mitochondrial DNA barcoding (Drosophilidae)

Knowledge graph centered on mitochondrial DNA barcoding (Drosophilidae) with 70 nodes and 164 connections. Top connected: Ligusticum porteri, Lepidoptera, Arabidopsis, Boechera stricta, Boechera.

Method synopsis

Time-calibrated phylogenetic analysis using multiple genes and both maximum likelihood and Bayesian approaches to estimate evolutionary relationships and timing of trait evolution.

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 — Evolution and genomic basis of the plant penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae (2022), Proceedings of the Royal Society B. The protocol was originally introduced by Mining the plant-insect interface with a leafmining <i>Drosophila</i> of <i>Arabidopsis</i> (2011), Molecular Ecology. Implementations in other papers (listed below) may differ.

1. Perform phylogenetic reconstruction
   Estimated a phylogeny of Scaptomyza including the sister clade of Hawaiian Drosophila, using 11 genes and 95 taxa. Used concatenated genes by maximum likelihood (ML) in RAxML, and a time-calibrated tree using Bayesian inference in MrBayes and BEAST. Complete phylogenies are reported in electronic supplementary material.
   Quantities: 11 genes, 95 taxa totalDuration: Not specifiedConditions: Computational phylogenetic analysis
   Equipment: RAxML software, MrBayes software, BEAST v2.4.6 software

Typical Equipment

• RAxML software
• MrBayes software
• BEAST v2.4.6 software

Output Measurements

• phylogenetic trees
• divergence times
• ancestral state reconstructions

Papers Using This Protocol (4)

Species Studied With This Protocol