1. Automated Barcoding Using the Characteristic Attribute Organization System Indra Neil Sarkar, PhD Divisions of Invertebrate Zoology & Library Services American Museum of Natural History Consortium for the Barcoding of Life Data Analysis Working Group Muséum National d’Histoire Naturelle July 06, 2006

2. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Ambition & Being BOLD http://www.jaestudio.com/

3. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Barcoding Identify Species –Recall –Precision Speed –Simplicity –Consistency

4. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Similarity Based Methods BLAST –Database Retrieval Clustering Algorithms –Phenetics

5. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Phenetic vs Cladistic Tree Topologies Are Often Different! –Which Is Right? –Does it Matter? Similarity Methods (Phenetic) –Evolution of Complete Sequences –FAST Character Methods (Cladistic) –Evolution of Individual Characters –SLOW

6. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 A Character Mindset MLAT MLBT MRBT MLCT MRCT MRCA MLAT MLBT MRBT MLCT MRCT MRCA

7. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 A Character Mindset MLAT MLBT MRBT MLCT MRCT MRCA Characters

8. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 A Character Mindset MLAT MLBT MRBT MLCT MRCT MRCA Character States

9. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 CAOS Characteristic –Character States Attribute –Characters Organization System Originally Designed as a Character- Based Heuristic for Phylogenetic Classification

10. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 CAOS A B C D

11. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 CAOS Pure (Pu) Private (Pr) Simple (s) Compound (c) ALL Members of One Group Have The Same Character State SOME Members of One Group Have The Same Character State CA’s with single position CA’s with multiple positions

12. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 CAOS Classification Rule Set Unclassified Sequence

13. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Characters vs Vectors Characters = Diagnostic –Apomorphies Vectors ≠ Diagnostic –Similarity Score Which approach provides a consistent phylogenetic representation of data?

14. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006

15. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Mopalia Test Case 569bp COI 19 In-Group Species 116 Individuals (~6/Species) What Happens to Classification Accuracy with Limited Sampling (e.g., 50%)?

16. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Entire Dataset Phenetic100% CAOS100% ABAB Phenetic 59% CAOS 96% AB BABA Phenetic 69% CAOS100%

17. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Proceeding BOLDly

18. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006

19. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 T atcgatcgatcgatcgatcgatcgTatcgatcgatcgatcgatcgatcg A atcgatcgatcgatcgatcgatcgAatcgatcgatcgatcgatcgatcg ------------------------T------------------------ ------------------------A------------------------ 12 ------------------------T------------------------ 1 ------------------------A------------------------ 2 T A

20. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 On Being Ambitious... Inter- vs. Intra- Species Classification Limited Sampling Strategies Accuracy at the Cost of Speed

21. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 On Being BOLD... Diagnostics Primers –Drop-Off –PCR –TAQ Assay Single Molecular Sequencing Oligos Diagnostic-Based Query Interface (In Addition to NJ Interface)

22. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Will the Real DNA Barcode Please Stand Up?

23. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Acknowledgments Rob DeSalle Ryan P Kelly Paul J Planet Mark Siddall Al Phillips MLA Donald A.B. Lindberg Research Fellowship National Science Foundation (IIS-0241229) Lewis B. & Dorothy Program for Molecular Systematics

24. © 2006 Indra Neil Sarkar, PhD CBoL DAWG 2006 Indra Neil Sarkar, PhD sarkar@amnh.org