Int. J. Mol. Sci. 2009, 10(11), 4723-4741; doi:10.3390/ijms10114723
Article

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

Daniel P. Faith 1,* email, Catherine A. Lozupone 2 email, David Nipperess 3 email and Rob Knight 2 email
1 The Australian Museum, 6 College St., Sydney, NSW, 2010, Australia 2 Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA 3 Department of Biological Sciences, Macquarie University, NSW, 2109, Australia
* Author to whom correspondence should be addressed.
Received: 23 July 2009; in revised form: 5 October 2009 / Accepted: 30 October 2009 / Published: 3 November 2009
(This article belongs to the Special Issue Cladistic Analysis and Molecular Evolution)
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Abstract: The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional specieslevel ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.
Keywords: bacteria; UniFrac; feature diversity; ordination; PD calculus; evolutionary features; GEO BON; climate change

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MDPI and ACS Style

Faith, D.P.; Lozupone, C.A.; Nipperess, D.; Knight, R. The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework. Int. J. Mol. Sci. 2009, 10, 4723-4741.

AMA Style

Faith DP, Lozupone CA, Nipperess D, Knight R. The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework. International Journal of Molecular Sciences. 2009; 10(11):4723-4741.

Chicago/Turabian Style

Faith, Daniel P.; Lozupone, Catherine A.; Nipperess, David; Knight, Rob. 2009. "The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework." Int. J. Mol. Sci. 10, no. 11: 4723-4741.

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