1. Barcoding the Birds of North America
Kevin C.R. Kerr
University of Guelph
Biodiversity Institute of Ontario
Canada
Collaborators: M.Y. Stoeckle, L.A. Weigt, C.J. Dove, C.M. Francis, P.D.N. Hebert

2. Introduction Preliminary birds study (Hebert et al. 2004)
Specimens obtained from the Royal Ontario Museum:
260 species
130 with >2 replicates
437 sequences in total

3. Introduction The next steps are straightforward: Increase taxon
density
Increase replicates
per species
Illustrations © I. Lewington
Map courtesy of “Birds of North American Online”

4. Analytical Chain Specimen Collection data Sample Photographs
Extract Amplify Sequence
Online barcode library

5. DNA sources Feathers were collected from banding stations
across the country
Tissues samples were
loaned from museums;
96 well format matrix boxes
facilitate the movement of
tissue specimens

6. DNA sources Contributing Institutions: Royal Ontario Museum
Burke Museum
Canadian Wildlife Service
Academy of Natural Sciences, Philadelphia
American Museum of Natural History
Field Museum
Museum of Comparative Zoology
Museum of Southwestern Biology
Museum of Vertebrate Zoology
National Museum of Natural History
University of Alaska – Fairbanks
University of Kansas

7. Methods The GenElute™ Mammalian Genomic DNA Purification Kit
(Sigma-Aldrich)
Silica-based membrane
Individual tube format
(2 ml tubes)
Spin down on bench top
centrifuge (allows 24
samples at a time)

8. Methods NucleoSpin® 96 Tissue (Machery-Nagel) Silica-based membrane
96-well plate format
Requires larger high-speed centrifuge (2 plates at a time facilitates balancing)
Supplemented in our lab with “Glass-Fibre” protocol
(MUCH lower cost!)

9. Methods
Biomek® NX automated workstation (Beckman Coulter)

10. Methods
Our study provides evidence of the presence of pseudogenes in a few species ( bp)
Not a problem with bidirectional sequencing
Reverse
Forward
Contig
Numt
Numt
5’ ’

11. Results Summary: 643 species (~93% coverage) 2,590 sequences
1-125 replicates per species
Mean intraspecific distance = 0.23%
(versus 0.27% from PLoS paper)
Mean congeneric distance = 5.91%
(versus 7.93% from PLoS paper)
n = 24
n = 125

12. Species identification
Example:
Somateria complex
Similar mtDNA sequences
Barcodes are shared
Horizontal transfer?

13. Species identification
Pairs (14)
= Species with unique barcodes
Species with shared or
overlapping barcodes =
6.4%
Triplets (2)
93.6%
White-headed gulls

14. Species “discovery”
Example: Troglodytes troglodytes
Of 405 new North American species inspected, 11 species harbour splits:
Fulmarus glacialis
Megascops kennicotti
Toxostoma curvirostre*
Psaltriparus minimus
Poecile gambeli*
Aphelocoma californica*
Aphelocoma ultramarina
Corvus corax*
Troglodytes troglodytes*
Thryomanes bewickii
Catharus guttatus
Eastern
Western
Outgroup 2%
Divergence
Western Eastern

15. Publication
These findings were published last month in Molecular Ecology Notes
(Kerr et al. 2007)

16. New results Summary: 654 species (up from 643)
3,412 sequences (up from 2,590)
(plus impending sequences from
collaborative projects on arctic
geese and ptarmigan)
n = 144
n > 300

17. Continued sampling
Adequate geographical coverage is essential for uncovering deep genetic splits
Range map of D. townsendi
Range map of G. trichas
Range map of C. americana

18. Continued sampling NJ tree for Certhia americana
(eastern and western forms are 3.2% divergent)

19. Practical applications
Unidentified hummingbird
overwintering in Ontario
Belongs to a complex of
species difficult to identify
DNA barcode was
obtained from a single
breast feather found in
the snow, identifying
this Rufous Hummingbird

20. Practical applications
Barrow’s Goldeneye
(B. islandica) is a rare
species in eastern Canada
DNA barcoding has been
used to distinguish nest sites
from its common cousin
Bucephala islandica Bucephala clangula
Barcodes are
obtained from
feathers used
for nest lining
© B. Gress

21. Future directions
Number of Replicates per Species

22. Future directions Proportion of NA birds barcoded: 7% Remaining
93% Completed
Map courtesy of “Birds of North American Online”, Image: © M. Danzenbaker

23. Acknowledgements Laboratory Collections Database Funding & Support
The Hebert Lab
Royal Ontario Museum
Smithsonian Institution
Burke Museum
Smithsonian Institution
Database
Museum of Vertebrate Zoology
BOLD
Philadelphia Academy of Sciences
Museum of Southwestern Biology
American Museum of Natural History
Funding &
Support
Louisiana State University
Museum of Comparative Zoology
The Moore Foundation
Field Museum of Natural History
Canadian Wildlife Service
University of Kansas
Federal Aviation Administration
Bird banding stations