Protocols & checklists

Protocols

Avian COI barcode primers and protocols with links to original papers, compiled august 2009, available at avian COI barcode primers.doc

For updated protocols and technical advances, see Canadian Center for DNA Barcoding (CCDB) website http://www.dnabarcoding.ca/pa/ge/research/protocols

Checklists

The target list of avian species is based on The Clements Checklist of Birds of the World, Sixth edition, plus updates as posted on Cornell University website. To assist with data submission, the following are available for download: 

  •  ABBI checklist (Excel, 6 MB) including most author names and ITIS numbers for the 9,933 world species 
  •  ABBI Name Lookup (Excel, 8 MB) file for converting synonyms, alternate spellings, and flagging extinct species (recognizes 2,462 alternate names and extinct forms)

Sequences files and analysis

North American birds fasta file (2569 sequences, 657 species) and Taxon ID tree pdf (neighbor-joining tree)

COI barcode sequences from published projects are available through GenBank and BOLD. BOLD has a suite of helpful software including for example geographic maps of collection locations, and sequence composition, neighbor-joining, and nearest neighbor analysis. Sequences, such as N American bird file above, and analytic results, such as N American birds Taxon ID tree, can be downloaded.