The generality of Constructive Neutral Evolution
@article{Brunet2018TheGO, title={The generality of Constructive Neutral Evolution}, author={Tyler D.P. Brunet and W. Ford Doolittle}, journal={Biology \& Philosophy}, year={2018}, volume={33}, pages={1-25} }
Constructive Neutral Evolution (CNE) is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or…
14 Citations
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References
SHOWING 1-10 OF 81 REFERENCES
On the Possibility of Constructive Neutral Evolution
- BiologyJournal of Molecular Evolution
- 1999
Nonselective factors in evolutionary innovation and directionality can be addressed in neutral models, such as those elaborated here with regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes.
How a neutral evolutionary ratchet can build cellular complexity
- BiologyIUBMB life
- 2011
It is suggested that CNE‐based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.
Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements
- BiologyGenome biology and evolution
- 2015
Here, general arguments for the importance of selection at levels above that of organisms in evolution are reviewed, and developed further for a common genomic feature: the carriage of transposable elements (TEs).
Nonadaptive origins of interactome complexity
- BiologyNature
- 2011
A phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits is demonstrated, leading to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein–protein interactions that stabilize key gene functions.
Genome reduction as the dominant mode of evolution
- BiologyBioEssays : news and reviews in molecular, cellular and developmental biology
- 2013
Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification, and a general model composed of two distinct evolutionary phases is proposed.
An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
- BiologyNature
- 2009
It is shown that the evolutionary path by which the vertebrate glucocorticoid receptor acquired its new function soon became inaccessible to reverse exploration, suggesting an important role for historical contingency in protein evolution.
Splendor and misery of adaptation, or the importance of neutral null for understanding evolution
- BiologyBMC Biology
- 2016
The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative…
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
- BiologymBio
- 2012
ABSTRACT Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically…
The probability of duplicate gene preservation by subfunctionalization.
- BiologyGenetics
- 2000
The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.
The evolutionary fate and consequences of duplicate genes.
- BiologyScience
- 2000
Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.