Multi-species life-history PCA analysis

Knowledge graph centered on Multi-species life-history PCA analysis with 46 nodes and 143 connections. Top connected: Marmota flaviventris, Spermophilus lateralis, Callospermophilus lateralis, Vatellus lateralis, Parus major.

Method synopsis

Principal component analysis applied across multiple species using demographic traits to identify major axes of life-history variation and test for slow-fast continuum patterns. Uses phylogenetically-informed approach to account for evolutionary relationships.

Synthesized from method descriptions across 1 paper 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 — Individual life histories: neither slow nor fast, just diverse (2023), Proceedings of the Royal Society B. Implementations in other papers (listed below) may differ.

1. Perform cross-species PCA
   Conducted PCA using species-mean values for the four life-history traits to identify the main structuring axes of variation across species. Used phylogenetically-informed PCA (pPCA) with 100 phylogenetic trees generated from the 'phytools' R package. Applied log-transformation to correct for allometric relationships and standardized variables (mean = 0, standard deviation = 1).
   Quantities: 100 phylogenetic trees, 4 life-history traits, 17 speciesDuration: Single analysis per phylogenetic treeConditions: Computational analysis using species-mean trait values
   Equipment: R software, phytools R package, phylogenetic trees
2. Test for slow-fast continuum using broken-stick model
   Applied broken-stick model to determine if first principal component was retained as main structuring axis. Used 52% variance explained as threshold - slow-fast continuum considered present if first PC explained more than 52% of variation and was characterized by opposition of time duration-related traits and time frequency-related traits.
   Quantities: 52% variance threshold, 4 conditions tested for slow-fast continuum presenceDuration: Applied to each PCA analysisConditions: Statistical significance testing using established model
   Equipment: broken-stick model, R software

Typical Equipment

• R software
• phytools R package
• broken-stick model

Output Measurements

• principal component loadings
• variance explained
• species scores on PC axes

Papers Using This Protocol (1)

Species Studied With This Protocol