DOI: 10.5061/dryad.7vh21
title: Data from: Extending the concept of diversity partitioning to characterize phenotypic complexity

description: Most components of an organism’s phenotype can be viewed as the expression
 of multiple traits. Many of these traits operate as complexes, where
 multiple subsidiary parts function and evolve together. As trait
 complexity increases, so does the challenge of describing complexity in
 intuitive, biologically meaningful ways. Traditional multivariate analyses
 ignore the phenomenon of individual complexity and provide relatively
 abstract representations of variation among individuals. We suggest
 adopting well-known diversity indices from community ecology to describe
 phenotypic complexity as the diversity of distinct subsidiary components
 of a trait. Using a hierarchical framework, we illustrate how total trait
 diversity can be partitioned into within-individual complexity (α
 diversity) and between-individual components (β diversity). This approach
 complements traditional multivariate analyses. The key innovations are (i)
 addition of individual complexity within the same framework as
 between-individual variation and (ii) a group-wise partitioning approach
 that complements traditional level-wise partitioning of diversity. The
 complexity-as-diversity approach has potential application in many fields,
 including physiological ecology, ecological and community genomics, and
 transcriptomics. We demonstrate the utility of this
 complexity-as-diversity approach with examples from chemical and microbial
 ecology. The examples illustrate biologically significant differences in
 complexity and diversity that standard analyses would not reveal.
description: Milkweed Cardenolide
 DataCardenolide
 concentration data originally published by Fordyce & Malcolm
 (2000)RhyssomatusCG.csvBaseline American Toad Bufadienolide ConcentrationsParotoid secretions were collected on pre-weighed filter paper after manual expression by compressing each gland between two fingers. Following an initial sampling, toads were randomly assigned to one of three expression-frequency treatments (N = 42)—frequent expression (5x), medium expression (1x), or low expression (0x)—and sampled over five months. At the experiment’s conclusion, toad glands were expressed one final time for comparison, followed by high-performance liquid chromatography (HPLC) of the secretions. Here we compare the baseline chemotypes to the final chemotypes among treatments.beginDat.csvFinal American Toad Bufadienolide Concentrations after 5 months of paratoid expressionParotoid secretions were collected on pre-weighed filter paper after manual expression by compressing each gland between two fingers. Following an initial sampling, toads were randomly assigned to one of three expression-frequency treatments (N = 42)—frequent expression (5x), medium expression (1x), or low expression (0x)—and sampled over five months. At the experiment’s conclusion, toad glands were expressed one final time for comparison, followed by high-performance liquid chromatography (HPLC) of the secretions. Here we compare the baseline chemotypes to the final chemotypes among treatments.endDat.csvPopulus Phospholipid Fatty Acid DatasetSchweitzer et al. (2008) used phospholipid fatty acid (PLFA) biomarkers to assess rhizosphere microbial community composition as a complex extended phenotype of Populus trees, asking whether PLFA profiles consistently differed among tree genotypes in a common garden. The dataset includes 3–4 clones each of four genotypes of Populus fremontii and five genotypes of Populus angustifolia.PopulusPLFA.csv