Phylomatic (Salicaceae)

Knowledge graph centered on Phylomatic (Salicaceae) with 17 nodes and 57 connections. Top connected: Spruce, Atriplex canescens, Asteraceae, Populus, native species.

Method synopsis

Construction of phylogenetic trees using Phylomatic web service with APG III megatree, followed by branch length assignment using BLADJ algorithm in Phylocom.

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 — Phylogenetic distance can predict susceptibility to attack by natural enemies (2011), Oikos. Implementations in other papers (listed below) may differ.

1. Phylogeny construction
   Used Phylomatic with APG III megatree (Angiosperm Phylogeny Group 2009) to construct base family-level phylogenies. Branch lengths were added using BLADJ algorithm in Phylocom. Node ages from Wikström et al. (2001) were used.
   Quantities: Eastern forest: 75 families with 63 exotics representing 31 families; Rocky Mountain: 63 families with 652 angiosperm species (603 natives, 49 exotics)Duration: Not specifiedConditions: Computational analysis
   Equipment: Phylomatic, Phylocom, APG III megatree, BLADJ algorithm

Typical Equipment

• Phylomatic
• Phylocom
• APG III megatree
• BLADJ algorithm

Output Measurements

• phylogenetic tree with branch lengths

Papers Using This Protocol (1)

Species Studied With This Protocol