An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

Rokyta, Darin R.; Joyce, Paul; Caudle, S. Brian; Wichman, Holly A.

doi:10.1038/ng1535

Cited by 180 publications

(255 citation statements)

References 16 publications

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“…Key parameters such as N 0 and r could be manipulated experimentally, while parameters like s b and u could be measured in nonpermissive conditions (e.g., measuring the mutation rate to an antibiotic resistance allele). In organisms such as bacteriophage that have sufficiently small genomes, wholegenome sequencing could be used to confirm that adaptation occurred via single substitutions (e.g., Rokyta et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…These efforts have largely focused on identifying patterns that might characterize adaptation through DNA sequence space (reviewed in Orr 2005). This work has revealed several interesting patterns (Gillespie 1984;Orr 2002Orr , 2005Rozen et al 2002) and has motivated a number of new experiments (Rozen et al 2002;Sanjuan et al 2004;Rokyta et al 2005;Barrett et al 2006;Kassen and Bataillon 2006). Nearly all work on the theory of adaptation, however, has been limited in at least one important way: it assumes that populations maintain a stable size following a sudden change in environment, a change to which the population must adapt.…”

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confidence: 99%

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Population Extinction and the Genetics of Adaptation

Orr

Unckless

2008

The American Naturalist

266

390

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Theories of adaptation typically ignore the effect of environmental change on population size. But some environmental challenges-challenges to which populations must adapt-may depress absolute fitness below 1, causing populations to decline. Under this scenario, adaptation is a race; beneficial alleles that adapt a population to the new environment must sweep to high frequency before the population becomes extinct. We derive simple, though approximate, solutions to the probability of successful adaptation (population survival) when adaptation involves new mutations, the standing genetic variation, or a mixture of the two. Our results show that adaptation to such environmental challenges can be difficult when relying on new mutations at one or a few loci, and populations will often decline to extinction.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Population Extinction and the Genetics of Adaptation

Orr

Unckless

2008

The American Naturalist

266

390

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“…The model explained these patterns by positing that most single mutations were near or in excess of the optimum and adding the second mutation therefore resulted in a movement away from the optimum. In the present work, we attempted to shift the wild-type genotype, ID11, and its nine previously described beneficial mutations (Rokyta et al 2005(Rokyta et al , 2008(Rokyta et al , 2011 closer to and farther from the optimal phenotype by changing the temperature at which fitness was measured, to quantify the changes in fitness effects and patterns of epistatic interactions between mutations. Previous work has shown that close relatives of ID11 in the G4-like group of microvirid coliphages (Rokyta et al 2006b) tend to have fitnesses inversely correlated with temperature (Knies et al 2009).…”

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confidence: 99%

Environment Determines Epistatic Patterns for a ssDNA Virus

2014

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Despite the accumulation of substantial quantities of information about epistatic interactions among both deleterious and beneficial mutations in a wide array of experimental systems, neither consistent patterns nor causal explanations for these interactions have yet emerged. Furthermore, the effects of mutations depend on the environment in which they are characterized, implying that the environment may also influence epistatic interactions. Recent work with beneficial mutations for the single-stranded DNA bacteriophage ID11 demonstrated that interactions between pairs of mutations could be understood by means of a simple model that assumes that mutations have additive phenotypic effects and that epistasis arises through a nonlinear phenotype-fitness map with a single intermediate optimum.To determine whether such a model could also explain changes in epistatic patterns associated with changes in environment, we measured epistatic interactions for these same mutations under conditions for which we expected to find the wild-type ID11 at different distances from its phenotypic optimum by assaying fitnesses at three different temperatures: 33°, 37°, and 41°. Epistasis was present and negative under all conditions, but became more pronounced as temperature increased. We found that the additive-phenotypes model explained these patterns as changes in the parameters of the phenotype-fitness map, but that a model that additionally allows the phenotypes to vary across temperatures performed significantly better. Our results show that ostensibly complex patterns of fitness effects and epistasis across environments can be explained by assuming a simple structure for the genotype-phenotype relationship.

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“…An earlier paper by John on the concept of a protein space (12) has also had contemporary influence, in the light of new ideas on how to model the process of adaptive evolution of protein and DNA sequences (Orr 2003), and the availability of data from viral systems on the detailed steps that actually occur during such evolution (Rokyta et al 2005). Another paper with John Haigh showed that data on human haemoglobin variants in European populations indicated a recent bottleneck of small population size (13).…”

Section: Research and Writings While Employed At The University Of Sumentioning

confidence: 99%

John Maynard Smith. 6 January 1920 – 19 April 2004

Charlesworth

Harvey

2005

Biogr. Mems Fell. R. Soc.

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Smith was born in London, the second child of Sidney Maynard Smith and Isobel Mary (née Pitman). In 1928 the family moved to the village of Hurst in Berkshire on the death of his father, a surgeon and freemason. John was immediately sent to boarding school-first to a preparatory school (St Peter's Court, Broadstairs) until 1933, then to Eton (until 1938. His holidays were invariably spent with his sister at their maternal grandfather's house in Exford on Exmoor, where John became an accomplished horse-rider, stag hunter and angler. Here, too, he developed his lifelong, self-taught interest in natural history, particularly bird-watching. This started during his childhood in London, when he was keen on visiting the Natural History Museum and Zoo, as well as reading any books about animals that he could find.He was very unhappy at school until the age of 16 years or so, and for the rest of his life was outspoken in his criticism of Eton and similar boarding schools. In reaction to the atmosphere at Eton, and to the advance of Fascism and Nazism in the late 1930s, John became an ardent Communist. (He had first-hand experience of Nazi Germany when he visited Berlin in 1938, where his uncle was British military attaché.) He had no formal science lessons at school, but used Eton's library to learn about science. It was here that he mastered the special theory of relativity and quantum theory, and enjoyed books about biology. His particular favourites were the essays of

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An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

Cited by 180 publications

References 16 publications

Population Extinction and the Genetics of Adaptation

Population Extinction and the Genetics of Adaptation

Environment Determines Epistatic Patterns for a ssDNA Virus

John Maynard Smith. 6 January 1920 – 19 April 2004

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