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Entropy 2011, 13(3), 570-594; doi:10.3390/e13030570

Towards an Evolutionary Model of Animal-Associated Microbiomes

1
Institute of Genomic Biology, University of Illinois, Urbana, IL 61801, USA
2
Department of Physics, University of Illinois, Urbana, IL 61801, USA
3
Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
4
Department of Anthropology, University of Illinois, Urbana, IL 61801, USA
5
J. Craig Venter Institute, Rockville, MD 20850, USA
6
Department of Animal Sciences, University of Illinois, IL 61801, USA
7
Department of Microbiology, University of Illinois, IL 61801, USA
*
Author to whom correspondence should be addressed.
Received: 16 December 2010 / Revised: 19 February 2011 / Accepted: 22 February 2011 / Published: 25 February 2011
(This article belongs to the Special Issue Emergence of Information in Evolutionary Processes)
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Abstract

Second-generation sequencing technologies have granted us greater access to the diversity and genetics of microbial communities that naturally reside endo- and ecto-symbiotically with animal hosts. Substantial research has emerged describing the diversity and broader trends that exist within and between host species and their associated microbial ecosystems, yet the application of these data to our evolutionary understanding of microbiomes appears fragmented. For the most part biological perspectives are based on limited observations of oversimplified communities, while mathematical and/or computational modeling of these concepts often lack biological precedence. In recognition of this disconnect, both fields have attempted to incorporate ecological theories, although their applicability is currently a subject of debate because most ecological theories were developed based on observations of macro-organisms and their ecosystems. For the purposes of this review, we attempt to transcend the biological, ecological and computational realms, drawing on extensive literature, to forge a useful framework that can, at a minimum be built upon, but ideally will shape the hypotheses of each field as they move forward. In evaluating the top-down selection pressures that are exerted on a microbiome we find cause to warrant reconsideration of the much-maligned theory of multi-level selection and reason that complexity must be underscored by modularity.
Keywords: microbiome; evolution; animal; multi-level selection; modularity; complexity; interdependency; ecology microbiome; evolution; animal; multi-level selection; modularity; complexity; interdependency; ecology
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Yeoman, C.J.; Chia, N.; Yildirim, S.; Miller, M.E.B.; Kent, A.; Stumpf, R.; Leigh, S.R.; Nelson, K.E.; White, B.A.; Wilson, B.A. Towards an Evolutionary Model of Animal-Associated Microbiomes. Entropy 2011, 13, 570-594.

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