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Origin of Life: Emergence, Self-organization and Evolution
A system-centered perspective on the origin and evolution of Life on Earth
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Between exploration and fixation III: From cells to molecules

Between exploration and fixation III: From cells to molecules | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

How long does it take to an RNA pool to find a particular structure through mutation and selection? In this computational study, Manrubia and Stich relate properties of the sequence-structure map, in particular the abundance of a given secondary structure in a random pool, with the number of replicative events that an initially random population of sequences needs to find that structure through mutation and selection. Search and fixation processes are more efficient in a wider range of mutation rates for common structures, thus indicating that evolvability of RNA populations is not simply determined by abundance.

 

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Stich M, Manrubia SC.

Motif frequency and evolutionary search times in RNA populations.

J Theor Biol. 2011 Jul 7;280(1):117-26. Epub 2011 Mar 21.

 

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Between exploration and fixation I

Between exploration and fixation I | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Evolution is a tricky game between exploration and fixation. Extremely high mutation rates (MRs) lead to error catastrophe. Conversely, unusually low MRs inhibit adaptation to changing environments.

Montero and co-workers investigate the time a phenotype takes to reach fitness peak as function of both fitness landscape and its mutation rate. Researchers evaluate the average time that the system takes to reach a final steady state of simple models of populations formed by self-replicative sequences (quasispecie).

 

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Arturo Marína, Héctor Tejeroa, Juan Carlos Nuñob, Francisco Monteroa.

Characteristic time in quasispecies evolution

Journal of Theoretical Biology Volume 303, 21 June 2012, Pages 25–32

 

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Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Evidence of non-random mutation rates suggests an evolutionary risk management strategy | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A central tenet in evolutionary theory is that mutations occur randomly in the genome, now Luscombe and co-workers show that “neutral mutation rate varies by more than an order of magnitude across 2,659 genes” and surprisingly this variation is not random. Researchers detected a lower rate in highly expressed genes and in those undergoing stronger purifying selection. These findings suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. It seems like that bacteria have evolved a mechanism that protects important genes from random mutation, effectively reducing the risk of self-destruction.

 

Source:

Iñigo Martincorena, Aswin S. N. Seshasayee & Nicholas M. Luscombe

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Nature, 22 April 2012

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Between exploration and fixation II: When you cannot stop

Between exploration and fixation II: When you cannot stop | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Evolution is a tricky game between exploration and fixation, we said. True, if you do not need to win the evolutionary arms race against your opponent (predator/parasite).

Yomo and Kashiwagi report about the phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli. They observed how the phenotypes and genotypes of coevolving parasite-host pairs change through the arms race. Copropagation experiments with Escherichia coli and the lytic RNA bacteriophage Qβ in a spatially unstructured environment revealed continuous adaptation and counter-adaptation: “E. coli first adapted by developing partial resistance to infection and later increasing specific growth rate. The phage counter-adapted by improving release efficiency with a change in host specificity and decrease in virulence. Whole-genome analysis indicated that the phage accumulated 7.5 mutations, mainly in the A2 gene, 3.4-fold faster than in Qβ propagated alone. E. coli showed fixation of two mutations (in traQ and csdA) faster than in sole E. coli experimental evolution.”

 

Source:

Kashiwagi A, Yomo T.

Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli.

PLoS Genet. 2011 Aug;7(8):e1002188. Epub 2011 Aug 4.

 

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Teaching old dogs new tricks: Biological adaptaion and exaptation

Teaching old dogs new tricks: Biological adaptaion and exaptation | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Adaptation and exaptation are two fundamental mechanisms for evolutionary success which play a pivotal role as much as innovation. Baliga and coworkers describe Halobacterium salinarum adaptation to new environments by reprogramming general transcription factors TFBs. Researchers have investigated the “implications of TFB expansions by correlating sequence variations, regulation, and physical interactions of all seven TFBs in Halobacterium salinarum NRC-1 to their fitness landscapes, functional hierarchies, and genetic interactions across 2488 experiments covering combinatorial variations in salt, pH, temperature, and Cu stress”. This study reveals how archea can generate completely novel fitness landscapes “by gene conversion events that introduce subtle changes to the regulation or physical interactions of duplicated TFBs.”

 

Source:

Serdar Turkarslan, David J Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J Christopher Bare, Christopher L Plaisier & Nitin S Baliga. Niche adaptation by expansion and reprogramming of general transcription factors. Molecular Systems Biology 7 Article number: 554
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