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Applying ecological models to communities of genetic elements: the case of neutral theory

Linquist, Stefan and Cottenie, Karl and Elliott, Tyler and Saylor, Brent and Kremer, Stefan and Gregory, T. Ryan (2015) Applying ecological models to communities of genetic elements: the case of neutral theory. [Preprint]

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Abstract

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size.


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Item Type: Preprint
Creators:
CreatorsEmailORCID
Linquist, Stefanlinquist"uoguelph.ca
Cottenie, Karlcottenie@uoguelph.ca
Elliott, Tylertelliott@uoguelph.ca
Saylor, Brentbsaylor@uoguelph.ca
Kremer, Stefanskremer@uoguelph.ca
Gregory, T. Ryanrgregory@uoguelph.ca
Keywords: ecological neutral theory, genome ecology, molecular neutral theory, mutation hazard model, transposon ecology.
Subjects: Specific Sciences > Biology
Specific Sciences > Biology > Ecology/Conservation
Specific Sciences > Biology > Evolutionary Theory
Specific Sciences > Biology > Molecular Biology/Genetics
Depositing User: Dr Stefan Linquist
Date Deposited: 26 Aug 2015 14:43
Last Modified: 26 Aug 2015 14:43
Item ID: 11635
Official URL: http://onlinelibrary.wiley.com/doi/10.1111/mec.132...
DOI or Unique Handle: 10.1111/mec.13219
Subjects: Specific Sciences > Biology
Specific Sciences > Biology > Ecology/Conservation
Specific Sciences > Biology > Evolutionary Theory
Specific Sciences > Biology > Molecular Biology/Genetics
Date: July 2015
URI: http://philsci-archive.pitt.edu/id/eprint/11635

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