Bayesian phylogenetic inference (Vespertilionidae)

Knowledge graph centered on Bayesian phylogenetic inference (Vespertilionidae) with 26 nodes and 90 connections. Top connected: Marmota flaviventris, Lepidoptera, Odocoileus, fish and wildlife, Detection, prevalence and phylogenetic relationshi.

Method synopsis

MCMC-based phylogenetic reconstruction using multiple gene fragments to establish evolutionary relationships among Prostigmata mites.

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 — Detection, prevalence and phylogenetic relationships of <i>Demodex</i> spp and further skin prostigmata mites (Acari, Arachnida) in wild and domestic mammals (2016), PLoS ONE. Implementations in other papers (listed below) may differ.

1. Phylogenetic analysis
   The Bayesian inference program MrBayes v3.2.5 was used to estimate phylogenetic trees. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. MODELTEST 3.7 was used to select the best evolutionary model among 56 models of evolution by the Akaike Information Criterion. MCMC sampling was performed with 1,000,000 iterations using by default a burn-in of 25%. Bootstrap results are shown as measures of tree repeatability and accuracy.
   Quantities: 25 sequences and 299 bp of 16S rRNA gene, 39 sequences and 483 bp of 18S rRNA gene, 11 sequences and 764 bp for combination data, 1,000,000 MCMC iterations, 25% burn-inDuration: 1,000,000 iterations per analysisConditions: Computational analysis
   Equipment: MrBayes v3.2.5, MODELTEST 3.7, FigTree software

Typical Equipment

• MrBayes v3.2.5
• MODELTEST 3.7
• FigTree software

Output Measurements

• phylogenetic trees
• bootstrap values
• genetic distances

Papers Using This Protocol (1)

Species Studied With This Protocol