulated in strain SZ5028 when cells were grown in l-arabinose, suggesting a regulatory role for l-arabinose or a metabolite of l-arabinose. These results suggest that the ability to metabolize l-arabinose reduces the virulence of B. pseudomallei and that the genes encoding arabinose assimilation may be considered antivirulence genes. The increase in virulence associated with the loss of these genes may have provided a selective advantage for B. pseudomallei as these organisms adapted to survival in animal hosts.

scholarly journals Commensalism or Cross-Species Adoption? A Critical Review of Theories of Wolf Domestication

2021 ◽  
Vol 8 ◽  
Author(s):  
James A. Serpell
Keyword(s):  
Social Relations ◽  
Selective Advantage ◽  
Domestic Dog ◽  
Ancestral Population ◽  
Alternative Account ◽  
Hunter Gatherers ◽  
Origin Stories ◽  
Eurasian Continent ◽  
Animal Remains ◽  
The Relationship

The work of archaeozoologists and molecular geneticists suggests that the domestication of the wolf (Canis lupus)—the ancestor of the domestic dog (C. familiaris)—probably occurred somewhere between 40,000 and 15,000 years ago somewhere on the Eurasian continent, perhaps in more than one location. Wolf domestication was therefore underway many millennia before the origins of agriculture and the domestication of food animals, such as sheep and goats. Currently, there are two predominant “origin stories” concerning the domestication of the wolf. The dominant narrative in recent literature is the commensal scavenger hypothesis which posits that wolves essentially domesticated themselves by invading ancient human settlements in search of animal remains and other edible waste discarded by hunter-gatherers. Over time, tolerance by humans gave a selective advantage to the bolder, less fearful wolves, which then diverged from the ancestral population as they adapted to the new scavenging niche. At some point in the process, humans also began to recognize the benefits of living with resident, semi-domestic wolves, either as guards or as hunting partners, thereby cementing the relationship. The alternative account of wolf domestication is very different. Sometimes known as the pet keeping or cross-species adoption hypothesis, this narrative draws heavily on anthropological observations of pet keeping among recent hunter-gatherers, and postulates that Paleolithic peoples were similarly inclined to capture, adopt and rear infant mammals, such as wolf pups, and that this habitual human nurturing behavior ultimately provided the basis for the evolution of a cooperative social system involving both species. This review critically examines and analyzes these two distinct domestication narratives and explores the underlying and sometimes erroneous assumptions they make about wolves, Pleistocene humans, and the original relationships that existed between the two species. The paper concludes that the commensal scavenger hypothesis is untenable based on what is known about recent and ancient hunter-gatherer societies, and that wolf domestication was predicated on the establishment of cooperative social relations between humans and wolves based on the early socialization of wolf pups.

scholarly journals Obstruction of adaptation in diploids by recessive, strongly deleterious alleles

2015 ◽  
Vol 112 (20) ◽  
pp. E2658-E2666 ◽  
Author(s):  
Zoe June Assaf ◽  
Dmitri A. Petrov ◽  
Jamie R. Blundell
Keyword(s):  
Genetic Disorders ◽  
Natural Populations ◽  
Selective Advantage ◽  
Adaptive Mutation ◽  
Heterozygote Advantage ◽  
Deleterious Mutations ◽  
Beneficial Mutation ◽  
Recessive Mutations ◽  
Deleterious Alleles ◽  
Signature Of Selection

Recessive deleterious mutations are common, causing many genetic disorders in humans and producing inbreeding depression in the majority of sexually reproducing diploids. The abundance of recessive deleterious mutations in natural populations suggests they are likely to be present on a chromosome when a new adaptive mutation occurs, yet the dynamics of recessive deleterious hitchhikers and their impact on adaptation remains poorly understood. Here we model how a recessive deleterious mutation impacts the fate of a genetically linked dominant beneficial mutation. The frequency trajectory of the adaptive mutation in this case is dramatically altered and results in what we have termed a “staggered sweep.” It is named for its three-phased trajectory: (i) Initially, the two linked mutations have a selective advantage while rare and will increase in frequency together, then (ii), at higher frequencies, the recessive hitchhiker is exposed to selection and can cause a balanced state via heterozygote advantage (the staggered phase), and (iii) finally, if recombination unlinks the two mutations, then the beneficial mutation can complete the sweep to fixation. Using both analytics and simulations, we show that strongly deleterious recessive mutations can substantially decrease the probability of fixation for nearby beneficial mutations, thus creating zones in the genome where adaptation is suppressed. These mutations can also significantly prolong the number of generations a beneficial mutation takes to sweep to fixation, and cause the genomic signature of selection to resemble that of soft or partial sweeps. We show that recessive deleterious variation could impact adaptation in humans and Drosophila.

Growth of an extracellular proteinase-deficient strain of Pseudomonas fluorescens on milk and milk proteins

1983 ◽  
Vol 50 (3) ◽  
pp. 365-374 ◽  
Author(s):  
Joan P. Torrie ◽  
Hilaire Cholette ◽  
Debbi A. Froehlich ◽  
Robin C. McKellar
Keyword(s):  
Pseudomonas Fluorescens ◽  
Enzyme Assay ◽  
Polyacrylamide Gel Electrophoresis ◽  
Skim Milk ◽  
Milk Proteins ◽  
Selective Advantage ◽  
Sole Source ◽  
Extracellular Proteinase ◽  
Cell Numbers ◽  
Mutant Cells

SummaryAn extracellular proteinase-and lipase-deficient mutant of a psychrotroph, Pseudomonas fluorescens strain 32A, has been isolated and the absence of the proteinase enzyme confirmed by growth on differential media, enzyme assay and polyacrylamide gel electrophoresis. Competition between the parent and the mutant was observed when equal numbers of the 2 strains were inoculated together into raw skim-milk at 6 °C. Bitterness was detected at 6 °C in pasteurized skim-milk inoculated with the parent cells concurrent with the detection of proteolytic activity. In the case of the mutant, slight bitterness which did not increase with increasing cell numbers was detected in the absence of proteolysis. Mutant cells failed to grow on Na caseinate as the sole source of carbon. It was concluded that the extracellular proteinase, while not essential for growth in milk, does provide a selective advantage to the producer organism. This enzyme is, however, essential for growth on milk proteins and contributes to the development of bitterness in pasteurized milk.

High production of pyoluteorin and 2,4-diacetylphloroglucinol by Pseudomonas fluorescens S272 grown on ethanol as a sole carbon source

1998 ◽  
Vol 86 (6) ◽  
pp. 559-563 ◽  
Author(s):  
Zhan Yuan ◽  
Song Cang ◽  
Motoko Matsufuji ◽  
Kuniho Nakata ◽  
Yasunori Nagamatsu ◽  
...  
Keyword(s):  
Carbon Source ◽  
Pseudomonas Fluorescens ◽  
Sole Carbon Source ◽  
High Production

The Functional Design of the Insect Excretory System

1981 ◽  
Vol 90 (1) ◽  
pp. 1-15 ◽  
Author(s):  
S. H. P. MADDRELL
Keyword(s):  
High Surface ◽  
High Surface Area ◽  
Volume Ratio ◽  
Selective Advantage ◽  
Excretory System ◽  
High Concentrations ◽  
Terrestrial Insects ◽  
Stressful Environments ◽  
Very High ◽  
Rate Of Movement

Insects have a slowly operating excretory system in which the passive rate of movement of haemolymph solutes into a slowly secreted primary excretory fluid is restricted by a reduction in the area available for passive transfer. They may have come to possess such an energy-saving system as a result of their evolution as small animals in osmotically and ionically stressful environments. Although the possession of a waxy cuticle is a major element in their ability to live in such environments, insects have a very high surface-area/volume ratio and this is likely to have conferred a selective advantage on individuals able to withstand unusually variable extracellular conditions. Among their major adaptations evolved to allow them to tolerate such conditions are the lack of a blood-borne respiratory pigment to be affected and the development of a system whereby their most sensitive tissues are protected by the regulatory activities of special covering epithelia. Because of these features it follows that there has been less evolutionary pressure for rapid excretory control of the haemolymph composition. With an excretory system that only slowly filters the haemolymph, less energy expenditure is involved in the production of the primary excretory fluid and in reabsorption of useful substances from it. In addition, insects are able to maintain in circulation high concentrations of substances such as amino acids, trehalose, and lipids. They can also eliminate excess fluid at very high rates with the loss of only trace amounts of haemolymph solutes. It is argued that terrestrial insects owe much of their success to their ability to recover virtually all the water from the slow flow of primary excretory fluid. The hindgut cells that are responsible for this recovery are aided by their cuticular lining which protects them from contact with the very high concentrations of potentially interfering compounds in the excretory material.

scholarly journals Involvement of Nitrate Reductase and Pyoverdine in Competitiveness of Pseudomonas fluorescens Strain C7R12 in Soil

2001 ◽  
Vol 67 (6) ◽  
pp. 2627-2635 ◽  
Author(s):  
Pascal Mirleau ◽  
Laurent Philippot ◽  
Thérèse Corberand ◽  
Philippe Lemanceau
Keyword(s):  
Nitrate Reductase ◽  
Pseudomonas Fluorescens ◽  
Type Strain ◽  
Wild Type Strain ◽  
Rhizosphere Soil ◽  
Selective Advantage ◽  
Site Directed Mutagenesis ◽  
Competitive Advantages ◽  
Wild Type ◽  
Rhizosphere Competence

ABSTRACT Involvement of nitrate reductase and pyoverdine in the competitiveness of the biocontrol strain Pseudomonas fluorescens C7R12 was determined, under gnotobiotic conditions, in two soil compartments (bulk and rhizosphere soil), with the soil being kept at two different values of matric potential (−1 and −10 kPa). Three mutants affected in the synthesis of either the nitrate reductase (Nar−), the pyoverdine (Pvd−), or both (Nar− Pvd−) were used. The Nar− and Nar− Pvd− mutants were obtained by site-directed mutagenesis of the wild-type strain and of the Pvd− mutant, respectively. The selective advantage given by nitrate reductase and pyoverdine to the wild-type strain was assessed by measuring the dynamic of each mutant-to-total-inoculant (wild-type strain plus mutant) ratio. All three mutants showed a lower competitiveness than the wild-type strain, indicating that both nitrate reductase and pyoverdine are involved in the fitness of P. fluorescens C7R12. The double mutant presented the lowest competitiveness. Overall, the competitive advantages given to C7R12 by nitrate reductase and pyoverdine were similar. However, the selective advantage given by nitrate reductase was more strongly expressed under conditions of lower aeration (−1 kPa). In contrast, the selective advantage given by nitrate reductase and pyoverdine did not differ in bulk and rhizosphere soil, indicating that these bacterial traits are not specifically involved in the rhizosphere competence but rather in the saprophytic ability of C7R12 in soil environments.

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