DNA barcoding (Apidae)

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

Method synopsis

Standard DNA extraction, amplification and sequencing of mitochondrial COI barcode region and nuclear PEPCK gene from museum and field specimens to generate phylogenetic data for species delimitation.

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. DNA extraction and sequencing
   Sequenced the 'barcode' region of the COI gene from recently collected specimens showing obvious morphological and colour variation. Most extraction, amplification, and sequencing work done at Biodiversity Institute of Ontario, Guelph, using standard protocols. Minority of specimens processed at Institute of Apicultural Research, Beijing.
   Quantities: 173 COI barcode samples, 903 PEPCK sequences obtainedDuration: Not specifiedConditions: Standard laboratory conditions
   Equipment: standard DNA extraction protocols, PCR primers, sequencing equipment
2. Sequence alignment and quality control
   Made sequence alignments using ClustalW function in MEGA (version 6.06) and checked amino acid translations using EMBOSS Transeq to verify sequence quality.
   Quantities: 46 unique haplotypes among 173 COI sequences, 92/658 nucleotide sites phylogenetically informativeDuration: Not specifiedConditions: Computational analysis
   Equipment: MEGA version 6.06, EMBOSS Transeq

Typical Equipment

• standard DNA extraction protocols
• PCR primers
• sequencing equipment
• MEGA version 6.06
• EMBOSS Transeq

Output Measurements

• COI sequences
• PEPCK sequences
• unique haplotypes

Papers Using This Protocol (1)

Species Studied With This Protocol