BEAST phylogenetic analysis (Apidae)

Knowledge graph centered on BEAST phylogenetic analysis (Apidae) with 32 nodes and 111 connections. Top connected: Bombus, Bombus terrestris, Bombus appositus, Bombus impatiens, B. appositus.

Method synopsis

BEAST analysis using linked mitochondrial and nuclear gene sequences with HKY substitution models and birth-death priors to estimate species-level phylogenetic relationships.

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 — Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees (2015), PLoS One. Implementations in other papers (listed below) may differ.

1. Phylogenetic analysis with BEAST
   Estimated species tree using BEAST linked trees from COI and PEPCK exon and intron sequences. Applied HKY nucleotide-substitution models, birth-death tree prior, and ran MCMC algorithm for 1.5 billion generations with sampling every 200,000 generations.
   Quantities: 1.5 billion MCMC generations, sampling every 200,000 generationsDuration: 1.5 billion generationsConditions: Computational analysis with birth-death process and HKY models
   Equipment: BEAST, Tracer version 1.6.0

Typical Equipment

• BEAST
• Tracer version 1.6.0

Output Measurements

• phylogenetic trees
• divergence time estimates
• posterior probabilities

Papers Using This Protocol (1)

Species Studied With This Protocol