Mantel test

Knowledge graph centered on Mantel test with 72 nodes and 103 connections. Top connected: Ligusticum porteri, Delphinium, Atriplex canescens, Asteraceae, Potentilla.

Method synopsis

Calculation of multiple phylogenetic diversity metrics for plant communities using established phylogenetic trees and null model approaches to test for phylogenetic clustering or overdispersion.

Synthesized from method descriptions across 10 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 — Rare species do not disproportionately contribute to phylogenetic diversity in a subalpine plant community (2025), American Journal of Botany. The protocol was originally introduced by Competitive hierarchy or niche packing? An examination of the effects of competition on community. (2014). Implementations in other papers (listed below) may differ.

1. Build phylogenetic tree
   Use the ALLMB.tre angiosperm phylogeny from Smith and Brown (2018). Replace missing species with closely related congeners when possible. Remove genera with multiple species (Senecio species and Erigonum species) that lacked genetic/phylogenetic information to avoid poor-to-genus resolution.
   Quantities: Final phylogeny included 55 of 68 species across all sitesDuration: One-time phylogeny constructionConditions: Used established angiosperm phylogeny as backbone
   Equipment: ALLMB.tre phylogeny file, phylogenetic analysis software
2. Calculate phylogenetic diversity metrics
   Calculate Faith's phylogenetic diversity (PD), mean phylogenetic distance (MPD), and mean nearest taxon distance (MNTD) for each community. Use picante R package and calculate standardized effect sizes (SES) using null models with 5000 randomizations.
   Quantities: Three phylogenetic metrics calculated for each of 15 plots, 5000 null model iterationsDuration: Computational analysis performed once for all communitiesConditions: Null models randomly draw species from regional species pool
   Equipment: R software, picante package

Typical Equipment

• R software
• picante package
• ALLMB.tre phylogeny file

Output Measurements

• Faith's phylogenetic diversity
• mean phylogenetic distance
• mean nearest taxon distance
• standardized effect sizes

Papers Using This Protocol (11)

Species Studied With This Protocol

Places Where Used