GMYC analysis (Apidae)

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

Method synopsis

Application of general mixed Yule/coalescent models to identify species boundaries in molecular phylogenies by detecting transitions between inter- and intraspecific branching rates.

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. GMYC species delimitation
   Applied single-threshold general mixed Yule/coalescent models using SPLITS library running on R platform. Used ultrametric estimate of phylogenetic tree including only unique haplotypes to avoid spurious inflation of terminal branching rates. Applied to tree using fastest evolving mitochondrial gene COI.
   Quantities: Applied to 46 unique haplotypes, recognized 9 candidate species with 95% confidence interval of 8-11 speciesDuration: Not specifiedConditions: Computational analysis
   Equipment: SPLITS library version 1.0-11, R platform version 2.12.1
2. Bayesian GMYC analysis
   Applied Bayesian GMYC analysis using bGMYC library on R platform to check robustness of GMYC results by accounting for uncertainty in phylogeny estimates. Applied to last 100 trees from BEAST run sample representing last 20 million trees.
   Quantities: Used sample of 10,000 trees from BEAST, applied to last 100 treesDuration: MCMC 50,000 generations, burn-in 40,000, thinning 100Conditions: Computational analysis with default settings
   Equipment: bGMYC library version 1.0.2, R platform

Typical Equipment

• SPLITS library version 1.0-11
• R platform version 2.12.1
• bGMYC library version 1.0.2

Output Measurements

• species delimitation
• confidence intervals for species number

Papers Using This Protocol (1)

Species Studied With This Protocol