title: Filling the gap - COI barcode resolution in eastern Palearctic birds.
abstract: BACKGROUND
  The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods.
  
  
  RESULTS
  We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots.
  
  
  CONCLUSIONS
  COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.
authors.affiliation: Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. kkerr@uoguelph.ca.
authors.forename: Kevin Cr
authors.initials: KC
authors.lastname: Kerr
authors.forename: Sharon M
authors.initials: SM
authors.lastname: Birks
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Kalyakin
authors.forename: Yaroslav A
authors.initials: YA
authors.lastname: Red'kin
authors.forename: Eugeny A
authors.initials: EA
authors.lastname: Koblik
authors.forename: Paul Dn
authors.initials: PD
authors.lastname: Hebert