Jessica A. Bryant, Frank J. Stewart, John M. Eppley, and Edward F. DeLong. 2012. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93:1659–1673. http://dx.doi.org/10.1890/11-1204.1

Supplement

R code used to normalize diversity measures (phylogenetic diversity [PD] and mean phylogenetic distance [MPD]) between samples with different sequencing depths and R code used to generate functional richness (FR) null models.
Ecological Archives E093-145-S1.

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Authors
File list (downloads)
Description

Author(s)

Jessica A. Bryant
Department of Civil and Environmental Engineering
Massachusetts Institute of Technology
Parsons Laboratory 48, 15 Vassar Street, Cambridge, MA 02139 USA

Frank J. Stewart
School of Biology
Georgia Institute of Technology
311 Ferst Drive, Atlanta, GA 30332 USA

John M. Eppley
Department of Civil and Environmental Engineering
Massachusetts Institute of Technology
Parsons Laboratory 48, 15 Vassar Street, Cambridge, MA 02139 USA

Edward F. DeLong
Department of Civil and Environmental Engineering
Massachusetts Institute of Technology
Parsons Laboratory 48, 15 Vassar Street, Cambridge, MA 02139 USA
E-mail: DeLong@mit.edu

File list

PDrarefy.r

MPDrarefy.r

FRrarefy.r

Description

PDrarefy.r

Description: R code used to normalize phylogenetic diversity (PD) across microbial communities with differing sequencing depths.

MPDrarefy.r

Description: R code used to normalize mean pairwise phylogenetic distance (MPD) across microbial communities with differing sequencing depths.

FRrarefy.r

Description: R code used to generate functional richness (FR) null models.