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Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
Success of DNA barcoding in distinguishing sister species of ...
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Success of DNA barcoding in distinguishing sister species of ...

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  • 1. Success of DNA barcoding in distinguishing sister species of diverse clades of birds Allan Baker, Erika Tavares, Rebecca Elbourne Department of Natural History, Royal Ontario Museum
  • 2. Organization of the talk
    • (1) Sister-species comparisons need to be tested
    • (2)10X rule for the ratio of intra- to interspecific distance fails to detect sister and cryptic species
    • (3) Multiple genes are needed to barcode species uniquely
    • (4) More extensive sampling of intra-specific diversity
    • (5) Problems with hybridization and paralogy in birds
    Aim is to address the following concerns about DNA barcoding:
  • 3. Barcoding sister-species of birds Multigene phylogenies Sister-species selection DNA extraction Amplification and sequencing of COI GenBank and BOLD search Map COI of sister-species in multigene phylogeny COI alignment Calculate COI corrected distances
  • 4. Multigene phylogeny of terns * Posterior Prob. = 1.00 Bayesian analysis 12S, Cytb, ND2, COI :3320 bp Bridge et al 2005, MPE 35: 459-469 COI:651 bp Distances
  • 5. Multigene phylogeny of shanks Bayesian analysis 12S and 16S rDNAs, ATPase8, ATPase6, COIII, ND1, tRNA-ISO, ND2, ND5, Cytb: 7664 bp . Pereira and Baker 2005 Condor 107. COI:651 bp Distances * Posterior Prob. = 1.00
  • 6. Multigene phylogeny of Calidridine sandpipers COI:~763 bp Distances Bayesian analysis RAG1 + mtDNA: 12,143 bp . Baker et al. In prep.
  • 7. Multigene phylogeny of penguins COI:~615 bp Distances Bayesian analysis RAG1, 12S, 16S, COI, Cytb: 5571 bp . Pereira and Baker et al (2006) Proc. Biol. Sci 273. * Posterior Prob. = 1.00
  • 8. Multigene phylogeny of kiwis Maximum Likelihood ATPAse 6, ATPase 8, CR, Cytb: 2267 bp . Burbidge et al (2003) Conservation Genetics 4. * Bootstrap proportion = 100% COI:~650 bp Distances
  • 9. Multigene phylogeny of Pteroglossus toucans COI:~615 bp Distances Bayesian analysis ATPase, COI, Cytb: 2168 bp . Eberhard and Bermingham (2005) MPE: 288-304 * Posterior Prob. = 1.00
  • 10. Multigene phylogeny of Woodpeckers Bayesian analysis COI, Cytb: 2580 bp . Moore et al (2006) Biol. J. Linn. Soc.87 * Posterior Prob. = 1.00 COI:~660 bp Distances
  • 11. Sister-species barcode comparisons Do many genes improve on COI barcoding of sister-species in 7 clades of birds? Multigene phylogenies Sister-species selection DNA extraction Amplification and sequencing of COI GenBank and BOLD search Test barcode in COI vs multigenes COI alignment of well sampled species Calculate COI distances and NJ topologies: K2P
  • 12. Success in barcoding sister-species of birds Sample of 812 sequences from 95 sister-species pairs Of the 6 “failures” 4 were known to be from hybridization Conclusion: No improvement using more genes 2 Clusters 1 Cluster COI 93.7% (89) 6.3%(6) Multigene 93.7% (89) 6.3%(6)
  • 13. Intraspecific versus among sister-species variation Sample of 812 sequences from 95 sister-species pairs. Conclusion: This is a potential problem for barcoding sister-species?
  • 14. Within-species variation in terns Terns Neighbour Joining (Kimura-2P) Node support: Posterior Prob. Bayesian analysis. COI (651 bp) Multigene 3220 bp) Intra-specific Between sister-species Within genera (above sister species level) Between genera
  • 15. New species of Little terns? 1.5% 1.3%
  • 16. http://www.birdguides.com Large-bill form Small-bill form 1.7% 1.8% New species of Gull-billed terns? Gull-billed Tern
  • 17. Within-species variation in Tringid sandpipers Neighbour Joining (model Kimura-2P) Node support: Posterior Prob. Bayesian analysis. COI (623 bp) Multigene (7664 bp) * Intra-specific Between sister-species Within genera (above sister species level) Between genera
  • 18. Within-species variation in penguins Penguins COI (bp) Multigene (bp) Neighbour Joining (model Kimura-2P) Node support: Posterior Prob. Bayesian analysis. Intra-specific Between sister-species Within genera (above sister species level) Between genera
  • 19. 2- White-Flippered Penguin Eudyptula m. albosignata (J.N. Davis and J.Busby) 3-Eudyptula m. novaehollandiae (J.N. Davis and J.Busby) 1-Little Penguin Eudyptula m. minor (J.N. Davis and J.Busby) Total Evidence Tree New species of Little blue penguins 1% a,b a,b c,d a,b e,f g,h Banks , JC. 2002 Notornis 49:29-38. Northern a Northern b Banks Peninsula b Banks Peninsula a Cook Strait c Cook Strait d Chatham Is. e Chatham Is. f Otago g Otago h Australia a Australia b COI barcode 3.56%
  • 20. New species of kiwis COI 650 bp Multigene phylogeny
  • 21. Threshold for sister-species Excluding putative new species and hybridizing species
  • 22. Threshold for sister-species
  • 23. Conclusion: Sister-species and intraspecific variation overlap slightly around 1% level Threshold for sister-species
  • 24. COI barcodes vs time of divergence of species Estimation of divergence times if not available with multidivtime Multigene phylogenies COI alignment COI distances vs divergence times Model choice
  • 25. Species barcode level varies with time since speciation
  • 26. Summary for these clades
    • The levels of distances between sister-species pairs varies from 1% to more than 20%.
    • When putative new species and hybridizing forms are excluded, COI distances (>1.3% ) between sister-species do not overlap with intraspecific variation
    • However, all sister-species have unique DNA barcodes that identify them
    • Results are specific to the clades we investigated, and potentially will vary with different rates of evolution in birds with faster rates of evolution
  • 27.  
  • 28.
    • These phenomena can be flagged with COI barcoding
    • By exposing these difficult cases barcoding will speed higher resolution studies required to make taxonomic decisions on species limits
    • Most species lose the ability to hybridize within 1-2 million years after divergence, so it should not be a pervasive problem in the tree of life
    • Even in closely related sister-species of birds less than 6% hybridize, so barcoding is highly effective in cataloguing species diversity and discovering putative new species.
    Hybridization, unsorted polymorphism and paralogy
  • 29. Acknowledgements
    • This research was supported by funding to the Canadian Barcode of Life Network from Genome Canada through the Ontario Genomics Institute, NSERC, and other sponsors listed at www.BOLNET.ca .
    • We thank Oliver Haddrath, Sergio Pereira, Eli Bridge and the Hebert lab for tips and assistance, and Rob Brumfield,Joel Cracraft and Bob Zink for permission to barcode loaned samples.

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