Phylogenetically independent contrasts

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Method synopsis

A standard comparative method that controls for evolutionary relationships among species by analyzing evolutionary changes along phylogenetic branches rather than raw species values. Uses software to test for phylogenetic signal and perform regression analyses on evolutionarily independent data points.

Synthesized from method descriptions across 4 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — A trait-based approach to the evolution of complex coalitions in male mammals (2009), Behavioral Ecology. Implementations in other papers (listed below) may differ.

1. Phylogenetically independent contrasts analysis
   Used Phylogenetic Independence 2.0 to determine whether variables under study were affected by their phylogenetic history. Selected the test for serial independence for continuous variables and runs test for discrete character state variables. Ran both types of tests with the 1000-simulation option and tested the likelihood of collaboration trait occurrences on areas of the tree where tolerance occurred, as well as likelihood of partner preference given the presence of collaboration.
   Quantities: 1000 simulation runs per testDuration: Not specifiedConditions: Computational analysis
   Equipment: Phylogenetic Independence 2.0 software
2. Statistical regression analysis
   Conducted multiple regression analysis with coalition complexity index as dependent variable and contrasts from all 6 social and environmental variables as independent variables. Used concentrated changes test to determine likelihood of evolutionary gains and tested likelihood that gains occurred more often than expected by chance. Calculated independent contrasts for each variable and used simple linear regression where contrasts from coalition complexity were dependent variable.
   Quantities: 37 species in analysis with 6 independent variablesDuration: Not specifiedConditions: Statistical analysis using 1000-simulation option
   Equipment: Compare Version 4.6b software, SPSS Version 10

Typical Equipment

• Phylogenetic Independence 2.0 software
• Compare Version 4.6b software

Output Measurements

• phylogenetically independent contrast values
• evolutionary correlation coefficients

Papers Using This Protocol (4)

Species Studied With This Protocol

Places Where Used