ITS phylogenetic reconstruction (Orobanchaceae)

Knowledge graph centered on ITS phylogenetic reconstruction (Orobanchaceae) with 40 nodes and 127 connections. Top connected: Hummingbird, Ipomopsis, Delphinium, I. aggregata, Ipomopsis aggregata.

Method synopsis

Standard molecular phylogenetic approach using ITS sequences to reconstruct evolutionary relationships and calculate phylogenetic distances between plant species. Includes sequence alignment, tree inference, and time calibration.

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 — Phylogeny does not predict the outcome of heterospecific pollen–pistil interactions in a species-rich alpine plant community (2025), American Journal of Botany. Implementations in other papers (listed below) may differ.

1. Calculate phylogenetic distances between species
   Generated a phylogeny from ITS sequences downloaded from NCBI, aligned sequences with the msa function in the R package msa, calculated distance alignment using the function dist.alignment in the multispecies ITS sequences alignment in the R package seqinr. Inferred a tree topology using neighbor joining via the BIONJ algorithm using the function bionj in the R package ape. Transformed the tree to be ultrametric with time-calibrated nodes using divergence time estimates from timetree.org.
   Quantities: ITS sequences from NCBI database, multiple sequence alignmentDuration: Computational analysis timeframe not specifiedConditions: Bioinformatic processing environment
   Equipment: R software, msa package, seqinr package, ape package, timetree.org database

Typical Equipment

• R software
• msa package
• seqinr package
• ape package

Output Measurements

• phylogenetic distance
• evolutionary relationships

Papers Using This Protocol (1)

Species Studied With This Protocol