GMYC analysis (Apidae)

Local Knowledge Graph (Top 53 entities)

Loading graph...

Knowledge graph centered on GMYC analysis (Apidae) with 53 nodes and 153 connections. Top connected: Two-form Bumble Bee, Bumble Bees, Yellow-fronted Bumble Bee, Buff-tailed Bumble Bee, Golden-belted Bumble Bee.

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.

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
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